Noncoding RNAs in apoptosis: identification and function

Özge TÜNCEL, (İzmir Yüksek Teknoloji Enstitüsü, Fen Fakültesi, Kodlamayan RNA Laboratuvarı, Moleküler Biyoloji ve Genetik Bölümü, İzmir, Türkiye)
Merve KARA, (İzmir Yüksek Teknoloji Enstitüsü, Fen Fakültesi, Kodlamayan RNA Laboratuvarı, Moleküler Biyoloji ve Genetik Bölümü, İzmir, Türkiye)
Bilge YAYLAK, (İzmir Yüksek Teknoloji Enstitüsü, Fen Fakültesi, Kodlamayan RNA Laboratuvarı, Moleküler Biyoloji ve Genetik Bölümü, İzmir, Türkiye)
İpek ERDOĞAN, (İzmir Yüksek Teknoloji Enstitüsü, Fen Fakültesi, Kodlamayan RNA Laboratuvarı, Moleküler Biyoloji ve Genetik Bölümü, İzmir, Türkiye)
Bünyamin AKGÜL (İzmir Yüksek Teknoloji Enstitüsü, Fen Fakültesi, Kodlamayan RNA Laboratuvarı, Moleküler Biyoloji ve Genetik Bölümü, İzmir, Türkiye)
Turkish Journal of Biology
14 0
Yıl: 2022 Cilt: 46 Sayı: 1 Sayfa Aralığı: 1 - 40 Metin Dili: İngilizce DOI: 10.3906/biy-2109-35 İndeks Tarihi: 20-06-2022

Noncoding RNAs in apoptosis: identification and function

Öz:
Apoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, proteincoding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis. However, recent genome annotations and transcriptomics studies have uncovered a plethora of regulatory noncoding RNAs that have the ability to modulate not only apoptosis but also many other biochemical processes in eukaryotes. In this review article, we will cover a brief summary of apoptosis and detection methods followed by an extensive discussion on microRNAs, circular RNAs, and long noncoding RNAs in apoptosis.
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  • Afford S, Randhawa S (2000). Apoptosis. Molecular Pathology 53: 55-63.
  • Agarwal V, Bell GW, Nam JW, Bartel DP (2015). Predicting effective microRNA target sites in mammalian mRNAs. eLife 4: e05005. Akgül B, Erdoğan İ (2018). Intracytoplasmic re-localization of miRISC complexes. Frontiers in Genetics 9: 403.
  • Alkan AH, Akgül B (2022). Endogenous miRNA sponges. Methods in Molecular Biology 2257: 91-104.
  • Alló M, Agirre E, Bessonov S, Bertucci P, Acuña LG et al. (2014). Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells. Proceedings of the National Academy of Sciences 111: 15622-15629.
  • Alwine JC, Kemp DJ, Stark GR (1977). Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethylpaper and hybridization with DNA probes. Proceedings of the National Academy of Sciences of the United States of America 74: 5350-5354.
  • Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS (2011). LncRNAdb: A reference database for long noncoding RNAs. Nucleic Acids Research 39: D146-51.
  • Anamika K, Verma S, Jere A, Desai A ((2016). Transcriptomic profiling using next generation sequencing. Advances, Advantages, and Challenges.
  • Andree HA, Reutelingsperger CP, Hauptmann R, Hemker HC, Hermens WT, Willems GM (1990). Binding of vascular anticoagulant alpha (VAC alpha) to planar phospholipid bilayers. The Journal of Biological Chemistry 265: 4923-4928.
  • Arrigoni A, Ranzani V, Rossetti G, Panzeri I, Abrignani S, Bonnal RJP, Pagani M (2016). Analysis RNA-seq and noncoding RNA. Methods in Molecular Biology 1480: 125-135.
  • Arya R, White K (2015). Cell death in development: Signaling pathways and core mechanisms. Seminars in Cell & Developmental Biology 39: 12-19.
  • Ashwal-Fluss R, Meyer M, Pamudurti NR, Ivanov A, Bartok O, Hanan M, Evantal N, Memczak S, Rajewsky N, Kadener S (2014). circRNA biogenesis competes with pre-mRNA splicing. Molecular Cell 56: 55-66.
  • Babarinde IA, Li Y, Hutchins AP (2019). Computational methods for mapping, assembly and quantification for coding and non-coding transcripts. Computational and Structural Biotechnology Journal 17: 628-637.
  • Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R (2008). Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes & Development 22: 2773-2785.
  • Balas MM, Johnson AM (2018). Exploring the mechanisms behind long noncoding RNAs and cancer. Non-coding RNA Research 3:108-117.
  • Banfalvi G (2017). Methods to detect apoptotic cell death. Apoptosis 22: 306-323.
  • Barrett SP, Salzman J (2016). Circular RNAs: analysis, expression and potential functions. Development 143: 1838-1847.
  • Bartel DP (2018). Metazoan MicroRNAs. Cell 173: 20-51.
  • Bartel DP (2009). MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
  • Bartolomei MS, Zemel S, Tilghman SM (1991). Parental imprinting of the mouse H19 gene. Nature 351: 153-155.
  • Bao Z, Yang Z, Huang Z, Zhou Y, Cui Q et al. (2019). LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Research 47: D1034-D1037.
  • Bazzini AA, Lee MT, Giraldez AJ (2012). Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in Zebrafish. Science 336: 233-237.
  • Bender T, Martinou J-C (2013). Where killers meet permeabilization of the outer mitochondrial membrane during apoptosis. Cold Spring Harbor Perspectives in Biology 5: a011106-a011106.
  • Benesova S, Kubista M, Valihrach L (2021). Small RNA-sequencing: approaches and considerations for miRNA analysis Diagnostics 11: 964.
  • Berghe TV, Linkermann A, Jouan-Lanhouet S, Walczak H, Vandenabeele P (2014). Regulated necrosis: the expanding network of non-apoptotic cell death pathways. Nature Reviews Molecular Cell Biology 15: 135-147.
  • Billen LP, Shamas-Din A, Andrews DW (2008). Bid: a Bax-like BH3 protein. Oncogene 27 Suppl 1: S93-104.
  • Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR et al. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
  • Blank M, Shiloh Y (2007). Programs for cell death: apoptosis is only one way to go. Cell Cycle 6: 686-695.
  • Bofill-De Ros X, Kasprzak WK, Bhandari Y, Fan L, Cavanaugh Q et al. (2019). Structural differences between pri-miRNA paralogs promote alternative Drosha cleavage and expand target repertoires. Cell Reports 26: 447-459.e4.
  • Bonnal S, Martinez C, Förch P, Bachi A, Wilm M et al. (2008). RBM5/ Luca-15/H37 regulates Fas alternative splice site pairing after exon definition. Molecular Cell 32: 81-95.
  • Borsani G, Tonlorenzi R, Simmler MC, Dandolo L, Arnuad D et al. (1991). Characterization of a murine gene expressed from the inactive X chromosome. Nature 351: 325-329.
  • Bose M, Barman B, Goswami A, Bhattacharyya SN (2017). Spatiotemporal uncoupling of microRNA-mediated translational repression and target RNA degradation controls microRNP recycling in mammalian cells. Molecular and Cellular Biology 37: e00464-16.
  • Bottini S, Hamouda-Tekaya N, Mategot R, Zaragosi L-E, Audebert S et al. (2017). Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq. Nature Communications 8: 1189.
  • Brannan CI, Dees EC, Ingram RS, Tilghman SM (1990). The product of the H19 gene may function as an RNA. Molecular and Cellular Biology 10: 28-36.
  • Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113: 25-36.
  • Bukhari SIA, Truesdell SS, Lee S, Kollu S, Classon A et al. (2016). A specialized mechanism of translation mediated by FXR1aassociated microRNP in cellular quiescence. Molecular Cell 61: 760-773.
  • Bumgarner R (2013). Overview of DNA microarrays: types, applications, and their future. Current Protocols in Molecular Biology Chapter 22: Unit 22.21.
  • Burattini S, Falcieri E (2013). Analysis of cell death by electron microscopy. Methods in Molecular Biology 1004: 77-89.
  • Caldas C, So CW, MacGregor A, Ford AM, McDonald B et al. (1998). Exon scrambling of MLL transcripts occur commonly and mimic partial genomic duplication of the gene. Gene 208: 167- 176.
  • Capel B, Swain A, Nicolis S, Hacker A, Walter Met al. (1993). Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell 73: 1019-1030.
  • Carlevaro-Fita J, Rahim A, Guigó R, Vardy LA, Johnson R (2016). Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. RNA 22: 867-867.
  • Carthew RW, Sontheimer EJ (2009). Origins and mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
  • Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik AE et al. (2006). A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 12: 913- 920.
  • Chao MP, Majeti R, Weissman IL (2012). Programmed cell removal: A new obstacle in the road to developing cancer. Nature Reviews Cancer 12: 58-67.
  • Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH et al. (2005). Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic acids research 33: e179.
  • Chen C, Yin P, Hu S, Sun X, Li B (2020). Circular RNA-9119 protects IL-1β-treated chondrocytes from apoptosis in an osteoarthritis cell model by intercepting the microRNA-26a/PTEN axis. Life Sciences 256: 117924.
  • Chen L-L, Yang L (2015). Regulation of circRNA biogenesis. RNA Biology 12: 381-388.
  • Chen P, Feng Y, Zhang H, Shi X, Li B et al. (2019). MicroRNA-192 inhibits cell proliferation and induces apoptosis in human breast cancer by targeting caveolin 1. Oncology Reports 42: 1667-1676.
  • Chen X-F, Liu Y (2016). MicroRNA-744 inhibited cervical cancer growth and progression through apoptosis induction by regulating Bcl-2. Biomedicine & pharmacotherapy 81: 379- 387.
  • Chen Y, Fu LL, Wen X, Liu B, Huang J et al. (2014). Oncogenic and tumor suppressive roles of microRNAs in apoptosis and autophagy. Apoptosis 19: 1177-1189.
  • Chen Q, Xu J, Li L, Li H, Mao S et al. (2014). MicroRNA-23a/b and microRNA-27a/b suppress Apaf-1 protein and alleviate hypoxia-induced neuronal apoptosis. Cell Death & Disease 5: e1132.
  • Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N et al. (2005). TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436: 740- 744.
  • Cheng C, Dong Y, Ru X, Xia Y, Ji Y (2020). LncRNA ANCR promotes glioma cells invasion, migration, proliferation and inhibits apoptosis via interacting with EZH2 and repressing PTEN expression. Cancer Gene Therapy 28: 1025-1034.
  • Cheng X, Zhang L, Zhang K, Zhang G, Hu Y et al. (2018). Circular RNA VMA21 protects against intervertebral disc degeneration through targeting miR-200c and X linked inhibitor-ofapoptosis protein. Annals of the Rheumatic Diseases 77: 770- 779.
  • Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N et al. (2010). Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes & Development 24: 992-1009.
  • Chou C-H, Shrestha S, Yang C-D, Chang N-W, Lin Y-L et al. (2018). miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Research 46: D296-D302.
  • Choucroun P, Gillet D, Dorange G, Sawicki B, Dewitte JD (2001). Comet assay and early apoptosis. Mutation Research 478: 89- 96.
  • Choudhuri S (2014). Chapter 7 - Additional Bioinformatic Analyses Involving Nucleic-Acid Sequences. Bioinformatics for Beginners 157-181.
  • Chu C-y, Rana TM (2006). Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54. PLOS Biology 4: e210.
  • Cimmino A, Calin GA, Fabbri M, Iorio MV, Ferracin M et al. (2005). miR-15 and miR-16 induce apoptosis by targeting BCL2. Proceedings of the National Academy of Sciences of the United States of America 102: 13944-13949.
  • Coccia E, Masanas M, López-Soriano J, Segura MF, Comella JX et al. (2020). FAIM Is Regulated by MiR-206, MiR-1-3p and MiR133b. Frontiers in Cell and Developmental Biology 0: 1609- 1609.
  • Cocquet J, Chong A, Zhang G, Veitia RA (2006). Reverse transcriptase template switching and false alternative transcripts. Genomics 88: 127-131.
  • Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M et al. (2015). The RNA binding protein quaking regulates formation of circRNAs. Cell 160: 1125-1134.
  • Corchete LA, Rojas EA, Alonso-López D, De Las Rivas J, Gutiérrez NC et al. (2020). Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis. Scientific Reports 10: 19737.
  • Cortez MA, Bueso-Ramos C, Ferdin J, Lopez-Berestein G, Sood AK et al. (2011). MicroRNAs in body fluids—the mix of hormones and biomarkers. Nature Reviews Clinical Oncology 8: 467-477.
  • Cosacak MI, Erdogan I, Nalbant A, Akgul B (2018). Re-arrangements in the cytoplasmic distribution of small RNAs following the maternal-to-zygotic transition in Drosophila embryos. Data in Brief 17:397-400
  • Cosacak MI, Yiğit H, Kizil C, Akgül B (2018). Re-Arrangements in the Cytoplasmic Distribution of Small RNAs Following the Maternal-to-Zygotic Transition in Drosophila Embryos. Genes 9: 82.
  • Costa FF (2007). Non-coding RNAs: Lost in translation? Gene 386: 1-10.
  • Davis-Dusenbery BN, Hata A (2010). Mechanisms of control of microRNA biogenesis. The Journal of Biochemistry 148: 381- 392.
  • Deng N, Li L, Gao J, Zhou J, Wang Y et al. (2018). Hsa_circ_0009910 promotes carcinogenesis by promoting the expression of miR449a target IL6R in osteosarcoma. Biochemical and Biophysical Research Communications 495: 189-196.
  • Denli AM, Tops BBJ, Plasterk RHA, Ketting RF, Hannon GJ (2004). Processing of primary microRNAs by the Microprocessor complex. Nature 432: 231-235.
  • Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S et al. (2012). The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Research 22: 1775-1789.
  • Dhanoa JK, Verma R, Sethi RS, Arora JS, Mukhopadhyay CS (2019). Biogenesis and biological implications of isomiRs in mammalsa review. ExRNA 2019 1: 3.
  • Ding X, Zhang S, Li X, Feng C, Huang Q et al. (2018). Profiling expression of coding genes, long noncoding RNA, and circular RNA in lung adenocarcinoma by ribosomal RNA-depleted RNA sequencing. FEBS Open Bio 8: 544-555.
  • Dinger ME, Pang KC, Mercer TR, Mattick JS (2008). Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLOS Computational Biology 4: e1000176.
  • Dodbele S, Mutlu N, Wilusz JE (2021). Best practices to ensure robust investigation of circular RNAs: pitfalls and tips. EMBO Reports 22: e52072.
  • Dong H, Lei J, Ding L, Wen Y, Ju H, Zhang X (2013). MicroRNA: function, detection, and bioanalysis. Chemical Reviews 113: 6207-6233.
  • Du WW, Fang L, Yang W, Wu N, Awan FM et al. (2017). Induction of tumor apoptosis through a circular RNA enhancing Foxo3 activity. Cell Death and Differentiation 24: 357-370.
  • Duan X, Han L, Peng D, Peng C, Xiao L, Bao Q et al. (2019). Bioinformatics analysis of a long non-coding RNA and mRNA regulation network in rats with middle cerebral artery occlusion based on RNA sequencing. Molecular Medicine Reports 20: 417-432.
  • Eichhorn SW, Guo H, McGeary SE, Rodriguez-Mias RA, Shin C et al. (2014). mRNA Destabilization Is the Dominant Effect of Mammalian MicroRNAs by the Time Substantial Repression Ensues. Molecular Cell 56: 104-115.
  • Eisenberg-Lerner A, Bialik S, Simon HU, Kimchi A (2009). mRNA destabilization Is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Cell Death & Differentiation 16: 966-975.
  • Elmore S (2007). Apoptosis: A review of programmed cell death. Toxicologic Pathology 35: 495-516.
  • Ender C, Krek A, Friedländer MR, Beitzinger M, Weinmann L et al. (2008). A human snoRNA with microRNA-like functions. Molecular Cell 32: 519-528.
  • Fadok VA, Voelker DR, Campbell PA, Cohen JJ, Bratton DL et al. (1992). Exposure of phosphatidylserine on the surface of apoptotic lymphocytes triggers specific recognition and removal by macrophages. Journal of Immunology 148: 2207- 2216.
  • Fan L, An G, Wang S, Chen X, Liu Y et al. (2019). Circular RNA expression profiling and selection of key circular RNAs in the hypothalamus of heat-acclimated rats. Frontiers in Physiology 10: 1112.
  • Fan L, Tan B, Li Y, Zhao Q, Yuan H et al. (2018). Upregulation of miR-185 promotes apoptosis of the human gastric cancer cell line MGC803. Molecular Medicine Reports 17: 3115-3122.
  • Fernandes JCR, Acuña SM, Aoki JI, Floeter-Winter LM, Muxel SM (2019). Long non-coding RNAs in the regulation of gene expression: physiology and disease. Non-Coding RNA 5: 17.
  • Filipowicz W, Bhattacharyya SN, Sonenberg N (2008). Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Reviews Genetics 9: 102-114.
  • Flynn RA, Pedram K, Malaker SA, Batista PJ, Smith BAH et al. (2021). Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell 184: 3109-3124.e3122.
  • Francis H, McDaniel K, Han Y, Liu X, Kennedy L et al., (2014). Regulation of the extrinsic apoptotic pathway by microRNA-21 in alcoholic liver injury. The Journal of Biological Chemistry 289: 27526-27539.
  • Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE et al. (2021). GENCODE 2021. Nucleic Acids Research 49: D916-D923.
  • Friedländer MR, Lizano E, Houben AJS, Bezdan D, Báñez-Coronel M et al. (2014). Evidence for the biogenesis of more than 1,000 novel human microRNAs. Genome Biology 15: R57.
  • Friedman RC, Farh KK-H, Burge CB, Bartel DP (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Research 19: 92-92.
  • Fritah S, Niclou SP, Azuaje F (2014). Databases for lncRNAs: A comparative evaluation of emerging tools. RNA 1655-1665.
  • Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C et al. (2006). The Abundance of Short Proteins in the Mammalian Proteome. PLOS Genetics 2: e52.
  • Frith MC, Pheasant M, Mattick JS (2005). The amazing complexity of the human transcriptome. European Journal of Human Genetics 13: 894-897.
  • Fu X, Dong D (2018). Bioinformatic Analysis of MicroRNA Sequencing Data. Methods in Molecular Biology 1751: 109- 125.
  • Fuchs Y, Steller H (2015). Live to die another way: modes of programmed cell death and the signals emanating from dying cells. Nature Reviews Molecular Cell Biology 16: 329-344.
  • Fujita Y, Kojima T, Kawakami K, Mizutani K, Kato T et al. (2015). miR-130a activates apoptotic signaling through activation of caspase-8 in taxane-resistant prostate cancer cells. The Prostate 75: 1568-1578.
  • Gagnon K, Li L, Chu Y, Janowski B, Corey D (2014). RNAi factors are present and active in human cell nuclei. Cell Reports 6: 211- 221.
  • Galindo MI, Pueyo JI, Fouix S, Bishop SA, Couso JP (2007). Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLOS Biology 5: e106.
  • Galluzzi L, Vitale I, Aaronson SA, Abrams JM, Adam D et al. (2018). Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018. Cell Death & Differentiation 25: 486-541.
  • Gao N, Li Y, Li J, Gao Z, Yang Z et al. (2020). Long non-coding RNAs: he regulatory mechanisms, research strategies, and future directions in cancers. Frontiers in Oncology 0: 2903-2903.
  • Gao X, Xia X, Li F, Zhang M, Zhou H et al. (2021). The circular RNA cdr1as promotes myocardial infarction by mediating the regulation of miR-7a on its target genes expression. Nature Cell Biology 23: 278-291.
  • Gebert LFR, MacRae IJ (2018). Regulation of microRNA function in animals. Nature Reviews Molecular Cell Biology 20: 21-37.
  • Geng H-H, Li R, Su Y-M, Xiao J, Pan M et al. (2016). The Circular RNA Cdr1as Promotes Myocardial Infarction by Mediating the Regulation of miR-7a on Its Target Genes Expression. PloS One 11: e0151753.
  • Gibbings DJ, Ciaudo C, Erhardt M, Voinnet O (2009). Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nature Cell Biology 11: 1143-1149.
  • Göktaş Ç, Yiğit H, Coşacak Mİ, Akgül B (2017). Differentially expressed tRNA-derived small RNAs co-sediment primarily with non-polysomal fractions in Drosophila. Genes 8: 333.
  • Gomes-Duarte A, Bauer S, Venø MT, Norwood BA, Henshall DC et al. (2021). Enrichment of circular RNA expression deregulation at the transition to recurrent spontaneous seizures in experimental temporal lobe epilepsy. Frontiers in Genetics 12: 33.
  • Gong Z, Zhang S, Zeng Z, Wu H, Yang Q et al. (2014). LOC401317, a p53-regulated long non-coding RNA, inhibits cell proliferation and induces apoptosis in the nasopharyngeal carcinoma cell line HNE2. PLOS One 9: e110674.
  • Guo C, Song WQ, Sun P, Jin L, Dai HY (2015). LncRNA-GAS5 induces PTEN expression through inhibiting MIR-103 in endometrial cancer cells. Journal of Biomedical Science 22: 1-9.
  • Guo H, Ingolia NT, Weissman JS, Bartel DP (2010). Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840.
  • Guo JU, Agarwal V, Guo H, Bartel DP (2014). Expanded identification and characterization of mammalian circular RNAs. Genome biology 15: 409.
  • Guo Y, Wei X, Peng Y (2020). Structure-mediated degradation of circRNAs. Trends in Cell Biology 30: 501-503.
  • Gupta RA, Shah N, Wang KC, Kim J, Horlings HM et al. (2010). Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464: 1071-1076.
  • Gurer DC, Erdogan İ, Ahmadov U, Basol M, Sweef O et al. (2021). Transcriptomics profiling identifies cisplatin-inducible death receptor 5 antisense long non-coding RNA as a modulator of proliferation and metastasis in HeLa cells. Frontiers in Cell and Developmental Biology 0: 2248-2248.
  • Ha M, Kim VN (2014). Regulation of microRNA biogenesis. Nature Reviews Molecular Cell Biology 15: 509-524.
  • Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T et al. (2008). Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44: 3-12.
  • Hall PA (1999). Assessing apoptosis: a critical survey. Endocrinerelated Cancer 6: 3-8.
  • Hamada S, Masamune A, Miura S, Satoh K, Shimosegawa T (2014). MiR-365 induces gemcitabine resistance in pancreatic cancer cells by targeting the adaptor protein SHC1 and pro-apoptotic regulator BAX. Cellular Signalling 26: 179-185.
  • Hamid SM, Akgül B (2014). Master regulators of posttranscriptional gene expression are subject to regulation. Methods Mol Biol 1107: 303-310.
  • Han J, Lee Y, Yeom K-H, Kim Y-K, Jin H et al. (2004). The DroshaDGCR8 complex in primary microRNA processing. Genes & Development 18: 3016-3027.
  • Han L, Zhang Eb, Yin Dd, Kong R, Xu Tp et al. (2015). Low expression of long noncoding RNA PANDAR predicts a poor prognosis of non-small cell lung cancer and affects cell apoptosis by regulating Bcl-2. Cell Death & Disease 6: e1665.
  • Han Y, Feng J, Ren Y, Wu L, Li H et al. (2020). Differential expression of microRNA between normally developed and underdeveloped female worms of Schistosoma japonicum. Veterinary Research 51: 126.
  • Handzlik JE, Tastsoglou S, Vlachos IS, Hatzigeorgiou AG (2020). Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data. Scientific Reports 10: 705.
  • Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B et al. (2013). Natural RNA circles function as efficient microRNA sponges. Nature 495: 384-388.
  • Hansen TB, Wiklund ED, Bramsen JB, Villadsen SB, Statham AL et al. (2011). miRNA-dependent gene silencing involving Ago2- mediated cleavage of a circular antisense RNA. The EMBO Journal 30: 4414-4422.
  • Harrow J, Denoeud F, Frankish A, Reymond A, Chen C-K et al. (2006). GENCODE: producing a reference annotation for ENCODE. Genome Biology 7: 1-9.
  • He R-Z, Luo D-X, Mo Y-Y (2019). Emerging roles of lncRNAs in the post-transcriptional regulation in cancer. Genes & Diseases 6: 6.
  • He SL, Green R (2013). Northern blotting. Methods in Enzymology 530: 75-87.
  • Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP et al. (2015). Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Reports 11: 1110-1122.
  • Hipfner DR, Weigmann K, Cohen SM (2002). The bantam gene regulates Drosophila growth. Genetics 161: 1527-1527.
  • Holdt LM, Stahringer A, Sass K, Pichler G, Kulak NA et al. (2016). Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans. Nature Communications 7: 12429.
  • Hong CF, Lin SY, Chou YT, Wu CW (2016). MicroRNA-7 compromises p53 protein-dependent apoptosis by controlling the expression of the chromatin remodeling factor SMARCD1. The Journal of Biological Chemistry 291: 1877-1889.
  • Hoon MJLd, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H et al. (2010). Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research 20: 257-264.
  • Horvitz HR, Sulston JE (1980). Isolation and genetic characterization of cell-lineage mutants of the nematode Genetics 96: 435-435.
  • Hotchkiss RS, Strasser A, McDunn JE, Swanson PE (2009). Cell Death 361: 1570-1583.
  • Wang HQ, Yu XD, Liu ZH, Cheng X, Samartzis D et al. (2011). Deregulated miR-155 promotes Fas-mediated apoptosis in human intervertebral disc degeneration by targeting FADD and caspase-3. The Journal of Pathology 225: 232-242.
  • Hsu MT, Coca-Prados M (1979). Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature 280: 339-340.
  • Hu X, Jiang H, Jiang X (2017). Downregulation of lncRNA ANRIL inhibits proliferation, induces apoptosis, and enhances radiosensitivity in nasopharyngeal carcinoma cells through regulating miR-125a. Cancer Biology and Therapy 18: 331-338.
  • Hu Y, Zhu Q, Tang L (2014). MiR-99a antitumor activity in human breast cancer cells through targeting of mTOR expression. PLOS One 9: e92099.
  • Huang G, Nishimoto K, Zhou Z, Hughes D, Kleinerman ES (2012). miR-20a encoded by the miR-17-92 cluster increases the metastatic potential of osteosarcoma cells by regulating Fas expression. Cancer Research 72: 908-916.
  • Huang A, Zheng H, Wu Z, Chen M, Huang Y (2020). Circular RNA-protein interactions: functions, mechanisms, and identification. Theranostics 10: 3503-3517.
  • Huang J, Zhao J, Geng X, Chu W, Li S et al. (2021). Long non-coding RNA lnc-CCNL1-3:1 promotes granulosa cell apoptosis and suppresses glucose uptake in women with polycystic ovary syndrome. Molecular Therapy - Nucleic Acids 23: 614-628.
  • Huang Y, Zhang J, Hou L, Wang G, Liu H et al. (2017). LncRNA AK023391 promotes tumorigenesis and invasion of gastric cancer through activation of the PI3K/Akt signaling pathway. Journal of Experimental & Clinical Cancer Research 36: 1-14.
  • Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y et al. (2011). Extensive and coordinated transcription of noncoding RNAs within cellcycle promoters. Nature Genetics 43: 621-629.
  • Hutvágner G, McLachlan J, Pasquinelli AE, Bálint É, Tuschl T et al. (2001). A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temporal RNA. Science 293: 834-838.
  • Igney FH, Krammer PH (2002). Death and anti-death: tumour resistance to apoptosis. Nature Reviews Cancer 2: 277-288.
  • Imanaka Y, Tsuchiya S, Sato F, Shimada Y, Shimizu K et al. (2011). MicroRNA-141 confers resistance to cisplatin-induced apoptosis by targeting YAP1 in human esophageal squamous cell carcinoma. Journal of Human Genetics 56: 270-276.
  • Ivanov A, Memczak S, Wyler E, Torti F, Porath Hagit T et al. (2015). Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Reports 10: 170-177.
  • Jarroux J, Morillon A, Pinskaya M (2017). History, discovery, and classification of lncRNAs. Advances in Experimental Medicine and Biology 1008: 1-46.
  • Jain AK, Xi Y, McCarthy R, Allton K, Akdemir KC et al. (2016). LncPRESS1 Is a p53-regulated lncRNA that safeguards pluripotency by disrupting SIRT6-dediated de-acetylation of histone H3K56. Molecular Cell 64: 967-981.
  • James BR, Griffith TS (2014). Tumor necrosis factor-related apoptosis-inducing ligand-induced apoptotic pathways in cancer immunosurveillance: molecular mechanisms and prospects for therapy. Research and Reports in Biochemistry 5: 1-10.
  • Jeck WR, Sharpless NE (2014). Detecting and characterizing circular RNAs. Nature Biotechnology 32: 453-461.
  • Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE et al. (2013). Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19: 141-157.
  • Jiang N, Zhang X, Gu X, Li X, Shang L (2021). Progress in understanding the role of lncRNA in programmed cell death. Cell Death Discovery 7: 1-11.
  • Jiang X, Liu W (2017). Long noncoding RNA highly upregulated in liver cancer activates p53-p21 pathway and promotes nasopharyngeal carcinoma cell growth. DNA Cell Biology 36: 596-602.
  • Jiao J, Zhang S (2019). Long non-coding RNA MEG-3 suppresses gastric carcinoma cell growth, invasion and migration via EMT regulation. Molecular Medicine Reports 20: 2685-2693.
  • Jonas S, Izaurralde E (2015). Towards a molecular understanding of microRNA-mediated gene silencing. Nature Reviews Genetics 16: 421-433.
  • Jones-Rhoades MW, Bartel DP, Bartel B (2006). MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology 57: 19-53.
  • Nishi K, Nishi A, Nagasawa T, Ui-Tei K (2013). Human TNRC6A is an Argonaute-navigator protein for microRNA-mediated gene silencing in the nucleus. RNA 19: 17-35.
  • Kamenska A, Simpson C, Vindry C, Broomhead H, Bénard M et al. (2016). The DDX6–4E-T interaction mediates translational repression and P-body assembly. Nucleic Acids Research 44: 6318-6334.
  • Karlen Y, McNair A, Perseguers S, Mazza C, Mermod N (2007). Statistical significance of quantitative PCR. BMC Bioinformatics 8: 131.
  • Kerr JFR, Wyllie AH, Currie AR (1972). A basic biological phenomenon with wideranging implications in tissue kinetics. British Journal of Cancer 26: 239-257.
  • Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS, Perera RJ (2011). The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Research 71: 3852-3862.
  • Kim SW, Li Z, Moore PS, Monaghan AP, Chang Y et al. (2010). A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Research 38: e98.
  • Kim Y-K, Kim B, Kim VN (2016). Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis. Proceedings of the National Academy of Sciences 113: E1881-E1889.
  • Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP (2010). Noncoding RNA Gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Science Signaling 3: ra8.
  • Kloc M, Wilk K, Vargas D, Shirato Y, Bilinski S et al. (2005). Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopusoocytes. Development 132: 3445-3457.
  • Knight SW, Bass BL (2001). A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293: 2269-2271.
  • Kong Z, Wan X, Zhang Y, Zhang P, Zhang Y et al. (2017). Androgenresponsive circular RNA circSMARCA5 is up-regulated and promotes cell proliferation in prostate cancer. Biochemical and Biophysical Research Communications 493: 1217-1223.
  • Kong Y, Zhang L, Huang Y, He T, Zhang L et al. (2017). Pseudogene PDIA3P1 promotes cell proliferation, migration and invasion, and suppresses apoptosis in hepatocellular carcinoma by regulating the p53 pathway. Cancer Letters 407: 76-83.
  • Koopman G, Reutelingsperger CP, Kuijten GA, Keehnen RM, Pals ST et al. (1994). Annexin V for flow cytometric detection of phosphatidylserine expression on B cells undergoing apoptosis. Blood 84: 1415-1420.
  • Kren BT, Wong PYP, Sarver A, Zhang X, Zeng Y et al. (2009). MicroRNAs identified in highly purified liver-derived mitochondria may play a role in apoptosis. RNA Biology 6: 65-72.
  • Kristensen LS, Okholm TLH, Venø MT, Kjems J (2018). Circular RNAs are abundantly expressed and upregulated during human epidermal stem cell differentiation. RNA Biology 15: 280-291.
  • Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A et al. (2017). High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nature Genetics 49: 1731-1740.
  • Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001). Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC et al. (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921.
  • Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J et al. (1999). A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 97: 17-27.
  • Lasda E, Parker R (2014). Circular RNAs: diversity of form and function. RNA 20: 1829-1842.
  • Lau NC, Lim LP, Weinstein EG, Bartel DP (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
  • Lee ECS, Elhassan SAM, Lim GPL, Kok WH, Tan SW et al. (2019). The roles of circular RNAs in human development and diseases. Biomedicine & Pharmacotherapy 111: 198-208.
  • Lee RC, Ambros V (2001). An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
  • Lee Y, Jeon K, Lee J-T, Kim S, Kim VN (2002). MicroRNA maturation: stepwise processing and subcellular localization. The EMBO Journal 21: 4663-4670.
  • Lee Y, Ahn C, Han J, Choi H, Kim J et al. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415- 419.
  • Lee RC, Feinbaum RL, Ambros V (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
  • Lei M, Zheng G, Ning Q, Zheng J, Dong D (2020). Translation and functional roles of circular RNAs in human cancer. Molecular Cancer 19: 30.
  • Leshkowitz D, Horn-Saban S, Parmet Y, Feldmesser E (2013). Differences in microRNA detection levels are technology and sequence dependent. RNA 19: 527-538.
  • Leung AKL, Calabrese JM, Sharp PA (2006). Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules. Proceedings of the National Academy of Sciences 103: 18125-18130.
  • Levine AJ, Oren M (2009). The first 30 years of p53: Growing ever more complex. Nature Reviews Cancer 9: 749-758.
  • Li B, Chen P, Qu J, Shi L, Zhuang W, Fu J, Li J, Zhang X, Sun Y, Zhuang W (2014). Activation of LTBP3 gene by a long noncoding RNA (lncRNA) MALAT1 transcript in mesenchymal stem cells from multiple myeloma. The Journal of Biological Chemistry 289: 29365-29375.
  • Li HW, Meng Y, Xie Q, Yi WJ, Lai XL et al. (2015). miR-98 protects endothelial cells against hypoxia/reoxygenation inducedapoptosis by targeting caspase-3. Biochemical and Biophysical Research Communications 467: 595-601.
  • Li Q, Wang X (2021). Differential expression analysis of long noncoding RNAs. Methods in Molecular Biology 2284: 193- 205.
  • Li R, Zhang H, Zheng X (2018). MiR-34c induces apoptosis and inhibits the viability of M4e cells by targeting BCL2. Oncology Letters 15: 3357-3361.
  • Li S, Teng S, Xu J, Su G, Zhang Y et al. (2019). Microarray is an efficient tool for circRNA profiling. Briefings in Bioinformatics 20: 1420-1433.
  • Li W, Ruan K (2009). MicroRNA detection by microarray. Analytical and Bioanalytical Chemistry 394: 1117-1124.
  • Li X, Wang H, Yao B, Xu W, Chen J et al. (2016). lncRNA H19/ miR-675 axis regulates cardiomyocyte apoptosis by targeting VDAC1 in diabetic cardiomyopathy. Scientific Reports 6: 1-9.
  • Li X, Zhang B, Li F, Yu K, Bai Y (2020). The mechanism and detection of alternative splicing events in circular RNAs. PeerJ 8: e10032.
  • Li X, Zhao Y, Yin J, Lin W (2020). Organic fluorescent probes for detecting mitochondrial membrane potential. Coordination Chemistry Reviews 420: 213419.
  • Li Z, Huang C, Bao C, Chen L, Lin M et al. (2015). Exon-intron circular RNAs regulate transcription in the nucleus. Nature Structural & Molecular Biology 22: 256-264.
  • Li Z, Kearse MG, Huang C (2019). The nuclear export of circular RNAs is primarily defined by their length. RNA Biology 16: 1-4.
  • Liang D, Wilusz JE (2014). Short intronic repeat sequences facilitate circular RNA production. Genes & Development 28: 2233- 2247.
  • Liao WT, Ye YP, Zhang NJ, Li TT, Wang SY et al. (2014). MicroRNA30b functions as a tumour suppressor in human colorectal cancer by targeting KRAS, PIK3CD and BCL2. The Journal of Pathology 232: 415-427.
  • Liu C-G, Calin GA, Volinia S, Croce CM (2008). MicroRNA expression profiling using microarrays. Nature Protocols 3: 563-578.
  • Liu D-W, Zhang J-H, Liu F-X, Wang X-T, Pan S-K et al. (2019). Silencing of long noncoding RNA PVT1 inhibits podocyte damage and apoptosis in diabetic nephropathy by upregulating FOXA1. Experimental & Molecular Medicine 51: 1-15.
  • Liu F, Gong J, Huang W, Wang Z, Wang M et al. (2013). MicroRNA106b-5p boosts glioma tumorigensis by targeting multiple tumor suppressor genes. Oncogene 33: 4813-4822.
  • Liu H, Zhou G, Fu X, Cui H, Pu G et al. (2017). Long noncoding RNA TUG1 is a diagnostic factor in lung adenocarcinoma and suppresses apoptosis via epigenetic silencing of BAX. Oncotarget 8: 101899-101910.
  • Liu J, Liu D, Zhao B, Jia C, Lv Y et al. (2020). Long non-coding RNA NEAT1 mediates MPTP/MPP+-induced apoptosis via regulating the miR-124/KLF4 axis in Parkinson’s disease. Open Life Sciences 15: 665-676.
  • Liu L, Ren W, Chen K (2017). MiR-34a Promotes Apoptosis and Inhibits Autophagy by Targeting HMGB1 in Acute Myeloid Leukemia Cells. Cellular Physiology and Biochemistry 41: 1981-1992.
  • Liu L, Zhang G, Liang Z, Liu X, Li T et al. (2013). MicroRNA15b enhances hypoxia/reoxygenation-induced apoptosis of cardiomyocytes via a mitochondrial apoptotic pathway. Apoptosis 19: 19-29.
  • Liu M, Jia J, Wang X, Liu Y, Wang C et al. (2018). Long non-coding RNA HOTAIR promotes cervical cancer progression through regulating BCL2 via targeting miR-143-3p. Cancer Biol Therapy 19: 391-399.
  • Liu T, Liu S, Xu Y, Shu R, Wang F et al. (2018). Circular RNA-ZFR Inhibited Cell Proliferation and Promoted Apoptosis in Gastric Cancer by Sponging miR-130a/miR-107 and Modulating PTEN. Cancer Research and Treatment 50: 1396-1417.
  • Liu X, Liu B, Zhou M, Fan F, Yu M et al. (2018). Circular RNA HIPK3 regulates human lens epithelial cells proliferation and apoptosis by targeting the miR-193a/CRYAA axis. Biochemical and Biophysical Research Communications 503: 2277-2285.
  • Liu X, Yan Z, Wu C, Yang Y, Li X et al. (2019). FastProNGS: fast preprocessing of next-generation sequencing reads. BMC Bioinformatics 20: 345.
  • Liu X, Zhong Y, Li J, Shan A (2017). Circular RNA circ-NT5C2 acts as an oncogene in osteosarcoma proliferation and metastasis through targeting miR-448. Oncotarget 8: 114829-114838.
  • Lockshin RA, Williams CM (1965). Programmed cell death—I. Cytology of degeneration in the intersegmental muscles of the Pernyi silkmoth. Journal of Insect Physiology 11: 123-133.
  • Long B, Li N, Xu XX, Li XX, Xu XJ et al. (2018). Long noncoding RNA FTX regulates cardiomyocyte apoptosis by targeting miR29b-1-5p and Bcl2l2. Biochemical and Biophysical Research Communications 495: 312-318.
  • Long J, Menggen Q, Wuren Q, Shi Q, Pi X (2018). Long noncoding RNA Taurine-Upregulated Gene1 (TUG1) promotes tumor growth and metastasis through TUG1/mir-129-5p/AstrocyteElevated Gene-1 (AEG-1) axis in malignant melanoma. Medical Science Monitor 24: 1547-1559.
  • Long Z, Gong F, Li Y, Fan Z, Li J (2020). Circ_0000285 regulates proliferation, migration, invasion and apoptosis of osteosarcoma by miR-409-3p/IGFBP3 axis. Cancer Cell International 20: 481.
  • Lorenzo Y, Costa S, Collins AR, Azqueta A (2013). The comet assay, DNA damage, DNA repair and cytotoxicity: hedgehogs are not always dead. Mutagenesis 28: 427-432.
  • Lu Y-M, Wang Y, Liu S-Q, Zhou M-Y, Guo Y-R (2018). Profile and validation of dysregulated long non-coding RNAs and mRNAs in ovarian cancer. Oncology Reports 40: 2964-2976.
  • Luciano DJ, Mirsky H, Vendetti NJ, Maas S (2004). RNA editing of a miRNA precursor. RNA 10: 1174-1177.
  • Lwin T, Lin J, Choi YS, Zhang X, Moscinski LC et al. (2010). Follicular dendritic cell-dependent drug resistance of nonHodgkin lymphoma involves cell adhesion-mediated Bim down-regulation through induction of microRNA-181a. Blood 116: 5228-5236.
  • Lynam-Lennon N, Maher SG, Reynolds JV (2009). The roles of microRNA in cancer and apoptosis. Biological Reviews 84: 55- 71.
  • Ma LY, Xie XW, Ma L, Pang JL, Xiong XM et al. (2017). Downregulated long non-coding RNA TRPM2-AS inhibits cisplatin resistance of non-small cell lung cancer cells via activation of p53- p66shc pathway. European Review for Medical and Pharmacological Sciences 21: 2626-2634.
  • Ma S, Kong S, Wang F, Ju S (2020). CircRNAs: biogenesis, functions, and role in drug-resistant Tumours. Molecular Cancer 19: 119.
  • Maghsoudi N, Zakeri Z, Lockshin R (2012). Programmed cell death and apoptosis--where it came from and where it is going: from Elie Metchnikoff to the control of caspases. Exp Oncol. 34: 146- 152.
  • Mansoori B, Mohammadi A, Ghasabi M, Shirjang S, Denghan R, Montazeri V, Holmskov U, Kazemi T, Duijf P, Gjerstorff, Baradadarn B (2019). miR-142-3p as tumor suppressor miRNA in the regulation of tumorigenicity, invasion and migration of human breast cancer by targeting Bach-1 expression. Journal of Cellular Physiology 234: 9816-9825.
  • Marques AC, Ponting CP (2014). Intergenic lncRNAs and the evolution of gene expression. Current Opinion in Genetics & Development 27: 48-53.
  • Martinez MM, Reif RD, Pappas D (2010). Detection of apoptosis: A review of conventional and novel techniques. Analytical Methods 2: 996-1004.
  • Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G et al. (2004). Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Molecular Cell 15: 185-197.
  • Melé M, Mattioli K, Mallar W, Shechner DM, Gerhardinger C et al. (2017). Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome research 27: 27-37.
  • Mello CC, Conte D (2004). Revealing the world of RNA interference. Nature 431: 338-342.
  • Memczak S, Jens M, Elefsinioti A, Torti F, Krueger Jet al. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495: 333-338.
  • Meng S, Zhou H, Feng Z, Xu Z, Tang Y et al. (2017). CircRNA: functions and properties of a novel potential biomarker for cancer. Molecular Cancer 16: 94-94.
  • Miao G, Zang X, Hou H, Sun H, Wang L et al. (2019). Bax targeted by miR-29a regulates chondrocyte apoptosis in osteoarthritis. BioMed Research International 2019: 1434538.
  • Miao H, Wang L, Zhan H, Dai J, Chang Y et al. (2019). A long noncoding RNA distributed in both nucleus and cytoplasm operates in the PYCARD-regulated apoptosis by coordinating the epigenetic and translational regulation. PLoS Genetics 15: e1008144.
  • Misawa A, Takayama K, Urano T, Inoue S (2016). Androgen-induced long noncoding RNA (lncRNA) SOCS2-AS1 promotes cell growth and inhibits apoptosis in prostate cancer cells. The Journal of Biological Chemistry 291: 17861-17880.
  • Molotski N, Soen Y (2012). Differential association of microRNAs with polysomes reflects distinct strengths of interactions with their mRNA targets. RNA 18:1612-1623.
  • Morey C, Avner P (2004). Employment opportunities for noncoding RNAs. FEBS Letters 567: 27-34.
  • Mott JL, Kobayashi S, Bronk SF, Gores GJ (2007). mir-29 regulates Mcl-1 protein expression and apoptosis. Oncogene 26: 6133- 6140.
  • Nan A, Chen L, Zhang N, Liu Z, Yang T et al. (2017). A novel regulatory network among LncRpa, CircRar1, MiR-671 and apoptotic genes promotes lead-induced neuronal cell apoptosis. Archives of Toxicology 91: 1671-1684.
  • Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T et al. (2014). The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505: 635-640.
  • Nigro JM, Cho KR, Fearon ER, Kern SE, Ruppert JM et al. (1991). Scrambled exons. Cell 64: 607-613.
  • Ning SB, Wang L, Song YC (2002). Identification of programmed cell death in situ in individual plant cells in vivo using a chromosome preparation technique. Journal of Experimental Botany 53: 651-658.
  • Nirmala JG, Lopus M (2020). Cell death mechanisms in eukaryotes. Cell Biology and Toxicology 36: 145-164.
  • Niu H, Hu Z, Liu H, Hu G, Yang B et al. (2016). Long non-coding RNA AK027294 involves in the process of proliferation, migration, and apoptosis of colorectal cancer cells. Tumor Biology 37: 10097-10105.
  • Niu H, Wang K, Zhang A, Yang S, Song Z et al. (2012). miR-92a is a critical regulator of the apoptosis pathway in glioblastoma with inverse expression of BCL2L11. Oncology Reports 28: 1771- 1777.
  • O’Brien J, Hayder H, Zayed Y, Peng C (2018). Overview of microRNA biogenesis, mechanisms of actions, and circulation. Frontiers in Endocrinology 9: 402.
  • Ohtsuka T, Ryu H, Minamishima YA, Macip S, Sagara J et al. (2004). ASC is a Bax adaptor and regulates the p53-Bax mitochondrial apoptosis pathway. Nature Cell Biology 6: 121-128.
  • Olsen PH, Ambros V (1999). The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Developmental Biology 216: 671-680.
  • Ormerod MG (2001). Using flow cytometry to follow the apoptotic cascade. Redox Report 6: 275-287.
  • Othumpangat S, Noti JD, Beezhold DH (2014). Lung epithelial cells resist influenza A infection by inducing the expression of cytochrome c oxidase VIc which is modulated by miRNA 4276. Virology 468-470: 256-264.
  • Otsuki Y, Li Z, Shibata M-A (2003). Apoptotic detection methods- -from morphology to gene. Progress in Histochemistry and Cytochemistry 38: 275-339.
  • Ouyang L, Shi Z, Zhao S, Wang FT, Zhou TT et al. (2012). Programmed cell death pathways in cancer: a review of apoptosis, autophagy and programmed necrosis. Cell Proliferation 45: 487-498.
  • Ouyang T, Liu Z, Han Z, Ge Q (2019). MicroRNA detection specificity: Recent advances and future perspective. Analytical Chemistry 91: 3179-3186.
  • Xu P, Vernooy SY, Guo M, Hay BA (2003). The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Current Biology 13: 790-795.
  • Pan F, Zhu L, Lv H, Pei C (2016). Quercetin promotes the apoptosis of fibroblast-like synoviocytes in rheumatoid arthritis by upregulating lncRNA MALAT1. International Journal of Molecular Medicine 38: 1507-1514.
  • Panda AC (2018). Circular RNAs act as miRNA sponges. Advances in Experimental Medicine and Biology 1087: 67-79.
  • Pang KC, Frith MC, Mattick JS (2006). Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function. Trends Genet 22: 1-5.
  • Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI et al. (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86-89
  • Patop IL, Wüst S, Kadener S (2019). Past, present, and future of circRNAs. The EMBO Journal 38: e100836.
  • Peng R, Liu Y, Cai Z, Shen F, Chen J et al. (2018). Characterization and analysis of whole transcriptome of giant panda spleens: Implying critical roles of long non-coding RNAs in immunity Cellular Physiology and Biochemistry 46: 1065-1077.
  • Peng W, Si S, Zhang Q, Li C, Zhao F et al. (2015). Long non-coding RNA MEG3 functions as a competing endogenous RNA to regulate gastric cancer progression. Journal of Experimental & Clinical Cancer Research 34: 1-10.
  • Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N (1996). Requirement for Xist in X chromosome inactivation. Nature 379: 131-137.
  • Perry SW, Norman JP, Barbieri J, Brown EB, Gelbard HA (2011). Mitochondrial membrane potential probes and the proton gradient: a practical usage guide. BioTechniques 50: 98-115.
  • Pickard MR, Williams GT (2016). The hormone response element mimic sequence of GAS5 lncRNA is sufficient to induce apoptosis in breast cancer cells. Oncotarget 7: 10104-10116.
  • Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N et al. (2005). Molecular biology: Inhibition of translational initiation by let-7 microRNA in human cells. Science 309: 1573-1576.
  • Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ et al. (2010). A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465: 1033-1038.
  • Potemkin N, Cawood SMF, Treece J, Guévremont D, Rand CJ et al. (2021). A workflow for simultaneous detection of coding and non-coding transcripts by ribosomal RNA-depleted RNA-Seq. bioRxiv 2021.2001.2004.425201
  • Prats A-C, David F, Diallo LH, Roussel E, Tatin F et al. (2020). Circular RNA, the key for translation. International Journal of Molecular Sciences 21: 8591.
  • Qi D, Li J, Que B, Su J, Li M et al. (2016). Long non-coding RNA DBCCR1-003 regulate the expression of DBCCR1 via DNMT1 in bladder cancer. Cancer Cell International 16: 1-13.
  • Ragan C, Goodall GJ, Shirokikh NE, Preiss T (2019). Insights into the biogenesis and potential functions of exonic circular RNA. Scientific reports 9: 2048.
  • Ramkissoon SH, Mainwaring LA, Sloand EM, Young NS, Kajigaya S (2006). Nonisotopic detection of microRNA using digoxigenin labeled RNA probes. Molecular and Cellular Probes 20: 1-4.
  • Ren S, Lin P, Wang J, Yu H, Lv T et al. (2020). Circular RNAs: promising molecular biomarkers of human aging-related diseases via functioning as an miRNA sponge. Molecular therapy Methods & Clinical Development 18: 215-229.
  • Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L et al. (2000). Estimate of human gene number provided by genomewide analysis using Tetraodon nigroviridis DNA sequence. Nature Genetics 25: 235-238.
  • Rong D, Sun H, Li Z, Liu S, Dong C et al. (2017). An emerging function of circRNA-miRNAs-mRNA axis in human diseases. Oncotarget 8: 73271-73281.
  • Rozpedek W, Pytel D, Mucha B, Leszczynska H, Diehl JA et al. (2016). The role of the PERK/eIF2α/ATF4/CHOP signaling pathway in tumor progression during endoplasmic reticulum stress. Current Molecular Medicine 16: 533-544.
  • Ruan H, Xiang Y, Ko J, Li S, Jing Y et al. (2019). Comprehensive characterization of circular RNAs in ~1000 human cancer cell lines. Genome Medicine 11: 55.
  • Ruby JG, Jan CH, Bartel DP (2007). Intronic microRNA precursors that bypass Drosha processing. Nature 448: 83-86.
  • Yekta S, Shih IH, Bartel DP (2004). MicroRNA-directed cleavage of HOXB8 mRNA. Science 304: 594-596.
  • Sacconi A, Biagioni F, Canu V, Mori F, Di Benedetto A et al. (2012). miR-204 targets Bcl-2 expression and enhances responsiveness of gastric cancer. Cell Death & Disease 3: e423.
  • Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO (2012). Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLOS one 7: e30733.
  • Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK (1976). Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proceedings of the National Academy of Sciences of the United States of America 73: 3852-3856.
  • Schena M, Shalon D, Davis RW, Brown PO (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
  • Schlackow M, Nojima T, Gomes T, Dhir A, Carmo-Fonseca M et al. (2017). Distinctive patterns of transcription and RNA processing for human lincRNAs. Molecular Cell 65: 25-38.
  • Schneider T, Hung L-H, Schreiner S, Starke S, Eckhof H et al. (2016). CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs. Scientific Reports 6: 31313.
  • Schneider T, Schreiner S, Preußer C, Bindereif A, Rossbach O (2018). Northern blot analysis of circular RNAs. Methods in Molecular Biology 1724: 119-133.
  • Sealfon SC, Chu TT (2011). RNA and DNA microarrays. Methods in Molecular Biology 671: 3-34.
  • Sehgal L, Mathur R, Braun FK, Wise JF, Berkova Z et al. (2014). FAS-antisense 1 lncRNA and production of soluble versus membrane Fas in B-cell lymphoma. Leukemia 28: 2376-2387.
  • Sekar S, Geiger P, Cuyugan L, Boyle A, Serrano G et al. (2019). Identification of circular RNAs using RNA sequencing. Journal of Visualized Experiments 153.
  • Shi H, Ji Y, Zhang D, Liu Y, Fang P (2016). MicroRNA-3666-induced suppression of SIRT7 inhibits the growth of non-small cell lung cancer cells. Oncology Reports 36: 3051-3057.
  • Shi H, Zhou Y, Jia E, Pan M, Bai Y, Ge Q (2021). Bias in RNA-seq library preparation: Current challenges and solutions. BioMed Research International 2021: 6647597.
  • Shi R, Chiang VL (2005). Facile means for quantifying microRNA expression by real-time PCR. BioTechniques 39: 519-525.
  • Shi W, Gerster K, Alajez NM, Tsang J, Waldron L et al. (2011). MicroRNA-301 mediates proliferation and invasion in human breast cancer. Cancer Research 71: 2926-2937.
  • Shi Y, Lv C, Shi L, Tu G (2018). MEG3 inhibits proliferation and invasion and promotes apoptosis of human osteosarcoma cells. Oncology Letters 15: 1917-1923.
  • Shingara J, Keiger K, Shelton J, Laosinchai-Wolf W, Powers P et al. (2005). An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 11: 1461-1470.
  • Shrestha RK, Lubinsky B, Bansode VB, Moinz MBJ, McCormack GP et al. (2014). QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform. BMC Bioinformatics 15: 33.
  • Singh RP, Waldron RT, Hahn BH (2012). Genes, tolerance and systemic autoimmunity. Autoimmunity Reviews 11: 664-669. Siomi H, Siomi MC (2009). RISC hitches onto endosome trafficking. Nature Cell Biology 11: 1049-1051.
  • Sivandzade F, Bhalerao A, Cucullo L (2019). Analysis of the mitochondrial membrane potential using the cationic JC-1 dye as a sensitive fluorescent probe. Bio-protocol 9: e3128.
  • Song Y-Z, Li J-F (2018). Circular RNA hsa_circ_0001564 regulates osteosarcoma proliferation and apoptosis by acting miRNA sponge. Biochemical and Biophysical Research Communications 495: 2369-2375.
  • Stark R, Grzelak M, Hadfield J (2019). RNA sequencing: the teenage years. Nature Reviews Genetics 20: 631-656.
  • Starke S, Jost I, Rossbach O, Schneider T, Schreiner S et al. (2015). Exon circularization requires canonical splice signals. Cell Reports 10: 103-111.
  • Statello L, Guo C-J, Chen L-L, Huarte M (2020). Gene regulation by long non-coding RNAs and its biological functions. Nature Reviews Molecular Cell Biology 22: 96-118.
  • Su Z, Yang Z, Xu Y, Chen Y, Yu Q et al. (2015). MicroRNAs in apoptosis, autophagy and necroptosis. Oncotarget 6: 8474- 8490.
  • Subramanian S, Steer CJ (2010). MicroRNAs as gatekeepers of apoptosis. Journal of Cellular Physiology 223: 289-298.
  • Subtelny AO, Eichhorn SW, Chen GR, Sive H, Bartel DP (2014). Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508: 66-71.
  • Sun L, Xue H, Jiang C, Zhou H, Gu L et al. (2016). LncRNA DQ786243 contributes to proliferation and metastasis of colorectal cancer both in vitro and in vivo. Bioscience Reports 36: e00328.
  • Sun X, Liu B, Zhao X-D, Wang L-Y, Ji W-Y (2015). MicroRNA-221 accelerates the proliferation of laryngeal cancer cell line Hep-2 by suppressing Apaf-1. Oncology Reports 33: 1221-1226.
  • Szabo L, Salzman J (2016). Detecting circular RNAs: bioinformatic and experimental challenges. Nature Reviews Genetics 17: 679-692.
  • Szondy Z, Garabuczi E, Joós G, Tsay GJ, Sarang Z (2014). Impaired clearance of apoptotic cells in chronic inflammatory diseases: therapeutic implications. Frontiers in Immunology 5: 354.
  • Siddika T, Heinemann IU (2021). Bringing microRNAs to light: Methods for microRNA quantification and visualization in live cells. Frontiers in Bioengineering and Biotechnology 8: 619583.
  • Takeiwa T, Ikeda K, Horie-Inoue K, Inoue S (2021). Mechanisms of apoptosis-related long non-coding RNAs in ovarian cancer. Frontiers in Cell and Developmental Biology 9: 641963.
  • Tang M, Kui L, Lu G, Chen W (2020). Disease-Associated Circular RNAs: From Biology to Computational Identification. BioMed Research International 2020: 6798590.
  • Tang Q, Chen Z, Zhao L, Xu H (2019). Circular RNA hsa_ circ_0000515 acts as a miR-326 sponge to promote cervical cancer progression through up-regulation of ELK1. Aging 11: 9982-9999.
  • Tang Y-Y, Zhao P, Zou T-N, Duan J-J, Zhi R et al. (2017). Diseaseassociated circular RNAs: From biology to computational identification. DNA and Cell Biology 36: 901-908.
  • Teng X, Hardwick JM (2015). promotes breast cancer cell carcinogenesis through decreasingSeminars in Cell & Developmental Biology 39: 3-11.
  • Thomson JM, Parker JS, Hammond SM (2007). Microarray analysis of miRNA gene expression. Methods in Enzymology 427: 107- 122.
  • Thornberry NA, Bull HG, Calaycay JR, Chapman KT, Howard AD et al. (1992). A novel heterodimeric cysteine protease is required for interleukin-1 beta processing in monocytes. Nature 356: 768-774.
  • Tian F, Yu CT, Ye WD, Wang Q (2017). Cinnamaldehyde induces cell apoptosis mediated by a novel circular RNA hsa_circ_0043256 in non-small cell lung cancer. Biochemical and Biophysical Research Communications 493: 1260-1266.
  • Truesdell SS, Mortensen RD, Seo M, Schroeder JC, Lee JH et al. (2012). MicroRNA-mediated mRNA translation activation in quiescent cells and oocytes involves recruitment of a nuclear microRNP. Scientific Reports 2: 1-12.
  • Tsai M-C, Manor O, Wan Y, Mosammaparast N, Wang JK et al. (2010). Long noncoding RNA as modular scaffold of histone modification complexes. Science 329: 689-693.
  • Turchinovich A, Weiz L, Langheinz A, Burwinkel B (2011). Characterization of extracellular circulating microRNA. Nucleic Acids Research 39: 7223-7233.
  • Tw N (2007). Mechanisms of microRNA-mediated gene regulation in animal cells. Trends in Genetics 23: 243-249.
  • Válóczi A, Hornyik C, Varga N, Burgyán J, Kauppinen S et al. (2004). Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Research 32: e175.
  • Vasudevan S, Steitz JA (2007). AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell 128: 1105-1118.
  • Veneziano D, Nigita G, Ferro A (2015). Computational approaches for the analysis of ncRNA through deep sequencing techniques. Frontiers in Bioengineering and Biotechnology 3: 77.
  • Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L et al., (2019). Lncipedia 5: Towards a reference set of human long non-coding RNAs. Nucleic Acids Research 47: D135-D139.
  • Walker JC, Harland RM (2009). microRNA-24a is required to repress apoptosis in the developing neural retina. Genes & Development 23: 1046-1051.
  • Wang F, Chen X, Sun B, Ma Y, Niu W et al. (2021). Hypermethylationmediated downregulation of lncRNA PVT1 promotes granulosa cell apoptosis in premature ovarian insufficiency via interacting with Foxo3a. Journal of Cellular Physiology 236: 5162-5175.
  • Wang H, Ach RA, Curry B (2007). Direct and sensitive miRNA profiling from low-input total RNA. RNA 13: 151-159.
  • Wang J, Ma R, Ma W, Chen J, Yang J et al. (2016). LncDisease: A sequence based bioinformatics tool for predicting lncRNAdisease associations. Nucleic Acids Research 44: e90.
  • Wang K, Liu F, Zhou LY, Ding SL, Long B et al. (2013). miR-874 regulates myocardial necrosis by targeting caspase-8. Cell Death & Disease 4: e709.
  • Wang KC, Chang HY (2011). Molecular mechanisms of long concoding RNAs. Molecular Cell. 43: 904-914.
  • Wang L-G, Ni Y, Su B-H, Mu X-R, Shen H-C et al. (2013). MicroRNA34b functions as a tumor suppressor and acts as a nodal point in the feedback loop with Met. International Journal of Oncology 42: 957-962.
  • Wang L, Wei Y, Yan Y, Wang H, Yang J et al. (2018). CircDOCK1 suppresses cell apoptosis via inhibition of miR-196a-5p by targeting BIRC3 in OSCC. Oncology Reports 39: 951-966.
  • Wang M, Guo C, Wang L, Luo G, Huang C et al. (2018). Long noncoding RNA GAS5 promotes bladder cancer cells apoptosis through inhibiting EZH2 transcription. Cell Death & Disease 9: 1-16.
  • Wang M, Shi J, Jiang H, Xu K, Huang Z (2020). Circ_0014130 participates in the proliferation and apoptosis of nonsmall cell lung cancer cells via the miR-142-5p/IGF-1 axis. Cancer Biotherapy & Radiopharmaceuticals 35: 233-240.
  • Wang N, Liang H, Zhou Y, Wang C, Zhang S et al. (2014). miR203 suppresses the proliferation and migration and promotes the apoptosis of lung cancer cells by targeting PLOS One 9: e105570.
  • Wang X, Liu H, Shi L, Yu X, Gu Y et al. (2018). LINP1 facilitates DNA damage repair through non-homologous end joining (NHEJ) pathway and subsequently decreases the sensitivity of cervical cancer cells to ionizing radiation. Cell Cycle 17: 439-447.
  • Wang Z, Liu M, Zhu H, Zhang W, He S et al. (2013). miR-106a is frequently upregulated in gastric cancer and inhibits the extrinsic apoptotic pathway by targeting FAS. Molecular Carcinogenesis 52: 634-646.
  • Wang P, Zhuang L, Zhang J, Fan J, Luo J et al. (2013). The serum miR-21 level serves as a predictor for the chemosensitivity of advanced pancreatic cancer, and miR-21 expression confers chemoresistance by targeting FasL. Molecular Oncology 7: 334-345.
  • Wang L, Li L, Guo R, Li X, Lu Y et al. (2014). miR-101 promotes breast cancer cell apoptosis by targeting Janus kinase 2. Cellular Physiology and Biochemistry 34: 413-422.
  • Wang JT, Wang ZH (2018). Role of miR-193a-5p in the proliferation and apoptosis of hepatocellular carcinoma. European Review For Medical and Pharmacological Sciences 22: 7233-7239.
  • Wei W, Shi L, Chen W, Hu L, Chen D et al. (2018). miR-200c regulates the proliferation, apoptosis and invasion of gastric carcinoma cells through the downregulation of EDNRA expression. International Journal of Molecular Medicine 41: 1619-1626.
  • Whitley SK, Horne WT, Kolls JK (2016). Research techniques made simple: Methodology and clinical applications of RNA sequencing. Journal of Investigative Dermatology 136: e77-e82.
  • Wilusz JE (2016). Long noncoding RNAs: Re-writing dogmas of RNA processing and stability. Biochimica et Biophysica Acta 1859: 128-138.
  • Wilusz JE (2018). A 360° view of circular RNAs: From biogenesis to functions. Wiley Interdisciplinary Reviews RNA 9: e1478.
  • Wilusz JE, Sunwoo H, Spector DL (2009). Long noncoding RNAs: functional surprises from the RNA world. Genes & Development 23: 1494-1504.
  • Wu E, Vashisht AA, Chapat C, Flamand MN, Cohen E et al. (2017). A continuum of mRNP complexes in embryonic microRNAmediated silencing. Nucleic Acids Research 45: 2081-2098.
  • Wu F, Huang W, Wang X (2015). microRNA-18a regulates gastric carcinoma cell apoptosis and invasion by suppressing hypoxiainducible factor-1α expression. Experimental and Therapeutic Medicine 10: 717-722.
  • Wu J-H, Yao Y-L, Gu T, Wang Z-Y, Pu X-Y et al. (2014). MiR421 regulates apoptosis of BGC-823 gastric cancer cells by targeting caspase-3. Asian Pacific Journal of Cancer Prevention 15: 5463-5468.
  • Wu M-Z, Fu T, Chen J-X, Lin Y-Y, Yang J-E et al. (2020). LncRNA GOLGA2P10 is induced by PERK/ATF4/CHOP signaling and protects tumor cells from ER stress-induced apoptosis by regulating Bcl-2 family members. Cell Death & Disease 11: 1-12.
  • Wu P-H, Isaji M, Carthew Richard W (2013). Functionally diverse microRNA effector complexes are regulated by extracellular signaling. Molecular Cell 52: 113-123.
  • Wu T, Chen W, Kong D, Li X, Lu H et al. (2015). miR-25 targets the modulator of apoptosis 1 gene in lung cancer. Carcinogenesis 36: 925-935.
  • Wu W, Zhang S, Li X, Xue M, Cao S et al. (2013). Ets-2 regulates cell apoptosis via the Akt pathway, through the regulation of Urothelial Cancer Associated 1, a long non-coding RNA, in bladder cancer cells. PLOS One 8: e73920.
  • Wu Y, Liang S, Xu B, Zhang R, Zhu M et al. (2017). Long noncoding RNA eosinophil granule ontogeny transcript inhibits cell proliferation and migration and promotes cell apoptosis in human glioma. Experimental and Therapeutic Medicine 14: 3817-3823.
  • Wu Z, Liu Y, Wei L, Han M (2021). LncRNA OIP5-AS1 promotes breast cancer progression by regulating miR-216a-5p/GLO1. Journal of Surgical Research 257: 501-510.
  • Xiao C, Rajewsky K (2009). MicroRNA control in the immune system: basic principles. Cell 136: 26-36.
  • Xiao M, Li J, Li W, Wang Y, Wu F et al. (2017). MicroRNAs activate gene transcription epigenetically as an enhancer trigger. RNA Biology 14: 1326-1334.
  • Xie L, Huang W, Fang Z, Ding F, Zou F et al. (2019). CircERCC2 ameliorated intervertebral disc degeneration by regulating mitophagy and apoptosis through miR-182-5p/SIRT1 axis. Cell Death & Disease 10: 751.
  • Xie M, Li M, Vilborg A, Lee N, Shu M-D et al. (2013). Mammalian 5′-capped microRNA precursors that generate a single microRNA. Cell 155: 1568-1580.
  • Xing M (2010). Genetic alterations in the phosphatidylinositol-3 kinase/Akt pathway in thyroid cancer. Thyroid 20: 697-706.
  • Xu C, Zhang J (2021). Mammalian circular RNAs result largely from splicing errors. Cell Reports 36: 109439.
  • Xu W, Chang J, Du X, Hou J (2017). Long non-coding RNA PCAT1 contributes to tumorigenesis by regulating FSCN1 via miR145-5p in prostate cancer. Biomedicine & Pharmacotherapy 95: 1112-1118.
  • Xu Y, Yao Y, Leng K, Li Z, Qin W et al. (2017). Long non-coding RNA UCA1 indicates an unfavorable prognosis and promotes tumorigenesis via regulating AKT/GSK-3β; signaling pathway in cholangiocarcinoma. Oncotarget 8: 96203-96214.
  • Xue M, Peng N, Zhu X, Zhang H (2021). Hsa_circ_0006872 promotes cigarette smoke-induced apoptosis, inflammation and oxidative stress in HPMECs and BEAS-2B cells through the miR-145-5p/NF-κB axis. Biochemical and Biophysical Research Communications 534: 553-560.
  • Yamada KM, Araki M (2001). Tumor suppressor PTEN: modulator of cell signaling, growth, migration and apoptosis. Journal of Cell Science 114: 2375-2382.
  • Yang F, Zhu P, Guo J, Liu X, Wang S et al. (2017). Circular RNAs in thoracic diseases. Journal of Thoracic Disease 9: 5382-5389.
  • Yang G, Gong Y, Wang Q, Wang L, Zhang X (2016). miR-100 antagonism triggers apoptosis by inhibiting ubiquitinationmediated p53 degradation. Oncogene 36: 1023-1037.
  • Yang R, Li P, Zhang G, Lu C, Wang H et al. (2017). Long non-coding RNA XLOC_008466 functions as an oncogene in human non-small cell lung cancer by targeting miR-874. Cellular Physiology and Biochemistry 42: 126-136.
  • Yang S-z, Xu F, Zhou T, Zhao X, McDonald JM et al. (2017). The long non-coding RNA HOTAIR enhances pancreatic cancer resistance to TNF-related apoptosis-inducing ligand. Journal of Biological Chemistry 292: 10390-10397.
  • Yang S, Sun Z, Zhou Q, Wang W, Wang G et al. (2018). MicroRNAs, long noncoding RNAs, and circular RNAs: potential tumor biomarkers and targets for colorectal cancer. Cancer Management and Research 10: 2249-2249.
  • Yang T, Zhang W, Wang L, Xiao C, Guo B et al. (2019). Long intergenic noncoding RNA-p21 inhibits apoptosis by decreasing PUMA expression in non-small cell lung cancer. The Journal of International Medical Research 47: 481-493.
  • Yang W, Li Y, He F, Wu H (2015). Microarray profiling of long non-coding RNA (lncRNA) associated with hypertrophic cardiomyopathy. BMC Cardiovascular Disorders 15: 62.
  • Yaylak B, Akgül B (2022). microRNA detection methods. Methods in Molecular Biology 2257: 33-55.
  • Yaylak B, Erdogan I, Akgul B (2019). Transcriptomics analysis of circular RNAs differentially expressed in apoptotic HeLa cells. Frontiers in Genetics 10: 176.
  • Ye H, Zhou Q, Zheng S, Li G, Lin Q et al. (2018). FEZF1-AS1/miR107/ZNF312B axis facilitates progression and Warburg effect in pancreatic ductal adenocarcinoma. Cell Death & Disease 9:1-19.
  • Yin F, Zhang JN, Wang SW, Zhou CH, Zhao MM et al. (2015). MiR125a-3p regulates glioma apoptosis and invasion by regulating Nrg1. PLOS One 10: e0116759.
  • Yin Y, Gao H, Guo J, Gao Y (2017). [Effect of circular RNA UBAP2 silencing on proliferation and invasion of human lung cancer A549 cells and its mechanism]. Chinese Journal of Lung Cancer 20: 800-807.
  • Yin Y, Lu JY, Zhang X, Shao W, Xu Y et al. (2020). U1 snRNP regulates chromatin retention of noncoding RNAs. Nature 580: 147-150.
  • Yoda M, Kawamata T, Paroo Z, Ye X, Iwasaki S et al. (2009). ATPdependent human RISC assembly pathways. Nature Structural & Molecular Biology 17: 17-23.
  • Yu B, Yang Z, Li J, Minakhina S, Yang M et al. (2005). Methylation as a crucial step in plant microRNA biogenesis. Science 307: 932-935.
  • Yu C-Y, Liu H-J, Hung L-Y, Kuo H-C, Chuang T-J (2014). Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro? Nucleic Acids Research 42: 9410-9423.
  • Yu L, Zhou GQ, Li DC (2018). MiR-136 triggers apoptosis in human gastric cancer cells by targeting AEG-1 and BCL2. European Review for Medical and Pharmacological Sciences 22: 7251- 7256.
  • Yuan L, Li S, Zhou Q, Wang D, Zou D et al. (2017). MiR-124 inhibits invasion and induces apoptosis of ovarian cancer cells by targeting programmed cell death 6. Oncology Letters 14: 7311- 7311.
  • Zamudio JR, Kelly TJ, Sharp PA (2014). Argonaute-bound small RNAs from promoter-proximal RNA polymerase II. Cell 156: 920-934.
  • Zalfa F, Achsel T, Bagni C (2006). mRNPs, polysomes or granules: FMRP in neuronal protein synthesis. Current Opinion in Neurobiology 16: 265-269.
  • Zeka F, Mestdagh P, Vandesompele J (2015). RT-qPCR-based quantification of small non-coding RNAs. Methods in Molecular Biology 1296: 85-102.
  • Zembruski NCL, Stache V, Haefeli WE, Weiss J (2012). 7-Aminoactinomycin D for apoptosis staining in flow cytometry. Analytical Biochemistry 429: 79-81.
  • Zeng Q, Wan H, Zhao S, Xu H, Tang T et al. (2020). Role of PIWIinteracting RNAs on cell survival: Proliferation, apoptosis, and cycle. IUBMB Life 72: 1870-1878.
  • Zhang B, Yi J, Zhang CL, Zhang QH, Xu JF et al. (2017). MiR146a inhibits proliferation and induces apoptosis in murine osteoblastic MC3T3-E1 by regulating Bcl2. European Review for Medical and Pharmacological Sciences 21: 3754-3762.
  • Zhang L, Xu HG, Lu C (2014). A novel long non-coding RNA T-ALL-R-LncR1 knockdown and Par-4 cooperate to induce cellular apoptosis in T-cell acute lymphoblastic leukemia cells. Leukemia & Lymphoma 55: 1373-1382.
  • Zhang C, Ge S, Gong W, Xu J, Guo Z et al. (2020). LncRNA ANRIL acts as a modular scaffold of WDR5 and HDAC3 complexes and promotes alteration of the vascular smooth muscle cell phenotype. Cell Death & Disease 11: 1-13.
  • Zhang H, Wang X, Huang H, Wang Y, Zhang F et al. (2019). Hsa_ circ_0067997 promotes the progression of gastric cancer by inhibition of miR-515-5p and activation of X chromosomelinked inhibitor of apoptosis (XIAP). Artificial Cells, Nanomedicine, and Biotechnology 47: 308-318.
  • Zhang R, Xu J, Zhao J, Wang X (2018). Silencing of hsa_circ_0007534 suppresses proliferation and induces apoptosis in colorectal cancer cells. European Review for Medical and Pharmacological Sciences 22: 118-126.
  • Zhang S, Zeng X, Ding T, Guo L, Li Y et al. (2018). Microarray profile of circular RNAs identifies hsa_circ_0014130 as a new circular RNA biomarker in non-small cell lung cancer. Scientific Reports 8: 2878.
  • Zhang X, Lu J, Zhang Q, Luo Q, Liu B (2021). CircRNA RSF1 regulated ox-LDL induced vascular endothelial cells proliferation, apoptosis and inflammation through modulating miR-135b5p/HDAC1 axis in atherosclerosis. Biological Research 54: 11.
  • Zhang X, Wang W, Zhu W, Dong J, Cheng Y et al. (2019). Mechanisms and functions of long non-coding RNAs at multiple regulatory levels. International Journal of Molecular Sciences 20: 5573.
  • Zhang Y, Zang Q, Xu B, Zheng W, Ban R et al. (2016). IsomiR Bank: a research resource for tracking IsomiRs. Bioinformatics 32: 2069-2071.
  • Zhang Y, Zou Y, Wang W, Zuo Q, Jiang Z et al. (2015). Downregulated long non-coding RNA MEG3 and its effect on promoting apoptosis and suppressing migration of trophoblast cells. Journal of Cellular Biochemistry 116: 542-550.
  • Zhang ZX, Liu ZQ, Jiang B, Lu XY, Ning XF et al. (2015). BRAF activated non-coding RNA (BANCR) promoting gastric cancer cells proliferation via regulation of NF-κB1. Biochemical and Biophysical Research Communications 465: 225-231.
  • Zhang H, Li Y, Huang Q, Hu H, Sheng H, Lai M (2011). MiR-148a promotes apoptosis by targeting Bcl-2 in colorectal cancer. Cell Death and Differentiation 18:1702-1710.
  • Zhao B, Ding S, Li W, Jin Y (2011). Hybridization kinetics analysis of an oligonucleotide microarray for microRNA detection. Acta Biochimica et Biophysica Sinica 43: 551-555.
  • Zhao B, Gong Z, Ma Z, Wang D, Jin Y (2015). Simple and sensitive microRNA labeling by terminal deoxynucleotidyl transferase. Acta Biochim Biophys Sin 44: 129-135.
  • Zhao F, Lin T, He W, Han J, Zhu D et al. (2014). Knockdown of a novel lincRNA AATBC suppresses proliferation and induces apoptosis in bladder cancer. Oncotarget 6: 1064-1078.
  • Zhao H, Zhang X, Frazao JB, Condino-Neto A, Newburger PE (2013). HOX antisense lincRNA HOXA-AS2 is an apoptosis repressor in all trans retinoic acid treated NB4 promyelocytic leukemia cells. Journal of Cellular Biochemistry 114: 2375- 2383.
  • Zhao J, Qi X, Bai J, Gao X, Cheng L (2020). A circRNA derived from linear HIPK3 relieves the neuronal cell apoptosis in spinal cord injury via ceRNA pattern. Biochemical and Biophysical Research Communications 528: 359-367.
  • Zhao J, Zou H, Han C, Ma J, Zhao J et al. (2018). Circlular RNA BARD1 (Hsa_circ_0001098) overexpression in breast cancer cells with TCDD treatment could promote cell apoptosis via miR-3942/BARD1 axis. Cell Cycle 17: 2731-2744.
  • Zhao S, Zhang Y, Gamini R, Zhang B, von Schack D (2018). Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion. Scientific Reports 8: 4781.
  • Zhao Y, Liu X, Lu YX (2017). MicroRNA-143 regulates the proliferation and apoptosis of cervical cancer cells by targeting HIF-1α. European Review for Medical And Pharmacological Sciences 21: 5580-5586.
  • Zheng C, Niu H, Li M, Zhang H, Yang Z et al. (2015). Cyclic RNA hsa-circ-000595 regulates apoptosis of aortic smooth muscle cells. Molecular medicine reports 12: 6656-6662.
  • Zheng J, Li XD, Wang P, Liu XB, Xue YX et al. (2015). CRNDE affects the malignant biological characteristics of human glioma stem cells by negatively regulating miR-186. Oncotarget 6: 25339- 25355.
  • Zheng Z, Qu J-Q, Yi H-M, Ye X, Huang W et al. (2017). MiR-125b regulates proliferation and apoptosis of nasopharyngeal carcinoma by targeting A20/NF-κB signaling pathway. Cell Death & Disease 8: e2855-e2855.
  • Zhong S, Wang J, Zhang Q, Xu H, Feng J (2018). CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers. BMC Bioinformatics 19: 292.
  • Zhou Y, Zhong Y, Wang Y, Zhang X, Batista DL et al. (2007). Activation of p53 by MEG3 non-coding RNA. Journal of Biological Chemistry 282: 24731-24742.
  • Zhu H, Li X, Song Y, Zhang P, Xiao Y et al. (2015). Long non-coding RNA ANRIL is up-regulated in bladder cancer and regulates bladder cancer cell proliferation and apoptosis through the intrinsic pathway. Biochemical and Biophysical Research Communications 467: 223-228.
APA Tüncel Ö, Kara M, Yaylak B, ERDOGAN VATANSEVER I, Akgül B (2022). Noncoding RNAs in apoptosis: identification and function. , 1 - 40. 10.3906/biy-2109-35
Chicago Tüncel Özge,Kara Merve,Yaylak Bilge,ERDOGAN VATANSEVER IPEK,Akgül Bünyamin Noncoding RNAs in apoptosis: identification and function. (2022): 1 - 40. 10.3906/biy-2109-35
MLA Tüncel Özge,Kara Merve,Yaylak Bilge,ERDOGAN VATANSEVER IPEK,Akgül Bünyamin Noncoding RNAs in apoptosis: identification and function. , 2022, ss.1 - 40. 10.3906/biy-2109-35
AMA Tüncel Ö,Kara M,Yaylak B,ERDOGAN VATANSEVER I,Akgül B Noncoding RNAs in apoptosis: identification and function. . 2022; 1 - 40. 10.3906/biy-2109-35
Vancouver Tüncel Ö,Kara M,Yaylak B,ERDOGAN VATANSEVER I,Akgül B Noncoding RNAs in apoptosis: identification and function. . 2022; 1 - 40. 10.3906/biy-2109-35
IEEE Tüncel Ö,Kara M,Yaylak B,ERDOGAN VATANSEVER I,Akgül B "Noncoding RNAs in apoptosis: identification and function." , ss.1 - 40, 2022. 10.3906/biy-2109-35
ISNAD Tüncel, Özge vd. "Noncoding RNAs in apoptosis: identification and function". (2022), 1-40. https://doi.org/10.3906/biy-2109-35
APA Tüncel Ö, Kara M, Yaylak B, ERDOGAN VATANSEVER I, Akgül B (2022). Noncoding RNAs in apoptosis: identification and function. Turkish Journal of Biology, 46(1), 1 - 40. 10.3906/biy-2109-35
Chicago Tüncel Özge,Kara Merve,Yaylak Bilge,ERDOGAN VATANSEVER IPEK,Akgül Bünyamin Noncoding RNAs in apoptosis: identification and function. Turkish Journal of Biology 46, no.1 (2022): 1 - 40. 10.3906/biy-2109-35
MLA Tüncel Özge,Kara Merve,Yaylak Bilge,ERDOGAN VATANSEVER IPEK,Akgül Bünyamin Noncoding RNAs in apoptosis: identification and function. Turkish Journal of Biology, vol.46, no.1, 2022, ss.1 - 40. 10.3906/biy-2109-35
AMA Tüncel Ö,Kara M,Yaylak B,ERDOGAN VATANSEVER I,Akgül B Noncoding RNAs in apoptosis: identification and function. Turkish Journal of Biology. 2022; 46(1): 1 - 40. 10.3906/biy-2109-35
Vancouver Tüncel Ö,Kara M,Yaylak B,ERDOGAN VATANSEVER I,Akgül B Noncoding RNAs in apoptosis: identification and function. Turkish Journal of Biology. 2022; 46(1): 1 - 40. 10.3906/biy-2109-35
IEEE Tüncel Ö,Kara M,Yaylak B,ERDOGAN VATANSEVER I,Akgül B "Noncoding RNAs in apoptosis: identification and function." Turkish Journal of Biology, 46, ss.1 - 40, 2022. 10.3906/biy-2109-35
ISNAD Tüncel, Özge vd. "Noncoding RNAs in apoptosis: identification and function". Turkish Journal of Biology 46/1 (2022), 1-40. https://doi.org/10.3906/biy-2109-35
Sayfa Oluşturulma Tarihi
02-04-2024 21:29

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