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Molecular insights into regulatory RNAs in the cellular machinery

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참고문헌

주제분류생화학

초록

It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.

Abstract

It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.

참고문헌 (252)

  1. Bizuayehu, T. T., "Long-read single-molecule RNA structure sequencing using nanopore", Nucleic Acids Res, 50, pp.e120~ (2022)
  2. Guh, C. Y., "Functions and properties of nuclear lncRNAs-from systematically mapping the interactomes of lncRNAs", J. Biomed. Sci, 27, pp.44~ (2020)
  3. Jones, C. P., "RNA quaternary structure and global sym metry", Trends Biochem. Sci, 40, pp.211~220 (2015)
  4. Chen, K., "LncRNA SNHG6 promotes glycolysis reprogramming in hepatocellular carcinoma by stabilizing the BOP1 protein", Anim. Cells Syst, 26, pp.369~379 (2022)
  5. Wright, B. W., "The dark proteome: translation from noncanonical open reading frames", Trends Cell Biol, 32, pp.243~258 (2022)
  6. Huang, Z., "The role of long noncoding RNAs in hepatocellular carcinoma", Mol. Cancer, 19, pp.77~ (2020)
  7. Kaikkonen, M. U., "Non-coding RNAs as regulators of gene expression and epigenetics", Cardiovasc. Res, 90, pp.430~440 (2011)
  8. Wei, L., "The emerging role of microRNAs and long noncoding RNAs in drug resistance of hepatocellular carcinoma", Mol. Cancer, 18, pp.147~ (2019)
  9. Morris, K. V., "The rise of regulatory RNA", Nat. Rev. Genet, 15, pp.423~437 (2014)
  10. Ransohoff, J. D., "The functions and unique features of long intergenic non-coding RNA", Nat. Rev. Mol. Cell Biol, 19, pp.143~157 (2018)
  11. Yang, S., "Molecular landscape of long noncoding RNAs in brain disorders", Mol. Psychiatry, 26, pp.1060~1074 (2021)
  12. Mattick, J. S., "Long non-coding RNAs : definitions, functions, challenges and recommendations", Nat. Rev. Mol. Cell Biol, 24, pp.430~447 (2023)
  13. Statello, L., "Gene regulation by long non coding RNAs and its biological functions", Nat. Rev. Mol. Cell Biol, 22, pp.96~118 (2021)
  14. Lim, K. H., "Discoveries for long non coding RNA dynamics in traumatic brain injury", Biology, 9 (2020)[DOI]
  15. Kim, S. H., "Long non-coding RNAs in brain tumors : roles and potential as therapeutic targets", J. Hematol. Oncol, 14, pp.77~ (2021)
  16. Sartorelli, V., "Enhancer RNAs are an important regulatory layer of the epigenome", Nat. Struct. Mol. Biol, 27, pp.521~528 (2020)
  17. Han, Z., "Enhancer RNA : what we know and what we can achieve", Cell Prolif, 55, pp.e13202~ (2022)
  18. Shang, R., "microRNAs in action : biogenesis, function and regulation", Nat. Rev. Genet, 24, pp.816~833 (2023)
  19. Khanbabaei, H., "Non-coding RNAs and epithelial mesenchymal transition in cancer : molecular mechanisms and clinical implications", J. Exp. Clin. Cancer Res, 41, pp.278~ (2022)
  20. O’Brien, J., "Overview of microRNA biogenesis, mechanisms of actions, and circulation", Front Endocrinol, 9, pp.402~ (2018)
  21. Ng, K. W., "Piwi-interacting RNAs in cancer : emerging functions and clinical utility", Mol. Cancer, 15, pp.5~ (2016)
  22. Cao, T., "Biology and clinical relevance of noncoding sno", scaRNAs, 2018, pp.28, 81~90
  23. Huang, Z. H., "snoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology", Cell Death Discov, 8, pp.259~ (2022)
  24. He, A. T., "Targeting circular RNAs as a therapeutic approach : current strategies and challenges", Signal. Transduct. Target Ther, 6, pp.185~ (2021)
  25. Kristensen, L. S., "The biogenesis, biology and characterization of circular RNAs", Nat. Rev. Genet, 20, pp.675~691 (2019)
  26. Sun, Y. M., "Principles and innovative technologies for decrypting noncoding RNAs : from discovery and functional prediction to clinical applica tion", J. Hematol. Oncol, 13, pp.109~ (2020)
  27. Hou, T. Y., "Spirits in the material world : enhancer RNAs in tran scriptional regulation", Trends Biochem. Sci, 46, pp.138~153 (2021)
  28. Li, Q., "Enhancer RNAs : mechanisms in transcriptional regulation and functions in diseases", Cell Commun. Signal, 21, pp.191~ (2023)
  29. Li, J., "An NGS workflow blueprint for DNA sequencing data and its application in individualized molecular oncology", Cancer Inf, 14, pp.87~107 (2015)
  30. Hess, J. F., "Library preparation for next generation sequencing : a review of automation strategies", Biotechnol. Adv, 41, pp.107537~ (2020)
  31. Mumbach, M. R., "HiChIRP reveals RNA-associated chromosome con formation", Nat. Methods, 16, pp.489~492 (2019)
  32. Jung, N., "Advances in higher-order chromatin architecture : the move towards 4D genome", BMB Rep, 54, pp.233~245 (2021)
  33. Bell, J. C., "Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts", Elife, 7 (2018)[DOI]
  34. Bonetti, A., "RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions", Nat. Commun, 11, pp.1018~ (2020)
  35. Horlacher, M., "Towards in silico CLIP-seq : predicting protein-RNA interac tion via sequence-to-signal learning", Genome Biol, 24, pp.180~ (2023)
  36. Jensen, K. B., "CLIP : crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins", Methods Mol. Biol, 488, pp.85~98 (2008)
  37. Spitzer, J., "PAR-CLIP(photoactivatable ribonucleoside-enhanced cross linking and immunoprecipitation) : a step-by-step protocol to the transcriptome wide identification of binding sites of RNA-binding proteins", Methods Enzymol, 539, pp.113~161 (2014)
  38. Garzia, A., "Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins", Methods, 118-119, pp.24~40 (2017)
  39. Konig, J., "iCLIP reveals the function of hnRNP particles in splicing at indi vidual nucleotide resolution", Nat. Struct. Mol. Biol, 17, pp.909~915 (2010)
  40. Huppertz, I., "iCLIP : protein-RNA interactions at nucleotide resolution", Methods, 65, pp.274~287 (2014)
  41. Cai, Z., "RIC-seq for global in situ profiling of RNA-RNA spatial interactions", Nature, 582, pp.432~437 (2020)
  42. Margasyuk, S., "RNA in situ conformation sequencing reveals novel long range RNA structures with impact on splicing", RNA, 29, pp.1423~1436 (2023)
  43. Nguyen, T. C., "Mapping RNA-RNA interactome and RNA structure in vivo by MARIO", Nat. Commun, 7, pp.12023~ (2016)
  44. Zubradt, M., "DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo", Nat. Methods, 14, pp.75~82 (2017)
  45. Jin, Q., "Probing in vivo RNA structure with optimized DMS-MaPseq in rice", Front. Plant Sci, 13, pp.869267~ (2022)
  46. Morandi, E., "Genome-scale deconvolution of RNA structure ensembles", Nat. Methods, 18, pp.249~252 (2021)
  47. Sanz, L. A., "High-resolution, strand-specific R-loop mapping via S9.6based DNA-RNA immunoprecipitation and high-throughput sequencing", Nat. Protoc, 14, pp.1734~1755 (2019)
  48. Halasz, L., "RNA-DNA hybrid(R-loop)immunoprecipitation mapping : an analytical workflow to evaluate inherent biases", Genome Res, 27, pp.1063~1073 (2017)
  49. Wahba, L., "S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation", Genes Dev, 30, pp.1327~1338 (2016)
  50. Sanz, L. A., "Prevalent, dynamic, and conserved r-loop structures associate with specific epigenomic signatures in mammals", Mol. Cell, 63, pp.167~178 (2016)
  51. Dumelie, J. G., "Defining the location of promoter-associated R loops at near-nucleotide resolution using bisDRIP-seq", Elife, 6 (2017)[DOI]
  52. Williams, C. G., "An intro duction to spatial transcriptomics for biomedical research", Genome Med, 14, pp.68~ (2022)
  53. Marx, V., "Method of the year : spatially resolved transcriptomics", Nat. Methods, 18, pp.9~14 (2021)
  54. Riba, A., "Cell cycle gene regulation dynamics revealed by RNA velocity and deep-learning", Nat. Commun, 13, pp.2865~ (2022)
  55. Kozomara, A., "miRBase : from microRNA sequences to function", Nucleic Acids Res, 47, pp.D155~D162 (2019)
  56. Zhao, L., "NONCODEV6 : an updated database dedicated to long non-coding RNA annotation in both animals and plants", Nucleic Acids Res, 49, pp.D165~D171 (2021)
  57. Kariuki, D., "Review of databases for experimentally validated human microRNA-mRNA interactions", Database (2023)[DOI]
  58. Kalvari, I., "Non-coding RNA analysis using the rfam database", Curr. Protoc. Bioinform, 62, pp.e51~ (2018)
  59. Amaral, P. P., "lncRNAdb:a reference database for long noncoding RNAs", Nucleic Acids Res, 39, pp.D146~D151 (2011)
  60. Lagarde, J., "High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing", Nat. Genet, 49, pp.1731~1740 (2017)
  61. Ganser, L. R., "The roles of structural dynamics in the cellular functions of RNAs", Nat. Rev. Mol. Cell Biol, 20, pp.474~489 (2019)
  62. Vicens, Q., "Thoughts on how to think(and talk)about RNA structure", Proc. Natl Acad. Sci. USA, 119, pp.e2112677119~ (2022)
  63. Lu, W., "Research on RNA secondary structure predicting via bidirectional recurrent neural network", BMC Bioinform, 22, pp.431~ (2021)
  64. Zhao, Q., "Review of machine learning methods for RNA secondary structure prediction", PLoS Comput. Biol, 17, pp.e1009291~ (2021)
  65. Wang, X. W., "RNA structure probing uncovers RNA structure-dependent biological functions", Nat. Chem. Biol, 17, pp.755~766 (2021)
  66. Kedde, M., "A pumilio-induced RNA structure switch in p27-3’ UTR controls miR-221 and miR-222 accessibility", Nat. Cell Biol, 12, pp.1014~1020 (2010)
  67. Imperatore, J. A., "Characterization of a G-quadruplex structure in pre-miRNA-1229 and in its Alzheimer’s disease associated variant rs2291418: implications for miRNA-1229 maturation", Int. J. Mol. Sci, 21 (2020)[DOI]
  68. Richard, P., "A common sequence motif determines the Cajal body-specific localization of box H", ACA scaRNAs, 2003, pp.22, 4283~4293
  69. Cerneckis, J., "Decoding pseudouridine : an emerging target for therapeutic development", Trends Pharm. Sci, 43, pp.522~535 (2022)
  70. Dethoff, E. A., "Functional complexity and regulation through RNA dynamics", Nature, 482, pp.322~330 (2012)
  71. Chaulk, S. G., "Role of pri-miRNA tertiary structure in miR-17~92 miRNA biogenesis", RNA Biol, 8, pp.1105~1114 (2011)
  72. Chakraborty, S., "Pri-miR-17-92a tran script folds into a tertiary structure and autoregulates its processing", RNA, 18, pp.1014~1028 (2012)
  73. Gan, H. H., "The role of tertiary structure in MicroRNA target recognition", Methods Mol. Biol, 1970, pp.43~64 (2019)
  74. Uroda, T., "Conserved pseudoknots in lncRNA MEG3 are essential for sti mulation of the p53 pathway", Mol. Cell, 75, pp.982~995 (2019)
  75. Fan, S., "lncRNA CISAL inhibits BRCA1 transcription by forming a tertiary structure at its promoter", iScience, 23, pp.100835~ (2020)
  76. Bernat, V., "RNA structures as mediators of neurological diseases and as drug targets", Neuron, 87, pp.28~46 (2015)
  77. Rybak-Wolf, A., "RNA dynamics in Alzheimer’s disease", Molecules, 26 (2021)[DOI]
  78. Liu, W., "Linking RNA dynamics to heart disease : the lncRNA", miRNA, Hypertens. Res, pp.2022, 45[DOI]
  79. Carlevaro-Fita, J., "Global positioning system : understanding long noncoding RNAs through subcellular localization", Mol. Cell, 73, pp.869~883 (2019)
  80. Mas-Ponte, D., "LncATLAS database for subcellular localization of long noncoding RNAs", RNA, 23, pp.1080~1087 (2017)
  81. Tong, C., "Localization of RNAs in the nucleus : cis-and trans-regulation", RNA Biol, 18, pp.2073~2086 (2021)
  82. Deng, S., "3D chromatin architecture and transcription regulation in cancer", J. Hematol. Oncol, 15, pp.49~ (2022)
  83. Limouse, C., "Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions", Nat. Commun, 14, pp.6073~ (2023)
  84. Li, X., "GRID-seq reveals the global RNA-chromatin interactome", Nat. Bio technol, 35, pp.940~950 (2017)
  85. Wang, K. C., "A long noncoding RNA maintains active chromatin to coor dinate homeotic gene expression", Nature, 472, pp.120~124 (2011)
  86. Singh, A. P., "A coordinated function of lncRNA HOTTIP and miRNA-196b underpinning leukemogenesis by targeting FAS signaling", Oncogene, 41, pp.718~731 (2022)
  87. Gupta, R. A., "Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis", Nature, 464, pp.1071~1076 (2010)
  88. Mozdarani, H., "The emerging role of the long non-coding RNA HOTAIR in breast cancer development and treatment", J. Transl. Med, 18, pp.152~ (2020)
  89. Portoso, M., "PRC2 is dispensable for HOTAIR-mediated transcriptional repression", EMBO J, 36, pp.981~994 (2017)
  90. Chen, C. K., "Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing", Science, 354, pp.468~472 (2016)
  91. Brockdorff, N., "Progress toward understanding chro mosome silencing by Xist RNA", Genes Dev, 34, pp.733~744 (2020)
  92. Dossin, F., "The molecular and nuclear dynamics of X-chromosome inactivation", Cold Spring Harb. Perspect. Biol, 14 (2022)[DOI]
  93. Engreitz, J. M., "Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression", Nat. Rev. Mol. Cell Biol, 17, pp.756~770 (2016)
  94. Sarkar, M. K., "An Xist-activating antisense RNA required for X-chromosome inactivation", Nat. Commun, 6, pp.8564~ (2015)
  95. Gjaltema, R. A. F., "Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus", Mol. Cell, 82, pp.190~208 (2022)
  96. Sun, S., "Jpx RNA activates Xist by evicting CTCF", Cell, 153, pp.1537~1551 (2013)
  97. Yang, F., "The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF andmaintainsH3K27me3 methylation", Genome Biol, 16, pp.52~ (2015)
  98. Kotzin, J. J., "The long non-coding RNA morrbid regulates Bim and short lived myeloid cell lifespan", Nature, 537, pp.239~243 (2016)
  99. Petermann, E., "Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids", Nat. Rev. Mol. Cell Biol, 23, pp.521~540 (2022)
  100. Skourti-Stathaki, K., "A double-edged sword : R loops as threats to genome integrity and powerful regulators of gene expression", Genes Dev, 28, pp.1384~1396 (2014)
  101. Boque-Sastre, R., "Head-to-head antisense transcription and R-loop forma tion promotes transcriptional activation", Proc. Natl Acad. Sci. USA, 112, pp.5785~5790 (2015)
  102. Gong, D., "Long noncoding RNA Lnc530 localizes on R-loops and regulates R-loop formation and genomic stability in mouse embryonic stem cells", Stem Cell Rep, 18, pp.952~968 (2023)
  103. Arab, K., "GADD45A binds R-loops and recruits TET1 to CpG island pro moters", Nat. Genet, 51, pp.217~223 (2019)
  104. Shlyueva, D., "Transcriptional enhancers : from properties to genome-wide predictions", Nat. Rev. Genet, 15, pp.272~286 (2014)
  105. Andersson, R., "Determinants of enhancer and promoter activities of regulatory elements", Nat. Rev. Genet, 21, pp.71~87 (2020)
  106. Joo, J. Y., "Stimulus-specific combinatorial functionality of neuronal c-fos enhancers", Nat. Neurosci, 19, pp.75~83 (2016)
  107. Mikhaylichenko, O., "The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription", Genes Dev, 32, pp.42~57 (2018)
  108. Kim, T. K., "Widespread transcription at neuronal activity-regulated enhan cers", Nature, 465, pp.182~187 (2010)
  109. Schaukowitch, K., "Enhancer RNA facilitates NELF release from immediate early genes", Mol. Cell, 56, pp.29~42 (2014)
  110. Tsai, P. F., "A muscle-specific enhancer RNA mediates cohesin recruitment and regulates transcription in trans", Mol. Cell, 71, pp.129~141 (2018)
  111. Gorbovytska, V., "Enhancer RNAs stimulate Pol II pause release by harnes sing multivalent interactions to NELF", Nat. Commun, 13, pp.2429~ (2022)
  112. Liang, L., "Complementary Alu sequences mediate enhancer-promoter selectivity", Nature, 619, pp.868~875 (2023)
  113. Pott, S., "What are super-enhancers?", Nat. Genet, 47, pp.8~12 (2015)
  114. Hnisz, D., "Super-enhancers in the control of cell identity and disease", Cell, 155, pp.934~947 (2013)
  115. Chen, H., "A high-resolution map of human enhancer RNA loci char acterizes super-enhancer activities in cancer", Cancer Cell, 38, pp.701~715 (2020)
  116. Fujinaga, K., "P-TEFb : the master regulator of tran scription elongation", Mol. Cell, 83, pp.393~403 (2023)
  117. Flynn, R. A., "7SK-BAF axis controls pervasive transcription at enhancers", Nat. Struct. Mol. Biol, 23, pp.231~238 (2016)
  118. Egloff, S., "The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression", EMBO J, 36, pp.934~948 (2017)
  119. Roberts, T. C., "The microRNA biology of the mammalian nucleus", Mol. Ther. Nucleic Acids, 3, pp.e188~ (2014)
  120. Kim, J. Y., "The role of microRNAs in the molecular link between circadian rhythm and autism spectrum disorder", Anim. Cells Syst, 27, pp.38~52 (2023)
  121. Leucci, E., "microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus", Sci. Rep, 3, pp.2535~ (2013)
  122. Hansen, T. B., "miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA", EMBO J, 30, pp.4414~4422 (2011)
  123. Laitinen, P., "Nuclear microRNA-466c regulates Vegfa expression in response to hypoxia", PLoS One, 17, pp.e0265948~ (2022)
  124. Chen, S., "The long non-coding RNA KLF3-AS1", miR-10a-3p, Cell Tissue Res, pp.2023, 393[DOI]
  125. Dinami, R., "MiR-182-3p targets TRF2 and impairs tumor growth of triple negative breast cancer", EMBO Mol. Med, 15, pp.e16033~ (2023)
  126. Hill, M., "Global miRNA to miRNA Interactions : Impacts for miR-21", Trends Cell Biol, 31, pp.3~5 (2021)
  127. Zhu, S., "MicroRNA-21 targets tumor suppressor genes in invasion and metastasis", Cell Res, 18, pp.350~359 (2008)
  128. Kartha, R. V., "Competing endogenous RNAs (ceRNAs): new entrants to the intricacies of gene regulation", Front. Genet, 5, pp.8~ (2014)
  129. Xu, S., "The multiple function of long noncoding RNAs in osteosarcoma progression, drug resistance and prognosis", Biomed. Pharmacother, 127, pp.110141~ (2020)
  130. Jang, W., "Hippo-YAP", TAZ pathway regulation : the crucial roles of lncRNAs in cancer, 2023, pp.27, 309~320
  131. Schmidt, K., "Targeting the oncogenic long non-coding RNA SLNCR1 by blocking its sequence-specific binding to the androgen receptor", Cell Rep, 30, pp.541~554 (2020)
  132. Castellanos-Rubio, A., "Cytoplasmic form of Carlr lncRNA facilitates inflam matory gene expression upon NF-kappaB activation", J. Immunol, 199, pp.581~588 (2017)
  133. Qin, M., "lncRNA PRR34-AS1 promotes HCC development via modulating Wnt", beta-catenin pathway by absorbing miR-296-5p and upregulating E2F2and SOX12, 2021, pp.25, 37~52
  134. Wang, Z., "Telomeric repeat-containing RNA(TERRA)constitutes a nucleo protein component of extracellular inflammatory exosomes", Proc. Natl Acad. Sci. USA, 112, pp.E6293~E6300 (2015)
  135. Jaenisch, R., "Epigenetic regulation of gene expression : how the gen ome integrates intrinsic and environmental signals", Nat. Genet, 33, pp.245~254 (2003)
  136. Baxter, E., "Epigenetic regulation in cancer progression", Cell Biosci, 4, pp.45~ (2014)
  137. Zhang, L., "Epigenetics in health and disease", Adv. Exp. Med. Biol, 1253, pp.3~55 (2020)
  138. Helm, M., "Detecting RNA modifications in the epitranscriptome : predict and validate", Nat. Rev. Genet, 18, pp.275~291 (2017)
  139. Roundtree, I. A., "Dynamic RNA modifications in gene expression regulation", Cell, 169, pp.1187~1200 (2017)
  140. Barbieri, I., "Role of RNA modifications in cancer", Nat. Rev. Cancer, 20, pp.303~322 (2020)
  141. Matsumura, Y., "Epitranscriptomics in metabolic disease", Nat. Metab, 5, pp.370~384 (2023)
  142. Shi, H., "Where, when, and how : context-dependent functions of RNA methylation writers, readers, and erasers", Mol. Cell, 74, pp.640~650 (2019)
  143. Ru, W., "Insight into m(6)A methylation from occurrence to functions", Open Biol, 10, pp.200091~ (2020)
  144. Lee, J. H., "Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation", Mol. Cell, 81, pp.3368~3385 (2021)
  145. Pendleton, K. E., "The U6 snRNA m(6)A methyltransferase METTL16 regulates SAM synthetase intron retention", Cell, 169, pp.824~835 (2017)
  146. van Tran, N., "The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112", Nucleic Acids Res, 47, pp.7719~7733 (2019)
  147. Ma, H., "N(6-)Methyladenosine methyltransferase ZCCHC4 mediates ribo somal RNA methylation", Nat. Chem. Biol, 15, pp.88~94 (2019)
  148. Alarcon, C. R., "HNRNPA2B1 is a mediator of m(6)A-dependent nuclear RNA processing events", Cell, 162, pp.1299~1308 (2015)
  149. Alarcon, C. R., "N6methyladenosine marks primary microRNAs for processing", Nature, 519, pp.482~485 (2015)
  150. Zhou, C., "Genome-wide maps of m6A circRNAs identify widespread and cell-type-specific methylation patterns that are distinct from mRNAs", Cell Rep, 20, pp.2262~2276 (2017)
  151. Yang, Y., "Extensive translation of circular RNAs driven by N(6)-methylade nosine", Cell Res, 27, pp.626~641 (2017)
  152. Chen, Y. G., "N6-Methyladenosine modification controls circular RNA immunity", Mol. Cell, 76, pp.96~109 (2019)
  153. Liu, N., "N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions", Nature, 518, pp.560~564 (2015)
  154. Yang, D., "N6-Methyladenosine modification of lincRNA 1281 is critically required for mESC differentiation potential", Nucleic Acids Res, 46, pp.3906~3920 (2018)
  155. Han, M., "Abnormality of m6A mRNA methylation is involved in Alzheimer’s disease", Front. Neurosci, 14, pp.98~ (2020)
  156. Liu, L., "N(6)-Methyladenosine : a potential breakthrough for human cancer", Mol. Ther. Nucleic Acids, 19, pp.804~813 (2020)
  157. Paramasivam, A., "N6adenosine methylation(m6A) : a promising new molecular target in hyperten sion and cardiovascular diseases", Hypertens. Res, 43, pp.153~154 (2020)
  158. Fang, D., "m6A modification-mediated lncRNA TP53TG1 inhibits gastric cancer progression by regulating CIP2A stability", Cancer Sci, 113, pp.4135~4150 (2022)
  159. Wang, X., "LncRNA FENDRR with m6A RNA methylation regulates hypoxia induced pulmonary artery endothelial cell pyroptosis by mediating DRP1 DNA methylation", Mol. Med, 28, pp.126~ (2022)
  160. Xue, C., "Advances in RNA cytosine-5 methylation : detection, regulatory mechanisms, biological functions and links to cancer", Biomark. Res, 8, pp.43~ (2020)
  161. Cui, L., "RNA modifications : importance in immune cell biology and related diseases", Signal Transduct. Target Ther, 7, pp.334~ (2022)
  162. Chen, Y. S., "Dynamic transcriptomic m(5)C and its regulatory role in RNA processing", Wiley Interdiscip. Rev. RNA, 12, pp.e1639~ (2021)
  163. Zhang, Y., "5-methylcytosine(m(5)C)RNA modification controls the innate immune response to virus infection by regulating type I interferons", Proc. Natl Acad. Sci. USA, 119, pp.e2123338119~ (2022)
  164. Yang, X., "RNA modifications in aging-associated cardiovascular diseases", Aging, 14, pp.8110~8136 (2022)
  165. Bohnsack, K. E., "Eukaryotic 5-methylcytosine (m(5)C) RNA methyltransferases: mechanisms, cellular functions, and links to disease", Genes, 10 (2019)[DOI]
  166. Song, H., "Biological roles of RNA m(5)C modification and its implications in cancer immunotherapy", Biomark. Res, 10, pp.15~ (2022)
  167. Sun, Z., "Aberrant NSUN2-mediated m(5)C modification of H19 lncRNA is associated with poor differentiation of hepatocellular carcinoma", Oncogene, 39, pp.6906~6919 (2020)
  168. Fang, L., "m5C-methylated lncRNA NR_033928 promotes gastric cancer proliferation by stabilizing GLS mRNA to promote glutamine metabolism reprogramming", Cell Death Dis, 14, pp.520~ (2023)
  169. Elliott, B. A., "Modification of messenger RNA by 2’-O-methylation regulates gene expression in vivo", Nat. Commun, 10, pp.3401~ (2019)
  170. Erales, J., "Evidence for rRNA 2’-O-methylation plasticity : control of intrinsic translational capabilities of human ribosomes", Proc. Natl Acad. Sci. USA, 114, pp.12934~12939 (2017)
  171. van Ingen, E., "C", D box snoRNA SNORD113-6 guides 2’-O-methylation and protects against site-specific fragmentation of tRNA(Leu)(TAA)in vascular remodeling, 2022, pp.30, 162~172
  172. Wu, H., "Long noncoding RNA ZFAS1 promoting small nucleolar RNA mediated 2’-O-methylation via NOP58 recruitment in colorectal cancer", Mol. Cancer, 19, pp.95~ (2020)
  173. Mao, L. H., "LncRNA-LALR1 upregulates small nucleolar RNA SNORD72 to promote growth and invasion of hepatocellular carcinoma", Aging, 12, pp.4527~4546 (2020)
  174. Zinshteyn, B., "Adenosine-to-inosine RNA editing", Wiley Interdiscip. Rev. Syst. Biol. Med, 1, pp.202~209 (2009)
  175. Gatsiou, A., "Adenosine-to inosine RNA editing in health and disease", Antioxid. Redox Signal, 29, pp.846~863 (2018)
  176. Huang, W., "The snoRNA-like lncRNA LNC-SNO49AB drives leukemia by activating the RNA-editing enzyme ADAR1", Cell Discov, 8, pp.117~ (2022)
  177. Borchardt, E. K., "Regulation and function of RNA pseudouridylation in human cells", Annu. Rev. Genet, 54, pp.309~336 (2020)
  178. Lin, T. Y., "Pseudouridines in RNAs: switching atoms means shifting paradigms", FEBS Lett, 595, pp.2310~2322 (2021)
  179. Kiss, D. J., "The structure-derived mechanism of box H", ACA pseudouridine synthase offers a plausible paradigm for programmable RNA editing, 2022, pp.12, 2756~2769
  180. Zacchini, F., "Human dyskerin binds to cytoplasmic H", ACA-box-containing transcripts affecting nuclear hormone receptor dependence, 2022, pp.23, 177~
  181. Badis, G., "A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advan tage in yeast", RNA, 9, pp.771~779 (2003)
  182. Breznak, S. M., "H", ACA snRNP-dependent ribosome biogenesis regulates translation of polyglutamine proteins, 2023, pp.9, eade5492~
  183. Jady, B. E., "Guide RNA acrobatics: positioning consecutive uridines for pseudouridylation by H", ACA pseudouridylation loops with dual guide capacity, 2022, pp.36, 70~83
  184. Hentze, M. W., "A brave new world of RNA binding proteins", Nat. Rev. Mol. Cell Biol, 19, pp.327~341 (2018)
  185. Romero-Barrios, N., "Splicing regulation by long noncoding RNAs", Nucleic Acids Res, 46, pp.2169~2184 (2018)
  186. Galganski, L., "Nuclear speckles : molecular organization, biological function and role in disease", Nucleic Acids Res, 45, pp.10350~10368 (2017)
  187. Morais, P., "Spliceosomal snRNA epitranscriptomics", Front. Genet, 12, pp.652129~ (2021)
  188. Shao, C., "Mechanisms for U2AF to define 3’ splice sites and regulate alternative splicing in the human genome", Nat. Struct. Mol. Biol, 21, pp.997~1005 (2014)
  189. Tholen, J., "Structural basis of branch site recognition by the human spliceosome", Science, 375, pp.50~57 (2022)
  190. Agrawal, A. A., "An extended U2AF(65)-RNA-binding domain recognizes the 3’ splice site signal", Nat. Commun, 7, pp.10950~ (2016)
  191. Bernard, D., "A long nuclear-retained non-coding RNA regulates synapto genesis by modulating gene expression", EMBO J, 29, pp.3082~3093 (2010)
  192. Tripathi, V., "The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation", Mol. Cell, 39, pp.925~938 (2010)
  193. Miao, H., "MALAT1 modulates alternative splicing by cooperating with the splicing factors PTBP1 and PSF", Sci. Adv, 8, pp.eabq7289~ (2022)
  194. Bhat, P., "Nuclear compartmentalization as a mechanism of quantitative control of gene expression", Nat. Rev. Mol. Cell Biol, 22, pp.653~670 (2021)
  195. Fox, A. H., "Paraspeckles : where long non coding RNA meets phase separation", Trends Biochem. Sci, 43, pp.124~135 (2018)
  196. Imamura, K., "Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli", Mol. Cell, 54, pp.1055~ (2014)
  197. Hirose, T., "NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies", Mol. Biol. Cell, 25, pp.169~183 (2014)
  198. Song, C., "Immunotherapy for Alzheimer’s disease : targeting beta-amyloid and beyond", Transl. Neurodegener, 11, pp.18~ (2022)
  199. Mittal, P., "The SWI", SNF complex in cancer—biology, bio markers and therapy, 2020, pp.17, 435~448
  200. Reddy, D., "Paraspeckles interact with SWI", SNF subunit ARID1B to regulate transcription and splicing, 2023, pp.24, e55345~
  201. McDonald, B., "Canonical BAF complex activity shapes the enhancer land scape that licenses CD8(+) T cell effector and memory fates", Immunity, 56, pp.1303~1319 (2023)
  202. Fujisawa, T., "Functions of bromodomain-containing pro teins and their roles in homeostasis and cancer", Nat. Rev. Mol. Cell Biol, 18, pp.246~262 (2017)
  203. Rahnamoun, H., "RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation", Nat. Struct. Mol. Biol, 25, pp.687~697 (2018)
  204. Pastori, C., "The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation", Proc. Natl Acad. Sci. USA, 112, pp.8326~8331 (2015)
  205. Pei, R., "JMJD6-BRD4 complex stimulates lncRNA HOTAIR transcription by binding to the promoter region of HOTAIR and induces radioresistance in liver cancer stem cells", J. Transl. Med, 21, pp.752~ (2023)
  206. Pistoni, M., "Longnoncoding RNA NEAT1 acts as a molecular switch for BRD4transcriptional activity and mediates repression of BRD4", WDR5 target genes, 2021, pp.19, 799~811
  207. Easton, A., "Identification and characterization of a MAPT-targeting locked nucleic acid antisense oligonucleotide therapeutic for tauopathies", Mol. Ther. Nucleic Acids, 29, pp.625~642 (2022)
  208. Grossi, E., "A lncRNA-SWI", SNF complex crosstalk controls transcriptional activation at specific promoter regions, 2020, pp.11, 936~
  209. Mancini, M., "Involvement of transcribed lncRNA uc.291 and SWI", SNF complex in cutaneous squamous cell carcinoma, 2021, pp.12, 14~
  210. Kim, Y. K., "RNA therapy : rich history, various applications and unlimited future prospects", Exp. Mol. Med, 54, pp.455~465 (2022)
  211. Lim, K. H., "Elevation of ACE2 as a SARS-CoV-2 entry receptor gene expression in Alzheimer’s disease", J. Infect, 81, pp.e33~e34 (2020)
  212. Lim, K. H., "Identifying new COVID-19 receptor neuropilin-1 in severe Alzheimer’s disease patients group brain using genome wide association study approach", Front. Genet, 12, pp.741175~ (2021)
  213. Feng, R., "RNA therapeutics—research and clinical advancements", Front. Mol. Biosci, 8, pp.710738~ (2021)
  214. Winkle, M., "Noncoding RNA therapeutics—challenges and potential solutions", Nat. Rev. Drug Discov, 20, pp.629~651 (2021)
  215. Rasul, M. F., "Strategies to overcome the main challenges of the use of CRISPR", Cas9 as a replacement for cancer therapy, 2022, pp.21, 64~
  216. Ledford, H., "Is CRISPR safe? Genome editing gets its first FDA scrutiny", Nature, 623, pp.234~235 (2023)
  217. Antonio-Aguirre, B., "Treating patients with geographic atrophy:are we there yet?", Int. J. Retin. Vitreous, 9, pp.72~ (2023)
  218. Kang, C., "Avacincaptad pegol : first approval", Drugs, 83, pp.1447~1453 (2023)
  219. Zhu, Y., "RNA-based therapeutics : an overview and prospectus", Cell Death Dis, 13, pp.644~ (2022)
  220. Sparmann, A., "RNA-based medicine : from molecular mechanisms to therapy", EMBO J, 42, pp.e114760~ (2023)
  221. Huang, C. K., "Preclinical and clinical development of noncoding RNA therapeutics for cardiovascular disease", Circ. Res, 126, pp.663~678 (2020)
  222. Paunovska, K., "Drug delivery systems for RNA therapeutics", Nat. Rev. Genet, 23, pp.265~280 (2022)
  223. Zhao, Y., "The development and improvement of ribonucleic acid therapy strategies", Mol. Ther. Nucleic Acids, 26, pp.997~1013 (2021)
  224. Azofeifa, J. G., "Enhancer RNA profiling predicts transcription factor activity", Genome Res, 28, pp.334~344 (2018)
  225. Marinus, T., "RNA framework for assaying the structure of RNAs by high-throughput sequencing", Methods Mol. Biol, 2284, pp.63~76 (2021)
  226. Shao, D., "An m6A", m5C, m7G-related long non-coding RNA signature to predict prognosis and immune features of glioma, pp.Front. Genet, 2022[DOI]
  227. Lim, K. H., "Advances in multiplex PCR for Alzheimer’s disease diagnostics targeting CDK genes", Neurosci. Lett, 749, pp.135715~ (2021)
  228. Kim, S. H., "Boosting of tau protein aggregation by CD40 and CD48 gene expression in Alzheimer’s disease", FASEB J, 37, pp.e22702~ (2023)
  229. Kim, S. H., "Prediction of Alzheimer’s disease-specific phospholipase c gamma-1 SNV bydeep learning-based approach for high-throughput screening", Proc. Natl Acad. Sci. USA, 118 (2021)[DOI]
  230. Joo, J. Y., "Prediction of genetic alteration of phospholipase C isozymes in brain disorders : Studies with deep learning", Adv. Biol. Regul, 82, pp.100833~ (2021)
  231. Yang, S., "Harnessing deep learning into hidden mutations of neurological disorders for therapeutic challenges", Arch. Pharm. Res, 46, pp.535~549 (2023)
  232. Lim, K. H., "Cryptic mutations of PLC family members in brain disorders : recent discoveries and a deep-learning-based approach", Brain, 146, pp.1267~1280 (2023)
  233. Kim, S. -H., "Potent of strategic approaches for tauopathies ranging from single-cell transcriptome to microbiome", Anim. Cells Syst, 27, pp.378~393 (2023)
  234. Sun, P. P., "DeepMRMP : a new predictor for multiple types of RNA mod ification sites using deep learning", Math. Biosci. Eng, 16, pp.6231~6241 (2019)
  235. Noviello, T. M. R., "Deep learning predicts short non-coding RNA functions from only raw sequence data", PLoS Comput. Biol, 16, pp.e1008415~ (2020)
  236. Liang, S., "Rm-LR : a long-range-based deep learning model for predicting multiple types of RNA modifications", Comput. Biol. Med, 164, pp.107238~ (2023)
  237. Mostavi, M., "Deep-2’-O-Me : predicting 2’-O-methylation sites by convolutional neural networks", Annu. Int. Conf. IEEE Eng. Med. Biol. Soc, 2018, pp.2394~2397 (2018)
  238. Zhuang, J., "PseUdeep : RNA pseudouridine site identification with deep learning algorithm", Front. Genet, 12, pp.773882~ (2021)
  239. Wang, H., "EMDLP : ensemble multiscale deep learning model for RNA methylation site prediction", BMC Bioinform, 23, pp.221~ (2022)
  240. Hasan, M. M., "Deepm5C : a deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy", Mol. Ther, 30, pp.2856~2867 (2022)
  241. Luo, Z., "DLm6Am: a deep-learning-based tool for identifying N6,2’-O dimethyladenosine sites in RNA sequences", Int. J. Mol. Sci, 23 (2022)[DOI]
  242. Wen, M., "DeepMirTar : a deep-learning approach for predicting human miRNA targets", Bioinformatics, 34, pp.3781~3787 (2018)
  243. Alam, T., "DeepDSSR : deep learning structure for human donor splice sites recognition", Stud. Health Technol. Inf, 262, pp.236~239 (2019)
  244. Pan, X., "RBPsuite : RNA-protein binding sites prediction suite based on deep learning", BMC Genom, 21, pp.884~ (2020)
  245. Zeng, M., "DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding", Brief Bioinform, 23 (2022)[DOI]
  246. Chaabane, M., "circDeep : deep learning approach for circular RNA classification from other long non-coding RNA", Bioinformatics, 36, pp.73~80 (2020)
  247. Chantsalnyam, T., "ncRDense : a novel com putational approach for classification of non-coding RNA family by deep learning", Genomics, 113, pp.3030~3038 (2021)
  248. Fu, L., "UFold : fast and accurate RNA secondary structure prediction with deep learning", Nucleic Acids Res, 50, pp.e14~ (2022)
  249. "NuFold : a novel tertiary RNA structure prediction method using deep learning with flexible nucleobase center representation" (2023)[URL]
  250. Nasaev, S. S., "AliNA—a deep learning program for RNA secondary structure prediction", Mol. Inform, 42, pp.e2300113~ (2023)
  251. Niu, M., "rBPDL : predicting RNA-binding proteins using deep learning", IEEE J. Biomed. Health Inf, 25, pp.3668~3676 (2021)
  252. Du, X., "DeepBtoD : improved RNA-binding proteins pre diction via integrated deep learning", J. Bioinform. Comput Biol, 20, pp.2250006~ (2022)

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