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Networks of mRNA Processing and Alternative Splicing Regulation in Health and Disease

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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1157))

Abstract

mRNA processing events introduce an intricate layer of complexity into gene expression processes, supporting a tremendous level of diversification of the genome’s coding and regulatory potential, particularly in vertebrate species. The recent development of massive parallel sequencing methods and their adaptation to the identification and quantification of different RNA species and the dynamics of mRNA metabolism and processing has generated an unprecedented view over the regulatory networks that are established at this level, which contribute to sustain developmental, tissue specific or disease specific gene expression programs. In this chapter, we provide an overview of the recent evolution of transcriptome profiling methods and the surprising insights that have emerged in recent years regarding distinct mRNA processing events – from the 5′ end to the 3′ end of the molecule.

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References

  1. Weake VM, Workman JL (2010) Inducible gene expression: diverse regulatory mechanisms. Nat Publ Group 11:426–437. https://doi.org/10.1038/nrg2781

    Article  CAS  Google Scholar 

  2. Pope SD, Medzhitov R (2018) Emerging principles of gene expression programs and their regulation. Mol Cell 71:389–397. https://doi.org/10.1016/j.molcel.2018.07.017

    Article  CAS  PubMed  Google Scholar 

  3. Heintzman ND, Ren B (2007) The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cell Mol Life Sci 64:386–400. https://doi.org/10.1007/s00018-006-6295-0

    Article  CAS  PubMed  Google Scholar 

  4. Soshnev AA, Josefowicz SZ, Allis CD (2016) Greater than the sum of parts: complexity of the dynamic epigenome. Mol Cell 62:681–694. https://doi.org/10.1016/j.molcel.2016.05.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Corbett AH (2018) Post-transcriptional regulation of gene expression and human disease. Curr Opin Cell Biol 52:96–104. https://doi.org/10.1016/j.ceb.2018.02.011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Schmid M, Jensen TH (2018) Controlling nuclear RNA levels. Nat Publ Group 19:518–529. https://doi.org/10.1038/s41576-018-0013-2

    Article  CAS  Google Scholar 

  7. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63. https://doi.org/10.1038/nrg2484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Blencowe BJ, Ahmad S, Lee LJ (2009) Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23:1379–1386. https://doi.org/10.1101/gad.1788009

    Article  CAS  PubMed  Google Scholar 

  9. Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Publ Group 13:840–852. https://doi.org/10.1038/nrg3306

    Article  CAS  Google Scholar 

  10. Daniel B, Nagy G, Nagy L (2014) The intriguing complexities of mammalian gene regulation: how to link enhancers to regulated genes. Are we there yet? FEBS Lett 588:2379–2391. https://doi.org/10.1016/j.febslet.2014.05.041

    Article  CAS  PubMed  Google Scholar 

  11. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487

    Article  CAS  PubMed  Google Scholar 

  12. Velculescu VE, Zhang L, Zhou W et al (1997) Characterization of the yeast transcriptome. Cell 88:243–251. https://doi.org/10.1016/S0092-8674(00)81845-0

    Article  CAS  PubMed  Google Scholar 

  13. Clark TA, Sugnet CW, Ares M (2002) Genome wide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296:907–910. https://doi.org/10.1126/science.1069415

    Article  CAS  PubMed  Google Scholar 

  14. Johnson JM, Castle J, Garrett-Engele P et al (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302:2141–2144. https://doi.org/10.1126/science.1090100

    Article  CAS  PubMed  Google Scholar 

  15. Pan Q, Shai O, Lee LJ et al (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413–1415. https://doi.org/10.1038/ng.259

    Article  CAS  PubMed  Google Scholar 

  16. Consortium TEP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74. https://doi.org/10.1038/nature11247

    Article  CAS  Google Scholar 

  17. Consortium TF, PMI TR, DGT C (2014) A promoter-level mammalian expression atlas. Nature 507:462–470. https://doi.org/10.1038/nature13182

    Article  CAS  Google Scholar 

  18. GTEx Consortium (2013) The Genotype-Tissue Expression (GTEx) project. Nat Genet 45:580–585. https://doi.org/10.1038/ng.2653

    Article  CAS  Google Scholar 

  19. Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA et al (2013) The cancer genome atlas pan-cancer analysis project. Nat Genet 45:1113–1120. https://doi.org/10.1038/ng.2764

    Article  CAS  PubMed Central  Google Scholar 

  20. Gerstein MB, Bruce C, Rozowsky JS et al (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17:669–681. https://doi.org/10.1101/gr.6339607

    Article  CAS  PubMed  Google Scholar 

  21. Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol 31:1009–1014. https://doi.org/10.1038/nbt.2705

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Garalde DR, Snell EA, Jachimowicz D et al (2018) Highly parallel direct RNA sequencing on an array of nanopores. Nat Methods 15:201–206. https://doi.org/10.1038/nmeth.4577

    Article  CAS  PubMed  Google Scholar 

  23. Kolodziejczyk AA, Kim JK, Svensson V et al (2015) The technology and biology of single-cell RNA sequencing. Mol Cell 58:610–620. https://doi.org/10.1016/j.molcel.2015.04.005

    Article  CAS  PubMed  Google Scholar 

  24. Amaral AJ, Brito FF, Chobanyan T et al (2014) Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models. Front Genet 5:43. https://doi.org/10.3389/fgene.2014.00043

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Hrdlickova R, Toloue M, Tian B (2017) RNA-Seq methods for transcriptome analysis. Wiley Interdiscip Rev RNA 8:e1364. https://doi.org/10.1002/wrna.1364

    Article  CAS  Google Scholar 

  26. SEQC/MAQC-III Consortium (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol 32:903–914. https://doi.org/10.1038/nbt.2957

    Article  CAS  Google Scholar 

  27. Sims D, Sudbery I, Ilott NE et al (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 15:121–132. https://doi.org/10.1038/nrg3642

    Article  CAS  PubMed  Google Scholar 

  28. Adey A, Morrison HG, Asan et al (2010) Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 11:R119. https://doi.org/10.1186/gb-2010-11-12-r119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Poptsova MS, Il’icheva IA, Nechipurenko DY et al (2014) Non-random DNA fragmentation in next-generation sequencing. Sci Rep 4:4532. https://doi.org/10.1038/srep04532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Aird D, Ross MG, Chen W-S et al (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12:R18. https://doi.org/10.1186/gb-2011-12-2-r18

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Parekh S, Ziegenhain C, Vieth B et al (2016) The impact of amplification on differential expression analyses by RNA-seq. Sci Rep 6:25533. https://doi.org/10.1038/srep25533

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671–682. https://doi.org/10.1038/nrg3068

    Article  CAS  PubMed  Google Scholar 

  33. Conesa A, Madrigal P, Tarazona S et al (2016) A survey of best practices for RNA-seq data analysis. Genome Biol 17:13. https://doi.org/10.1186/s13059-016-0881-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lianoglou S, Garg V, Yang JL et al (2013) Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev 27:2380–2396. https://doi.org/10.1101/gad.229328.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Carninci P, Kasukawa T, Katayama S et al (2005) The transcriptional landscape of the mammalian genome. Science 309:1559–1563. https://doi.org/10.1126/science.1112014

    Article  CAS  PubMed  Google Scholar 

  36. FANTOM Consortium, Suzuki H, Forrest ARR et al (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41:553–562. https://doi.org/10.1038/ng.375

    Article  CAS  PubMed Central  Google Scholar 

  37. Hoskins RA, Landolin JM, Brown JB et al (2011) Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res 21:182–192. https://doi.org/10.1101/gr.112466.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Takahashi H, Lassmann T, Murata M, Carninci P (2012) 5′ end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 7:542–561. https://doi.org/10.1038/nprot.2012.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Arribere JA, Gilbert WV (2013) Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res 23:977–987. https://doi.org/10.1101/gr.150342.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Kruesi WS, Core LJ, Waters CT et al (2013) Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. elife 2:e00808. https://doi.org/10.7554/eLife.00808

    Article  PubMed  PubMed Central  Google Scholar 

  41. Core LJ, Martins AL, Danko CG et al (2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46:1311–1320. https://doi.org/10.1038/ng.3142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845–1848. https://doi.org/10.1126/science.1162228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Duttke SHC, Lacadie SA, Ibrahim MM et al (2015) Human promoters are intrinsically directional. Mol Cell 57:674–684. https://doi.org/10.1016/j.molcel.2014.12.029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Schwanhäusser B, Busse D, Li N et al (2011) Global quantification of mammalian gene expression control. Nature 473:337–342. https://doi.org/10.1038/nature10098

    Article  CAS  PubMed  Google Scholar 

  45. Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218–223. https://doi.org/10.1126/science.1168978

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Arava Y, Wang Y, Storey JD et al (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci 100:3889–3894. https://doi.org/10.1073/pnas.0635171100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Mata J, Marguerat S, Bähler J (2005) Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci 30:506–514. https://doi.org/10.1016/j.tibs.2005.07.005

    Article  CAS  PubMed  Google Scholar 

  48. Gama-Carvalho M, Barbosa-Morais NL, Brodsky AS et al (2006) Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biol 7:R113. https://doi.org/10.1186/gb-2006-7-11-r113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Zhao J, Ohsumi TK, Kung JT et al (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40:939–953. https://doi.org/10.1016/j.molcel.2010.12.011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Ule J, Jensen K, Mele A, Darnell RB (2005) CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37:376–386. https://doi.org/10.1016/j.ymeth.2005.07.018

    Article  CAS  PubMed  Google Scholar 

  51. König J, Zarnack K, Luscombe NM, Ule J (2011) Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 13:77–83. https://doi.org/10.1038/nrg3141

    Article  CAS  Google Scholar 

  52. Nussbacher JK, Batra R, Lagier-Tourenne C, Yeo GW (2015) RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci 38:226–236. https://doi.org/10.1016/j.tins.2015.02.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Keene JD (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8:533–543. https://doi.org/10.1038/nrg2111

    Article  CAS  PubMed  Google Scholar 

  54. Ule J, Stefani G, Mele A et al (2006) An RNA map predicting Nova-dependent splicing regulation. Nature 444:580–586. https://doi.org/10.1038/nature05304

    Article  CAS  PubMed  Google Scholar 

  55. Barash Y, Calarco JA, Gao W et al (2010) Deciphering the splicing code. Nature 465:53–59. https://doi.org/10.1038/nature09000

    Article  CAS  PubMed  Google Scholar 

  56. Zhao BS, Roundtree IA, He C (2017) Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol 18:31–42. https://doi.org/10.1038/nrm.2016.132

    Article  CAS  PubMed  Google Scholar 

  57. Meyer KD, Saletore Y, Zumbo P et al (2012) Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149:1635–1646. https://doi.org/10.1016/j.cell.2012.05.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Lovejoy AF, Riordan DP, Brown PO (2014) Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One 9:e110799. https://doi.org/10.1371/journal.pone.0110799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Carlile TM, Rojas-Duran MF, Zinshteyn B et al (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515:143–146. https://doi.org/10.1038/nature13802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Roundtree IA, Evans ME, Pan T, He C (2017) Dynamic RNA modifications in gene expression regulation. Cell 169:1187–1200. https://doi.org/10.1016/j.cell.2017.05.045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Sultan M, Schulz M, Richard H et al (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956. https://doi.org/10.1126/science.1160342

    Article  CAS  PubMed  Google Scholar 

  62. Wang ET, Sandberg R, Luo S et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476. https://doi.org/10.1038/nature07509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Shiraki T, Kondo S, Katayama S et al (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci 100:15776–15781. https://doi.org/10.1073/pnas.2136655100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Katayama S, Tomaru Y, Kasukawa T et al (2005) Antisense transcription in the mammalian transcriptome. Science 309:1564–1566. https://doi.org/10.1126/science.1112009

    Article  PubMed  Google Scholar 

  65. Lizio M, Harshbarger J, Shimoji H et al (2015) Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol 16:22. https://doi.org/10.1186/s13059-014-0560-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Almada AE, Wu X, Kriz AJ et al (2013) Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499:360–363. https://doi.org/10.1038/nature12349

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Pal S, Gupta R, Kim H et al (2011) Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development. Genome Res 21:1260–1272. https://doi.org/10.1101/gr.120535.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Reyes A, Huber W (2018) Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Nucleic Acids Res 46:582–592. https://doi.org/10.1093/nar/gkx1165

    Article  CAS  PubMed  Google Scholar 

  69. Ramanathan A, Robb GB, Chan S-H (2016) mRNA capping: biological functions and applications. Nucleic Acids Res 44:7511–7526. https://doi.org/10.1093/nar/gkw551

    Article  PubMed  PubMed Central  Google Scholar 

  70. Galloway A, Cowling VH (2018) mRNA cap regulation in mammalian cell function and fate. Biochim Biophys Acta Gene Regul Mech. https://doi.org/10.1016/j.bbagrm.2018.09.011

    Article  CAS  Google Scholar 

  71. Daffis S, Szretter KJ, Schriewer J et al (2010) 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members. Nature 468:452–456. https://doi.org/10.1038/nature09489

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Hyde JL, Diamond MS (2015) Innate immune restriction and antagonism of viral RNA lacking 2′-O methylation. Virology 479–480:66–74. https://doi.org/10.1016/j.virol.2015.01.019

    Article  CAS  PubMed  Google Scholar 

  73. Cowling VH, Cole MD (2007) The Myc transactivation domain promotes global phosphorylation of the RNA polymerase II carboxy-terminal domain independently of direct DNA binding. Mol Cell Biol 27:2059–2073. https://doi.org/10.1128/MCB.01828-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Mezquita P, Parghi SS, Brandvold KA, Ruddell A (2005) Myc regulates VEGF production in B cells by stimulating initiation of VEGF mRNA translation. Oncogene 24:889–901. https://doi.org/10.1038/sj.onc.1208251

    Article  CAS  PubMed  Google Scholar 

  75. Aregger M, Cowling VH (2014) E2F1-dependent methyl cap formation requires RNA pol II phosphorylation. Cell Cycle 11:2146–2148. https://doi.org/10.4161/cc.20620

    Article  CAS  Google Scholar 

  76. Lombardi O, Varshney D, Phillips NM, Cowling VH (2016) c-Myc deregulation induces mRNA capping enzyme dependency. Oncotarget 7:82273–82288. https://doi.org/10.18632/oncotarget.12701

    Article  PubMed  PubMed Central  Google Scholar 

  77. Aregger M, Kaskar A, Varshney D et al (2016) CDK1-cyclin B1 activates RNMT, coordinating mRNA cap methylation with G1 phase transcription. Mol Cell 61:734–746. https://doi.org/10.1016/j.molcel.2016.02.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Grasso L, Suska O, Davidson L et al (2016) mRNA cap methylation in pluripotency and differentiation. CellReports 16:1352–1365. https://doi.org/10.1016/j.celrep.2016.06.089

    Article  CAS  Google Scholar 

  79. Inesta-Vaquera F, Chaugule VK, Galloway A et al (2018) DHX15 regulates CMTR1-dependent gene expression and cell proliferation. Life Sci Alliance 1:e201800092. https://doi.org/10.26508/lsa.201800092

    Article  PubMed  PubMed Central  Google Scholar 

  80. Furuichi Y, Morgan M, Shatkin AJ et al (1975) Methylated, blocked 5 termini in HeLa cell mRNA. Proc Natl Acad Sci 72:1904–1908. https://doi.org/10.1073/pnas.72.5.1904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Perry RP, Kelley DE (1976) Kinetics of formation of 5′ terminal caps in mRNA. Cell 8:433–442. https://doi.org/10.1016/0092-8674(76)90156-2

    Article  CAS  PubMed  Google Scholar 

  82. Werner M, Purta E, Kaminska KH et al (2011) 2′-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. Nucleic Acids Res 39:4756–4768. https://doi.org/10.1093/nar/gkr038

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Wei C, Gershowitz A, Moss B (1975) N6, O2“-dimethyladenosine a novel methylated ribonucleoside next to the 5” terminal of animal cell and virus mRNAs. Nature 257:251–253. https://doi.org/10.1038/257251a0

    Article  CAS  PubMed  Google Scholar 

  84. Kruse S, Zhong S, Bodi Z et al (2011) A novel synthesis and detection method for cap-associated adenosine modifications in mouse mRNA. Sci Rep 1:54. https://doi.org/10.1038/srep00126

    Article  CAS  Google Scholar 

  85. Tamarkin-Ben-Harush A, Vasseur J-J, Debart F et al (2017) Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress. elife 6:977. https://doi.org/10.7554/eLife.21907

    Article  Google Scholar 

  86. Abdelhamid RF, Plessy C, Yamauchi Y et al (2014) Multiplicity of 5′ cap structures present on short RNAs. PLoS One 9:e102895. https://doi.org/10.1371/journal.pone.0102895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Wetzel C, Limbach PA (2016) Mass spectrometry of modified RNAs: recent developments. Analyst 141:16–23. https://doi.org/10.1039/c5an01797a

    Article  CAS  PubMed  Google Scholar 

  88. Bird JG, Zhang Y, Tian Y et al (2016) The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature 535:444–447. https://doi.org/10.1038/nature18622

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Jiao X, Doamekpor SK, Bird JG et al (2017) 5′ end nicotinamide adenine dinucleotide cap in human cells promotes RNA decay through DXO-mediated deNADding. Cell 168:1015–1027.e10. https://doi.org/10.1016/j.cell.2017.02.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Kiledjian M (2018) Eukaryotic RNA 5′-end NAD + capping and DeNADding. Trends Cell Biol 28:454–464. https://doi.org/10.1016/j.tcb.2018.02.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Schoenberg DR, Maquat LE (2012) Regulation of cytoplasmic mRNA decay. Nat Publ Group 13:246–259. https://doi.org/10.1038/nrg3160

    Article  CAS  Google Scholar 

  92. Jiao Y, Riechmann JL, Meyerowitz EM (2008) Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. Plant Cell 20:2571–2585. https://doi.org/10.1105/tpc.108.062786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Karginov FV, Cheloufi S, Chong MMW et al (2010) Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol Cell 38:781–788. https://doi.org/10.1016/j.molcel.2010.06.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Mercer TR, Dinger ME, Bracken CP et al (2010) Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res 20:1639–1650. https://doi.org/10.1101/gr.112128.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Otsuka Y, Kedersha NL, Schoenberg DR (2009) Identification of a cytoplasmic complex that adds a cap onto 5′-monophosphate RNA. Mol Cell Biol 29:2155–2167. https://doi.org/10.1128/MCB.01325-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Mukherjee C, Bakthavachalu B, Schoenberg DR (2014) The cytoplasmic capping complex assembles on adapter protein nck1 bound to the proline-rich C-terminus of Mammalian capping enzyme. PLoS Biol 12:e1001933. https://doi.org/10.1371/journal.pbio.1001933

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Trotman JB, Schoenberg DR (2018) A recap of RNA recapping. Wiley Interdiscip Rev RNA 10:e1504. https://doi.org/10.1002/wrna.1504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Mukherjee C, Patil DP, Kennedy BA et al (2012) Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. CellReports 2:674–684. https://doi.org/10.1016/j.celrep.2012.07.011

    Article  CAS  Google Scholar 

  99. Gregory BD, O’Malley RC, Lister R et al (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 14:854–866. https://doi.org/10.1016/j.devcel.2008.04.005

    Article  CAS  PubMed  Google Scholar 

  100. Kiss DL, Oman KM, Dougherty JA et al (2016) Cap homeostasis is independent of poly(A) tail length. Nucleic Acids Res 44:304–314. https://doi.org/10.1093/nar/gkv1460

    Article  CAS  PubMed  Google Scholar 

  101. Chen P, Zhou Z, Yao X et al (2017) Capping enzyme mRNA-cap/RNGTT regulates hedgehog pathway activity by antagonizing protein kinase A. Sci Rep 7:2891. https://doi.org/10.1038/s41598-017-03165-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Sharp PA (1994) Split genes and RNA splicing. Cell 77:805–815

    Article  CAS  PubMed  Google Scholar 

  103. Nilsen TW, Graveley BR (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463:457–463. https://doi.org/10.1038/nature08909

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Wahl MC, Will CL, Lührmann R (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136:701–718. https://doi.org/10.1016/j.cell.2009.02.009

    Article  CAS  PubMed  Google Scholar 

  105. Matera AG, Wang Z (2014) A day in the life of the spliceosome. Nat Rev Mol Cell Biol 15:108–121. https://doi.org/10.1038/nrm3742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Will CL, Lührmann R (2011) Spliceosome structure and function. Cold Spring Harb Perspect Biol 3:a003707–a003707. https://doi.org/10.1101/cshperspect.a003707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Baralle M, Baralle FE (2018) The splicing code. Biosystems 164:39–48. https://doi.org/10.1016/j.biosystems.2017.11.002

    Article  CAS  PubMed  Google Scholar 

  108. Smith CW, Valcárcel J (2000) Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem Sci 25:381–388

    Article  CAS  PubMed  Google Scholar 

  109. Hertel KJ (2008) Combinatorial control of exon recognition. J Biol Chem 283:1211–1215. https://doi.org/10.1074/jbc.R700035200

    Article  CAS  PubMed  Google Scholar 

  110. Wang Z, Burge CB (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14:802–813. https://doi.org/10.1261/rna.876308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Lee Y, Rio DC (2015) Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem 84:291–323. https://doi.org/10.1146/annurev-biochem-060614-034316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Savarese M, Jonson PH, Huovinen S et al (2018) The complexity of titin splicing pattern in human adult skeletal muscles. Skelet Muscle 8:11. https://doi.org/10.1186/s13395-018-0156-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. da Costa PJ, Menezes J, Romão L (2017) The role of alternative splicing coupled to nonsense-mediated mRNA decay in human disease. Int J Biochem Cell Biol 91:168–175. https://doi.org/10.1016/j.biocel.2017.07.013

    Article  CAS  PubMed  Google Scholar 

  114. Ni JZ, Grate L, Donohue JP et al (2007) Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 21:708–718. https://doi.org/10.1101/gad.1525507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Lareau LF, Inada M, Green RE et al (2007) Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446:926–929. https://doi.org/10.1038/nature05676

    Article  CAS  PubMed  Google Scholar 

  116. Saltzman AL, Kim YK, Pan Q et al (2008) Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol 28:4320–4330. https://doi.org/10.1128/MCB.00361-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Mayr C, Bartel DP (2009) Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138:673–684. https://doi.org/10.1016/j.cell.2009.06.016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Ogorodnikov A, Kargapolova Y, Danckwardt S (2016) Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end. Pflugers Arch 468:993–1012. https://doi.org/10.1007/s00424-016-1828-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Long JC, Cáceres JF (2009) The SR protein family of splicing factors: master regulators of gene expression. Biochem J 417:15–27. https://doi.org/10.1042/BJ20081501

    Article  CAS  PubMed  Google Scholar 

  120. Weatheritt RJ, Sterne-Weiler T, Blencowe BJ (2016) The ribosome-engaged landscape of alternative splicing. Nat Struct Mol Biol 23:1117–1123. https://doi.org/10.1038/nsmb.3317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Venables JP (2006) Unbalanced alternative splicing and its significance in cancer. BioEssays 28:378–386. https://doi.org/10.1002/bies.20390

    Article  CAS  PubMed  Google Scholar 

  122. Srebrow A, Kornblihtt AR (2006) The connection between splicing and cancer. J Cell Sci 119:2635–2641. https://doi.org/10.1242/jcs.03053

    Article  CAS  PubMed  Google Scholar 

  123. Matos P, Collard JG, Jordan P (2003) Tumor-related alternatively spliced Rac1b is not regulated by Rho-GDP dissociation inhibitors and exhibits selective downstream signaling. J Biol Chem 278:50442–50448. https://doi.org/10.1074/jbc.M308215200

    Article  CAS  PubMed  Google Scholar 

  124. Scherr A-L, Gdynia G, Salou M et al (2016) Bcl-xL is an oncogenic driver in colorectal cancer. Cell Death Dis 7:e2342–e2342. https://doi.org/10.1038/cddis.2016.233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Ghigna C, Giordano S, Shen H et al (2005) Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Mol Cell 20:881–890. https://doi.org/10.1016/j.molcel.2005.10.026

    Article  CAS  PubMed  Google Scholar 

  126. Chen M, Zhang J, Manley JL (2010) Turning on a fuel switch of cancer: hnRNP proteins regulate alternative splicing of pyruvate kinase mRNA. Cancer Res 70:8977–8980. https://doi.org/10.1158/0008-5472.CAN-10-2513

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Sibley CR, Emmett W, Blazquez L et al (2015) Recursive splicing in long vertebrate genes. Nature 521:371–375. https://doi.org/10.1038/nature14466

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Kelly S, Greenman C, Cook PR, Papantonis A (2015) Exon skipping is correlated with exon circularization. J Mol Biol 427:2414–2417. https://doi.org/10.1016/j.jmb.2015.02.018

    Article  CAS  PubMed  Google Scholar 

  129. Duff MO, Olson S, Wei X, Garrett SC, Osman A, Bolisetty M et al (2015) Genome-wide identification of zero nucleotide recursive splicing in Drosophila. Nature 521:376–379. https://doi.org/10.1038/nature14475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Georgomanolis T, Sofiadis K, Papantonis A (2016) Cutting a long intron short: recursive splicing and its implications. Front Physiol 7:598. https://doi.org/10.3389/fphys.2016.00598

    Article  PubMed  PubMed Central  Google Scholar 

  131. Starke S, Jost I, Rossbach O et al (2015) Exon circularization requires canonical splice signals. CellReports 10:103–111. https://doi.org/10.1016/j.celrep.2014.12.002

    Article  CAS  Google Scholar 

  132. Jeck WR, Sharpless NE (2014) Detecting and characterizing circular RNAs. Nat Biotechnol 32:453–461. https://doi.org/10.1038/nbt.2890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Barrett SP, Salzman J (2016) Circular RNAs: analysis, expression and potential functions. Development 143:1838–1847. https://doi.org/10.1242/dev.128074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Wang M, Yu F, Wu W et al (2017) Circular RNAs: a novel type of non-coding RNA and their potential implications in antiviral immunity. Int J Biol Sci 13:1497–1506. https://doi.org/10.7150/ijbs.22531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Chuang T-J, Chen Y-J, Chen C-Y et al (2018) Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells. Nucleic Acids Res 46:3671–3691. https://doi.org/10.1093/nar/gky032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Chen L-L (2016) The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol 17:205–211. https://doi.org/10.1038/nrm.2015.32

    Article  CAS  PubMed  Google Scholar 

  137. Zhang Z-C, Guo X-L, Li X (2018) The novel roles of circular RNAs in metabolic organs. Genes Dis 5:16–23. https://doi.org/10.1016/j.gendis.2017.12.002

    Article  CAS  PubMed  Google Scholar 

  138. Han B, Chao J, Yao H (2018) Circular RNA and its mechanisms in disease: from the bench to the clinic. Pharmacol Ther 187:31–44. https://doi.org/10.1016/j.pharmthera.2018.01.010

    Article  CAS  PubMed  Google Scholar 

  139. Xiao SH, Manley JL (1997) Phosphorylation of the ASF/SF2 RS domain affects both protein-protein and protein-RNA interactions and is necessary for splicing. Genes Dev 11:334–344

    Article  CAS  PubMed  Google Scholar 

  140. Stamm S (2008) Regulation of alternative splicing by reversible protein phosphorylation. J Biol Chem 283:1223–1227. https://doi.org/10.1074/jbc.R700034200

    Article  CAS  PubMed  Google Scholar 

  141. Gonçalves V, Pereira JFS, Jordan P (2017) Signaling pathways driving aberrant splicing in cancer cells. Gene 9:9. https://doi.org/10.3390/genes9010009

    Article  CAS  Google Scholar 

  142. Goren A, Kim E, Amit M et al (2010) Overlapping splicing regulatory motifs--combinatorial effects on splicing. Nucleic Acids Res 38:3318–3327. https://doi.org/10.1093/nar/gkq005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Zahler AM, Damgaard CK, Kjems J, Caputi M (2004) SC35 and heterogeneous nuclear ribonucleoprotein A/B proteins bind to a juxtaposed exonic splicing enhancer/exonic splicing silencer element to regulate HIV-1 tat exon 2 splicing. J Biol Chem 279:10077–10084. https://doi.org/10.1074/jbc.M312743200

    Article  CAS  PubMed  Google Scholar 

  144. Zhang XH-F, Arias MA, Ke S, Chasin LA (2009) Splicing of designer exons reveals unexpected complexity in pre-mRNA splicing. RNA 15:367–376. https://doi.org/10.1261/rna.1498509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Pagani F, Baralle FE (2004) Genomic variants in exons and introns: identifying the splicing spoilers. Nat Rev Genet 5:389–396. https://doi.org/10.1038/nrg1327

    Article  CAS  PubMed  Google Scholar 

  146. Baralle D, Baralle M (2005) Splicing in action: assessing disease causing sequence changes. J Med Genet 42:737–748. https://doi.org/10.1136/jmg.2004.029538

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Ghigna C, Moroni M, Porta C et al (1998) Altered expression of heterogenous nuclear ribonucleoproteins and SR factors in human colon adenocarcinomas. Cancer Res 58:5818–5824

    CAS  PubMed  Google Scholar 

  148. David CJ, Manley JL (2010) Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev 24:2343–2364. https://doi.org/10.1101/gad.1973010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Karni R, de Stanchina E, Lowe SW et al (2007) The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat Struct Mol Biol 14:185–193. https://doi.org/10.1038/nsmb1209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Naftelberg S, Schor IE, Ast G, Kornblihtt AR (2015) Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 84:165–198. https://doi.org/10.1146/annurev-biochem-060614-034242

    Article  CAS  PubMed  Google Scholar 

  151. Luco RF, Pan Q, Tominaga K et al (2010) Regulation of alternative splicing by histone modifications. Science 327:996–1000. https://doi.org/10.1126/science.1184208

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Blaustein M, Pelisch F, Srebrow A (2007) Signals, pathways and splicing regulation. Int J Biochem Cell Biol 39:2031–2048. https://doi.org/10.1016/j.biocel.2007.04.004

    Article  CAS  PubMed  Google Scholar 

  153. Valacca C, Bonomi S, Buratti E et al (2010) Sam68 regulates EMT through alternative splicing-activated nonsense-mediated mRNA decay of the SF2/ASF proto-oncogene. J Cell Biol 191:87–99. https://doi.org/10.1083/jcb.201001073

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. van der Houven, van Oordt W, Diaz-Meco MT, Lozano J et al (2000) The MKK(3/6)-p38-signaling cascade alters the subcellular distribution of hnRNP A1 and modulates alternative splicing regulation. J Cell Biol 149:307–316

    Article  Google Scholar 

  155. Allemand E, Guil S, Myers M et al (2005) Regulation of heterogenous nuclear ribonucleoprotein A1 transport by phosphorylation in cells stressed by osmotic shock. Proc Natl Acad Sci 102:3605–3610. https://doi.org/10.1073/pnas.0409889102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Gonçalves V, Henriques A, Pereira J et al (2014) Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells. RNA. https://doi.org/10.1261/rna.041376.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Licatalosi DD, Darnell RB (2010) RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 11:75–87. https://doi.org/10.1038/nrg2673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Kalsotra A, Cooper TA (2011) Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet 12:715–729. https://doi.org/10.1038/nrg3052

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Buljan M, Chalancon G, Eustermann S et al (2012) Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 46:871–883. https://doi.org/10.1016/j.molcel.2012.05.039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Ellis JD, Barrios-Rodiles M, Çolak R et al (2012) Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell 46:884–892. https://doi.org/10.1016/j.molcel.2012.05.037

    Article  CAS  PubMed  Google Scholar 

  161. Barbosa-Morais NL, Irimia M, Pan Q et al (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338:1587–1593. https://doi.org/10.1126/science.1230612

    Article  CAS  PubMed  Google Scholar 

  162. Traunmüller L, Gomez AM, Nguyen T-M, Scheiffele P (2016) Control of neuronal synapse specification by a highly dedicated alternative splicing program. Science 352:982–986. https://doi.org/10.1126/science.aaf2397

    Article  CAS  PubMed  Google Scholar 

  163. Calarco JA, Zhen M, Blencowe BJ (2011) Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts. RNA 17:775–791. https://doi.org/10.1261/rna.2603911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Baralle FE, Giudice J (2017) Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol 18:437–451. https://doi.org/10.1038/nrm.2017.27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Gallego-Paez LM, Bordone MC, Leote AC et al (2017) Alternative splicing: the pledge, the turn, and the prestige: the key role of alternative splicing in human biological systems. Hum Genet 136:1015–1042. https://doi.org/10.1007/s00439-017-1790-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Li M, Izpisua Belmonte JC (2018) Deconstructing the pluripotency gene regulatory network. Nat Cell Biol 20:382–392. https://doi.org/10.1038/s41556-018-0067-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Abdel-Wahab O, Levine R (2011) The spliceosome as an indicted conspirator in myeloid malignancies. Cancer Cell 20:420–423. https://doi.org/10.1016/j.ccr.2011.10.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Scott LM, Rebel VI (2013) Acquired mutations that affect pre-mRNA splicing in hematologic malignancies and solid tumors. J Natl Cancer Inst 105:1540–1549. https://doi.org/10.1093/jnci/djt257

    Article  CAS  PubMed  Google Scholar 

  169. Dittmar KA, Jiang P, Park JW et al (2012) Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol Cell Biol 32:1468–1482. https://doi.org/10.1128/MCB.06536-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Warzecha CC, Carstens RP (2012) Complex changes in alternative pre-mRNA splicing play a central role in the epithelial-to-mesenchymal transition (EMT). Semin Cancer Biol 22:417–427. https://doi.org/10.1016/j.semcancer.2012.04.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Hollander D, Donyo M, Atias N et al (2016) A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1. Genome Res 26:541–553. https://doi.org/10.1101/gr.193169.115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Kim HK, Pham MHC, Ko KS et al (2018) Alternative splicing isoforms in health and disease. Pflugers Arch 470:995–1016. https://doi.org/10.1007/s00424-018-2136-x

    Article  CAS  PubMed  Google Scholar 

  173. Mayr C (2017) Regulation by 3′-untranslated regions. Annu Rev Genet 51:171–194. https://doi.org/10.1146/annurev-genet-120116-024704

    Article  CAS  PubMed  Google Scholar 

  174. Xie X, Lu J, Kulbokas EJ et al (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434:338–345. https://doi.org/10.1038/nature03441

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Siepel A, Bejerano G, Pedersen JS et al (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15:1034–1050. https://doi.org/10.1101/gr.3715005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Bartel DP (2018) Metazoan MicroRNAs. Cell 173:20–51. https://doi.org/10.1016/j.cell.2018.03.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Guo H, Ingolia NT, Weissman JS, Bartel DP (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835–840. https://doi.org/10.1038/nature09267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Eichhorn SW, Guo H, McGeary SE et al (2014) mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell 56:104–115. https://doi.org/10.1016/j.molcel.2014.08.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Marson A, Levine SS, Cole MF et al (2008) Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134:521–533. https://doi.org/10.1016/j.cell.2008.07.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Liu N, Olson EN (2010) MicroRNA regulatory networks in cardiovascular development. Dev Cell 18:510–525. https://doi.org/10.1016/j.devcel.2010.03.010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Gama-Carvalho M, Andrade J, Bras-Rosario L (2014) Regulation of cardiac cell fate by microRNAs: implications for heart regeneration. Cell 3:996–1026. https://doi.org/10.3390/cells3040996

    Article  CAS  Google Scholar 

  182. Chen C-YA, Shyu A-B (2017) Emerging themes in regulation of global mRNA turnover in cis. Trends Biochem Sci 42:16–27. https://doi.org/10.1016/j.tibs.2016.08.014

    Article  CAS  PubMed  Google Scholar 

  183. Andreassi C, Riccio A (2009) To localize or not to localize: mRNA fate is in 3′UTR ends. Trends Cell Biol 19:465–474. https://doi.org/10.1016/j.tcb.2009.06.001

    Article  CAS  PubMed  Google Scholar 

  184. Berkovits BD, Mayr C (2015) Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization. Nature 522:363–367. https://doi.org/10.1038/nature14321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Tian B, Manley JL (2017) Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol 18:18–30. https://doi.org/10.1038/nrm.2016.116

    Article  CAS  PubMed  Google Scholar 

  186. Tian B, Hu J, Zhang H, Lutz CS (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33:201–212. https://doi.org/10.1093/nar/gki158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Mayr C (2016) Evolution and biological roles of alternative 3′ UTRs. Trends Cell Biol 26:227–237. https://doi.org/10.1016/j.tcb.2015.10.012

    Article  CAS  PubMed  Google Scholar 

  188. Smibert P, Miura P, Westholm JO et al (2012) Global patterns of tissue-specific alternative polyadenylation in Drosophila. CellReports 1:277–289. https://doi.org/10.1016/j.celrep.2012.01.001

    Article  CAS  Google Scholar 

  189. Ulitsky I, Shkumatava A, Jan CH et al (2012) Extensive alternative polyadenylation during zebrafish development. Genome Res 22:2054–2066. https://doi.org/10.1101/gr.139733.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  190. Ji Z, Lee JY, Pan Z et al (2009) Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 106:7028–7033. https://doi.org/10.1073/pnas.0900028106

    Article  PubMed  PubMed Central  Google Scholar 

  191. Sandberg R, Neilson JR, Sarma A et al (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320:1643–1647. https://doi.org/10.1126/science.1155390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Elkon R, Drost J, van Haaften G et al (2012) E2F mediates enhanced alternative polyadenylation in proliferation. Genome Biol 13:R59. https://doi.org/10.1186/gb-2012-13-7-r59

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Spies N, Burge CB, Bartel DP (2013) 3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res 23:2078–2090. https://doi.org/10.1101/gr.156919.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Gruber AR, Martin G, Müller P et al (2014) Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells. Nat Commun 5:5465. https://doi.org/10.1038/ncomms6465

    Article  CAS  PubMed  Google Scholar 

  195. Geisberg JV, Moqtaderi Z, Fan X et al (2014) Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast. Cell 156:812–824. https://doi.org/10.1016/j.cell.2013.12.026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Oikonomou P, Goodarzi H, Tavazoie S (2014) Systematic identification of regulatory elements in conserved 3′ UTRs of human transcripts. Cell Rep 7:281–292. https://doi.org/10.1016/j.celrep.2014.03.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Malka Y, Steiman-Shimony A, Rosenthal E et al (2017) Post-transcriptional 3′-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments. Nat Commun 8:2029. https://doi.org/10.1038/s41467-017-02099-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Kocabas A, Duarte T, Kumar S, Hynes MA (2015) Widespread differential expression of coding region and 3′ UTR sequences in neurons and other tissues. Neuron 88:1149–1156. https://doi.org/10.1016/j.neuron.2015.10.048

    Article  CAS  PubMed  Google Scholar 

  199. Sudmant PH, Lee H, Dominguez D et al (2018) Widespread accumulation of ribosome-associated isolated 3′ UTRs in neuronal cell populations of the aging brain. CellReports 25:2447–2456.e4. https://doi.org/10.1016/j.celrep.2018.10.094

    Article  CAS  Google Scholar 

  200. Salmena L, Poliseno L, Tay Y et al (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146:353–358. https://doi.org/10.1016/j.cell.2011.07.014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Li X, Yang L, Chen L-L (2018) The biogenesis, functions, and challenges of circular RNAs. Mol Cell 71:428–442. https://doi.org/10.1016/j.molcel.2018.06.034

    Article  CAS  PubMed  Google Scholar 

  202. Wu Y, Zhao W, Liu Y et al (2018) Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response. EMBO J 37:e99017. https://doi.org/10.15252/embj.201899017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Maharana S, Wang J, Papadopoulos DK et al (2018) RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science 360:918–921. https://doi.org/10.1126/science.aar7366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Ma W, Mayr C (2018) A membraneless organelle associated with the endoplasmic reticulum enables 3′UTR-mediated protein-protein interactions. Cell 175:1492–1506.e19. https://doi.org/10.1016/j.cell.2018.10.007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Jordan, P., Gonçalves, V., Fernandes, S., Marques, T., Pereira, M., Gama-Carvalho, M. (2019). Networks of mRNA Processing and Alternative Splicing Regulation in Health and Disease. In: Romão, L. (eds) The mRNA Metabolism in Human Disease. Advances in Experimental Medicine and Biology, vol 1157. Springer, Cham. https://doi.org/10.1007/978-3-030-19966-1_1

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