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A census of human RNA-binding proteins

Nature Reviews Genetics volume 15, pages 829845 (2014) | Download Citation

Abstract

Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. The introduction of large-scale quantitative methods, such as next-generation sequencing and modern protein mass spectrometry, has renewed interest in the investigation of PTGR and the protein factors involved at a systems-biology level. Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.

Key points

  • Recent advances in next-generation sequencing methods and quantitative mass spectrometry have renewed the interest in RNA biology and the genome-wide investigation of post-transcriptional gene regulatory proteins. A global census that systematically lists the number of factors involved in post-transcriptional gene regulation (PTGR) is currently not available. Here, we provide an overall summary of the proteins involved in interactions with all classes of RNAs based on our current knowledge of PTGR; this will guide future systems-wide studies of PTGR.

  • RNA-binding proteins (RBPs) are evolutionarily deeply conserved, and their structural domains diversified early in evolution.

  • RBPs are among the most abundant proteins in the cell and are generally ubiquitously expressed, which mirrors their central and conserved role in gene regulation.

  • Only ~2% of RBPs are tissue-specific, and most of these are mRNA- and non-coding RNA-binding proteins.

  • Diseases involving RBPs show characteristic phenotypes depending on the type of RNA (for example, mRNA, ribosomal RNA and tRNA) predominantly bound by the RBPs.

  • Correlated expression of RBPs across developmental processes can identify factors in shared PTGR pathways.

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References

  1. 1.

    & The noncoding RNA revolution — trashing old rules to forge new ones. Cell 157, 77–94 (2014). This is a concise overview of the different RNA classes in bacteria, archaea and eukaryotes, highlighting their discovery and regulatory roles.

  2. 2.

    , , & Protein–RNA interactions: new genomic technologies and perspectives. Nature Rev. Genet. 13, 77–83 (2011).

  3. 3.

    , , , & Identification of RNA–protein interaction networks using PAR-CLIP. Wiley Interdiscip. Rev. RNA 3, 159–177 (2011).

  4. 4.

    , & Learning the language of post-transcriptional gene regulation. Genome Biol. 14, 130 (2013).

  5. 5.

    Functional and quantitative proteomics using SILAC. Nature Rev. Mol. Cell. Biol. 7, 952–958 (2006).

  6. 6.

    , & RNA-seq: a revolutionary tool for transcriptomics. Nature Rev. Genet. 10, 57–63 (2009).

  7. 7.

    , & SELEX — a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Engineer. 24, 381–403 (2007).

  8. 8.

    et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172–177 (2013).

  9. 9.

    , , , & Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33, D514–D517 (2005).

  10. 10.

    , & Characterization of heterogeneous nuclear RNA–protein complexes in vivo with monoclonal antibodies. Mol. Cell. Biol. 4, 1104–1114 (1984).

  11. 11.

    , , & Immunopurification of heterogeneous nuclear ribonucleoprotein particles reveals an assortment of RNA-binding proteins. Genes Dev. 2, 215–227 (1988).

  12. 12.

    , , & Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc. Natl Acad. Sci. USA 97, 14085–14090 (2000).

  13. 13.

    , & Multi-disciplinary methods to define RNA–protein interactions and regulatory networks. Curr. Opin. Genet. Dev. 23, 20–28 (2013).

  14. 14.

    , & Methods for comprehensive experimental identification of RNA–protein interactions. Genome Biol. 15, 203 (2014).

  15. 15.

    , , & SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536–540 (1995).

  16. 16.

    , & SMART 6: recent updates and new developments. Nucleic Acids Res. 37, D229–D232 (2009).

  17. 17.

    et al. The Pfam protein families database. Nucleic Acids Res. 38, D211–D222 (2010).

  18. 18.

    et al. SUPERFAMILY — sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res. 37, D380–D386 (2009).

  19. 19.

    et al. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 41, D348–D352 (2013).

  20. 20.

    , , & The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000).

  21. 21.

    et al. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29, 41–43 (2001).

  22. 22.

    et al. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. BMC Dev. Biol. 5, 14 (2005).

  23. 23.

    , , , & RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. 39, D301–D308 (2011).

  24. 24.

    et al. A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation. RNA Biol. 6, 426–433 (2009).

  25. 25.

    , & Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 30, 1427–1464 (2002). This is one of the first genome-wide comparative studies profiling the proteins involved in RNA metabolism, which concluded that RNA metabolism is the most evolutionary conserved of all cellular systems. It gives a detailed account of the structural, functional and phylogenetic relationships of protein domains in RNA metabolism, and analyses the number of genes containing RBDs across 30 different organisms.

  26. 26.

    et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25–29 (2000).

  27. 27.

    et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149, 1393–1406 (2012).

  28. 28.

    et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 46, 674–690 (2012). References 27 and 28 describe the first large-scale crosslinking studies combined with quantitative mass spectrometry for the proteome-wide identification of poly(A)-RBPs.

  29. 29.

    et al. The RNA-binding protein repertoire of embryonic stem cells. Nature Struct. Mol. Biol. 20, 1122–1130 (2013).

  30. 30.

    , , & Global analysis of yeast mRNPs. Nature Struct. Mol. Biol. 20, 127–133 (2013).

  31. 31.

    Profile hidden Markov models. Bioinformatics 14, 755–763 (1998).

  32. 32.

    , & RNA-binding proteins: modular design for efficient function. Nature Rev. Mol. Cell. Biol. 8, 479–490 (2007). This review summarizes the most commonly found RBDs and gives an overview of their structural characteristics and binding modes.

  33. 33.

    & Conserved structures and diversity of functions of RNA-binding proteins. Science 265, 615–621 (1994).

  34. 34.

    OB-fold domains: a snapshot of the evolution of sequence, structure and function. Curr. Opin. Struct. Biol. 12, 794–801 (2002).

  35. 35.

    & SAM domains: uniform structure, diversity of function. Trends Biochem. Sci. 28, 625–628 (2003).

  36. 36.

    et al. RNA chaperones, RNA annealers and RNA helicases. RNA Biol. 4, 118–130 (2007).

  37. 37.

    , , & RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett. 582, 1977–1986 (2008).

  38. 38.

    Activities of cold-shock domain proteins in translation control. Bioessays 21, 319–325 (1999).

  39. 39.

    , , & Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression. Bioessays 32, 109–118 (2010).

  40. 40.

    , , & Getting to the end of RNA: structural analysis of protein recognition of 5′ and 3′ termini. Biochim. Biophys. Acta. 1789, 653–666 (2009).

  41. 41.

    , & Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res. 34, 4943–4959 (2006). This is a highly detailed review on the structural determinants of RNA binding for ssRBDs.

  42. 42.

    & Building specificity with nonspecific RNA-binding proteins. Nature Struct. Mol. Biol. 12, 645–653 (2005).

  43. 43.

    , , , & Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Nucleic Acids Res. 37, 7701–7714 (2009).

  44. 44.

    , & Structure and function of KH domains. FEBS J. 275, 2712–2726 (2008).

  45. 45.

    , & RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence. Cell. Mol. Life Sci. 70, 1875–1895 (2013).

  46. 46.

    & The double-stranded RNA-binding motif, a versatile macromolecular docking platform. FEBS J. 272, 2109–2117 (2005).

  47. 47.

    & Eukaryotic Lsm proteins: lessons from bacteria. Nature Struct. Mol. Biol. 12, 1031–1036 (2005).

  48. 48.

    Roles of eukaryotic Lsm proteins in the regulation of mRNA function. Int. Rev. Cell. Mol. Biol. 272, 149–189 (2009).

  49. 49.

    , , & Modular recognition of RNA by a human pumilio-homology domain. Cell 110, 501–512 (2002).

  50. 50.

    & From unwinding to clamping — the DEAD box RNA helicase family. Nature Rev. Mol. Cell. Biol. 12, 505–516 (2011).

  51. 51.

    RNA helicases at work: binding and rearranging. Trends Biochem. Sci. 36, 19–29 (2011).

  52. 52.

    & DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol. Cell 8, 251–262 (2001).

  53. 53.

    & DEAD-box proteins: the driving forces behind RNA metabolism. Nature Rev. Mol. Cell. Biol. 5, 232–241 (2004).

  54. 54.

    Argonaute proteins: functional insights and emerging roles. Nature Rev. Genet. 14, 447–459 (2013).

  55. 55.

    & RNA binding strategies of ribosomal proteins. Nucleic Acids Res. 27, 381–388 (1999).

  56. 56.

    , & Alternative splicing and evolution: diversification, exon definition and function. Nature Rev. Genet. 11, 345–355 (2010).

  57. 57.

    & Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nature Rev. Mol. Cell. Biol. 10, 741–754 (2009).

  58. 58.

    , , & A census of human transcription factors: function, expression and evolution. Nature Rev. Genet. 10, 252–263 (2009). Analogous to this Analysis, this article presents a catalogue for curated human TFs. It describes a census of ~1,400 TFs and gives an overview of common structural domains, tissue-specific expression and evolutionary conservation.

  59. 59.

    & Dissecting the expression landscape of RNA-binding proteins in human cancers. Genome Biol. 15, R14 (2014).

  60. 60.

    , , & The multifunctional nucleolus. Nature Rev. Mol. Cell. Biol. 8, 574–585 (2007).

  61. 61.

    , & Nucleolus, ribosomes, and cancer. Am. J. Pathol. 173, 301–310 (2008).

  62. 62.

    & Does the ribosome translate cancer? Nature Rev. Cancer 3, 179–192 (2003).

  63. 63.

    et al. Suppression of eIF2α kinases alleviates Alzheimer's disease-related plasticity and memory deficits. Nature Neurosci. 16, 1299–1305 (2013).

  64. 64.

    et al. Ribosomal protein s15 phosphorylation mediates LRRK2 neurodegeneration in Parkinson's disease. Cell 157, 472–485 (2014).

  65. 65.

    & Genetics of Parkinson's disease. Cold Spring Harb. Perspect. Med. 2, a008888 (2012).

  66. 66.

    , & Translation matters: protein synthesis defects in inherited disease. Nature Rev. Genet. 8, 711–723 (2007). This is a comprehensive review of mRNA-binding, tRNA-binding and ribosomal proteins involved in translation, genetic mutations of which cause human diseases.

  67. 67.

    , & Translational control in cancer. Nature Rev. Cancer 10, 254–266 (2010). This article discusses dysregulation of translation in human cancers and the factors involved, the loss or increased expression of which are found in different cancers, as well as the relevant druggable targets.

  68. 68.

    , , , & The nucleolus: an emerging target for cancer therapy. Trends Mol. Med. 19, 643–654 (2013).

  69. 69.

    et al. Inhibition of mitochondrial translation as a therapeutic strategy for human acute myeloid leukemia. Cancer Cell 20, 674–688 (2011).

  70. 70.

    & Translation regulation as a therapeutic target in cancer. Cancer Res. 72, 3891–3900 (2012). This paper describes different druggable targets for regulating aberrant protein translation in diseases such as cancers.

  71. 71.

    et al. DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nature Struct. Mol. Biol. 19, 760–766 (2012).

  72. 72.

    et al. Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition. RNA 19, 613–626 (2013).

  73. 73.

    et al. LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol. Cell 48, 195–206 (2012).

  74. 74.

    et al. LIN28A is a suppressor of ER-associated translation in embryonic stem cells. Cell 151, 765–777 (2012).

  75. 75.

    et al. The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of pre-rRNA processing factors. Mol. Cell 51, 539–551 (2013).

  76. 76.

    et al. The post-transcriptional steps of eukaryotic ribosome biogenesis. Cell. Mol. Life Sci. 65, 2334–2359 (2008).

  77. 77.

    & The many faces of small nucleolar RNAs. Biochim. Biophys. Acta. 1839, 438–443 (2014).

  78. 78.

    et al. Long noncoding RNAs with snoRNA ends. Mol. Cell 48, 219–230 (2012).

  79. 79.

    & tRNA biology charges to the front. Genes Dev. 24, 1832–1860 (2010).

  80. 80.

    , & Cellular dynamics of tRNAs and their genes. FEBS Lett. 584, 310–317 (2010).

  81. 81.

    Biogenesis of small nuclear RNPs. J. Cell Sci. 117, 5949–5951 (2004).

  82. 82.

    , & The small subunit processome in ribosome biogenesis — progress and prospects. Wiley Interdiscip. Rev. RNA 2, 1–21 (2011).

  83. 83.

    et al. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 4, 255–261 (2013).

  84. 84.

    , & Mapping and significance of the mRNA methylome. Wiley Interdiscip. Rev. RNA 4, 397–422 (2013).

  85. 85.

    et al. Exaggerated behavioral phenotypes in Fmr1/Fxr2 double knockout mice reveal a functional genetic interaction between fragile X-related proteins. Hum. Mol. Genet. 15, 1984–1994 (2006).

  86. 86.

    , & Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307, 1113–1143 (2001).

  87. 87.

    & Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 195, 643–681 (2013).

  88. 88.

    et al. EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 19, 327–335 (2009).

  89. 89.

    , & SF1 and SF2 helicases: family matters. Curr. Opin. Struct. Biol. 20, 313–324 (2010).

  90. 90.

    , & Structural classification of zinc fingers: survey and summary. Nucleic Acids Res. 31, 532–550 (2003).

  91. 91.

    , , , & Evolution of RNA-binding proteins in animals: insights from genome-wide analysis in the sponge Amphimedon queenslandica. Mol. Biol. Evol. 28, 2289–2303 (2011).

  92. 92.

    & Ribosome biogenesis: of knobs and RNA processing. Exp. Cell Res. 296, 43–50 (2004).

  93. 93.

    , & Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res. 14, 54–61 (2004).

  94. 94.

    et al. Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins. Genome Biol. 6, R56 (2005).

  95. 95.

    , , & An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol. 5, e1000598 (2009). This is one of the first RNA-seq studies to investigate the tissue specificity of genes based on mRNA expression levels in 16 human tissues and cell types.

  96. 96.

    et al. A comprehensive functional analysis of tissue specificity of human gene expression. BMC Biol. 6, 49 (2008).

  97. 97.

    , , & Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466, 835–840 (2010).

  98. 98.

    et al. Global quantification of mammalian gene expression control. Nature 473, 337–342 (2011).

  99. 99.

    & The biogenesis and function of PIWI proteins and piRNAs: progress and prospect. Annu. Rev. Cell Dev. Biol. 25, 355–376 (2009).

  100. 100.

    , & Neuronal regulation of alternative pre-mRNA splicing. Nature Rev. Neurosci. 8, 819–831 (2007).

  101. 101.

    et al. Digital genome-wide ncRNA expression, including snoRNAs, across 11 human tissues using polyA-neutral amplification. PLoS ONE 5, e11779 (2010).

  102. 102.

    , & Tissue-specific differences in human transfer RNA expression. PLoS Genet. 2, e221 (2006).

  103. 103.

    & Synonymous but not the same: the causes and consequences of codon bias. Nature Rev. Genet. 12, 32–42 (2011).

  104. 104.

    & How common are extraribosomal functions of ribosomal proteins? Mol. Cell 34, 3–11 (2009).

  105. 105.

    & Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nature Rev. Mol. Cell. Biol. 13, 355–369 (2012).

  106. 106.

    & PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nature Rev. Genet. 14, 523–534 (2013).

  107. 107.

    , , & PIWI-interacting small RNAs: the vanguard of genome defence. Nature Rev. Mol. Cell. Biol. 12, 246–258 (2011).

  108. 108.

    & Pathway to totipotency: Lessons from germ cells. Cell 127, 891–904 (2006).

  109. 109.

    & The chromatoid body: a germ-cell-specific RNA-processing centre. Nature Rev. Mol. Cell. Biol. 8, 85–90 (2007).

  110. 110.

    , , & RNA granules in germ cells. Cold Spring Harb. Perspect. Biol. 3, a002774 (2011).

  111. 111.

    & Post-transcriptional and post-translational regulation during mouse oocyte maturation. BMB Rep. 44, 147–157 (2011).

  112. 112.

    et al. Global gene expression in the human fetal testis and ovary. Biol. Reprod. 81, 438–443 (2009).

  113. 113.

    , & The DAZL and PABP families: RNA-binding proteins with interrelated roles in translational control in oocytes. Reproduction 137, 595–617 (2009).

  114. 114.

    & Role of the DAZ genes in male fertility. Reprod. Biomed. Online 10, 72–80 (2005).

  115. 115.

    The DEAD-box helicase Vasa: evidence for a multiplicity of functions in RNA processes and developmental biology. Biochim. Biophys. Acta. 1829, 810–816 (2013).

  116. 116.

    et al. MOV10L1 is necessary for protection of spermatocytes against retrotransposons by PIWI-interacting RNAs. Proc. Natl Acad. Sci. USA 107, 11847–11852 (2010).

  117. 117.

    et al. Mouse MOV10L1 associates with PIWI proteins and is an essential component of the PIWI-interacting RNA (piRNA) pathway. Proc. Natl Acad. Sci. USA 107, 11841–11846 (2010).

  118. 118.

    & Gonadotropin-regulated testicular helicase (GRTH/DDX25): an essential regulator of spermatogenesis. Trends Endocrinol. Metab. 18, 314–320 (2007).

  119. 119.

    in Ribonucleases Ch. 2 (ed. Nicholson, A. W.) 35–53 (Springer, 2011).

  120. 120.

    VICKZ proteins: a multi-talented family of regulatory RNA-binding proteins. Biol. Cell 97, 87–96 (2005).

  121. 121.

    & Mechanisms coordinating ELAV/Hu mRNA regulons. Curr. Opin. Genet. Dev. 23, 35–43 (2013).

  122. 122.

    et al. FMRP targets distinct mRNA sequence elements to regulate protein expression. Nature 492, 382–386 (2012). References 2, 14 and 122 give comprehensive and balanced accounts of different methods developed for the genome-wide identification of RBPs and RBP-binding sites.

  123. 123.

    , & New perspectives on the biology of fragile X syndrome. Curr. Opin. Genet. Dev. 22, 256–263 (2012).

  124. 124.

    et al. Fxr1 knockout mice show a striated muscle phenotype: implications for Fxr1p function in vivo. Hum. Mol. Genet. 13, 1291–1302 (2004).

  125. 125.

    & Ribosomopathies: human disorders of ribosome dysfunction. Blood 115, 3196–3205 (2010).

  126. 126.

    , , & RNA-binding proteins in human genetic disease. Trends Genet. 24, 416–425 (2008).

  127. 127.

    , & RNA and disease. Cell 136, 777–793 (2009). This is a comprehensive overview of RNA- and RBP-based genetic diseases caused by mutations in RNAs and RBPs, and highlights the most prominent examples.

  128. 128.

    , & Altered ribostasis: RNA–protein granules in degenerative disorders. Cell 154, 727–736 (2013). This paper highlights prion-like RBP aggregation in human diseases caused by mutations in RBPs.

  129. 129.

    , , & Eukaryotic stress granules are cleared by autophagy and Cdc48/VCP function. Cell 153, 1461–1474 (2013).

  130. 130.

    et al. Local RNA translation at the synapse and in disease. J. Neurosci. 31, 16086–16093 (2011).

  131. 131.

    , & TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration. Hum. Mol. Genet. 19, R46–R64 (2010).

  132. 132.

    et al. Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature 495, 467–473 (2013).

  133. 133.

    et al. Expansion of an unstable trinucleotide CAG repeat in spinocerebellar ataxia type 1. Nature Genet. 4, 221–226 (1993).

  134. 134.

    et al. Identification and characterization of the gene causing type 1 spinocerebellar ataxia. Nature Genet. 7, 513–520 (1994).

  135. 135.

    et al. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474, 380–384 (2011).

  136. 136.

    & RNA-binding proteins in microsatellite expansion disorders: mediators of RNA toxicity. Brain Res. 1462, 100–111 (2012).

  137. 137.

    et al. tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia. Nature Genet. 40, 1113–1118 (2008).

  138. 138.

    & Aminoacyl-tRNA synthetases in medicine and disease. EMBO Mol. Med. 5, 332–343 (2013).

  139. 139.

    et al. Mutations involved in Aicardi–Goutières syndrome implicate SAMHD1 as regulator of the innate immune response. Nature Genet. 41, 829–832 (2009).

  140. 140.

    et al. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi–Goutières syndrome and mimic congenital viral brain infection. Nature Genet. 38, 910–916 (2006).

  141. 141.

    , & Messenger-RNA-binding proteins and the messages they carry. Nature Rev. Mol. Cell. Biol. 3, 195–205 (2002).

  142. 142.

    & How cells get the message: dynamic assembly and function of mRNA–protein complexes. Nature Rev. Genet. 14, 275–287 (2013).

  143. 143.

    RNA regulons: coordination of post-transcriptional events. Nature Rev. Genet. 8, 533–543 (2007).

  144. 144.

    & Principles and properties of eukaryotic mRNPs. Mol. Cell 54, 547–558 (2014).

  145. 145.

    et al. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nature Rev. Mol. Cell. Biol. 14, 153–165 (2013).

  146. 146.

    & Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci. 25, 381–388 (2000).

  147. 147.

    , & The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701–718 (2009).

  148. 148.

    & Functional consequences of developmentally regulated alternative splicing. Nature Rev. Genet. 12, 715–729 (2011).

  149. 149.

    et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664–668 (2010).

  150. 150.

    et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53–64 (2012).

  151. 151.

    et al. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol. Cell 43, 327–339 (2011).

  152. 152.

    et al. A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility. Nature Cell Biol. 12, 1014–1020 (2010).

  153. 153.

    & RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nature Rev. Mol. Cell. Biol. 10, 430–436 (2009).

  154. 154.

    , & Pluripotency and cellular reprogramming: facts, hypotheses, unresolved issues. Cell 143, 508–525 (2010).

  155. 155.

    et al. Constitutive patterns of gene expression regulated by RNA-binding proteins. Genome Biol. 15, R13 (2014).

  156. 156.

    , , & Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks. Proc. Natl Acad. Sci. USA 106, 20300–20305 (2009).

  157. 157.

    Cytoplasmic RNA: a case of the tail wagging the dog. Nature Rev. Cancer 13, 643–653 (2013).

  158. 158.

    , , , & Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev. 27, 2380–2396 (2013). This is a detailed study profiling genome-wide alternative polyadenylation sites in mRNAs across 12 human cell lines and tissues. The authors conclude that genes with multiple 3′UTRs tend to vary 3′UTR ratios across tissues, whereas genes with single 3′UTRs vary mRNA expression levels.

  159. 159.

    , & Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853–866 (2011).

  160. 160.

    & Tissue-specific mechanisms of alternative polyadenylation: testis, brain, and beyond. Wiley Interdiscip. Rev. RNA 1, 494–501 (2010).

  161. 161.

    & Understanding follicle growth in vivo. Hum. Reprod. 25, 2944–2954 (2010).

  162. 162.

    et al. Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs): post-transcriptional drivers of cancer progression? Cell. Mol. Life Sci. 70, 2657–2675 (2013).

  163. 163.

    , , , & Human DAZL, DAZ and BOULE genes modulate primordial germ-cell and haploid gamete formation. Nature 462, 222–225 (2009).

  164. 164.

    & Dendritic mRNA: transport, translation and function. Nature Rev. Neurosci. 8, 776–789 (2007).

  165. 165.

    , , & Remote control of gene function by local translation. Cell 157, 26–40 (2014).

  166. 166.

    , & The molecular and systems biology of memory. Cell 157, 163–186 (2014).

  167. 167.

    & Dendritic protein synthesis, synaptic plasticity, and memory. Cell 127, 49–58 (2006).

  168. 168.

    et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489, 391–399 (2012).

  169. 169.

    et al. Transcriptional landscape of the prenatal human brain. Nature 508, 199–206 (2014).

  170. 170.

    et al. Genome-wide gene expression profiles of the developing mouse hippocampus. Proc. Natl Acad. Sci. USA 98, 8862–8867 (2001).

  171. 171.

    & How does Lin28 let-7 control development and disease? Trends Cell Biol. 22, 474–482 (2012).

  172. 172.

    et al. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nature Genet. 43, 706–711 (2011).

  173. 173.

    & Human fetal hippocampal development: I. Cytoarchitecture, myeloarchitecture, and neuronal morphologic features. J. Comp. Neurol. 367, 274–292 (1996).

  174. 174.

    et al. ANG mutations segregate with familial and 'sporadic' amyotrophic lateral sclerosis. Nature Genet. 38, 411–413 (2006).

  175. 175.

    et al. RNASET2-deficient cystic leukoencephalopathy resembles congenital cytomegalovirus brain infection. Nature Genet. 41, 773–775 (2009).

  176. 176.

    , , & Structural and molecular insights into the mechanism of action of human angiogenin-ALS variants in neurons. Nature Commun. 3, 1121 (2012).

  177. 177.

    et al. Motoneurons secrete angiogenin to induce RNA cleavage in astroglia. J. Neurosci. 32, 5024–5038 (2012).

  178. 178.

    et al. Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biol. 15, R12 (2014).

  179. 179.

    et al. miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4–NOT. Nature Struct. Mol. Biol. 18, 1211–1217 (2011).

  180. 180.

    & Tristetraprolin (TTP): Interactions with mRNA and proteins, and current thoughts on mechanisms of action. Biochim. Biophys. Acta. 1829, 666–679 (2013).

  181. 181.

    Immune proteins in brain development and synaptic plasticity. Neuron 64, 93–109 (2009).

  182. 182.

    & Cytokines and CNS development. Neuron 64, 61–78 (2009).

  183. 183.

    et al. The spatio-temporal expression of MHC class I molecules during human hippocampal formation development. Brain Res. 1529, 26–38 (2013).

  184. 184.

    & The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nature Rev. Mol. Cell. Biol. 15, 313–326 (2014).

  185. 185.

    & lincRNAs: Genomics, evolution, and mechanisms. Cell 154, 26–46 (2013). This is a detailed review on the emerging roles of lncRNAs in gene regulation.

  186. 186.

    Ribosome profiling: new views of translation, from single codons to genome scale. Nature Rev. Genet. 15, 205–213 (2014). This article gives an overview of ribosome profiling, which is a method to measure actively translating RNAs genome-wide. Next to mass spectrometry, ribosome profiling allows the quantification of expressed proteins in the cell and also the measurement of translation rates of mRNAs.

  187. 187.

    et al. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505, 706–709 (2014).

  188. 188.

    et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505, 696–700 (2014).

  189. 189.

    , , , & Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505, 701–705 (2014).

  190. 190.

    & RNA sequencing: advances, challenges and opportunities. Nature Rev. Genet. 12, 87–98 (2011).

  191. 191.

    , & MicroRNA profiling: approaches and considerations. Nature Rev. Genet. 13, 358–369 (2012). References 189 and 191 describe transcriptome-wide methods for determining RNA structures in vivo, which give insights into RNA accessibility and regulation.

  192. 192.

    , , & Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs. Nature 469, 97–101 (2011). This study describes one of the first RNA-seq methods to accurately profile alternative polyadenylation sites genome-wide.

  193. 193.

    , , & TAIL-seq: Genome-wide determination of poly(A) tail length and 3′ end modifications. Mol. Cell 53, 1044–1052 (2014).

  194. 194.

    , , , & Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508, 66–71 (2014). This paper details a protocol to map genome-wide mRNA poly(A) tail length in vivo.

  195. 195.

    & 3′ processing of eukaryotic precursor tRNAs. Wiley Interdiscip. Rev. RNA 2, 362–375 (2011).

  196. 196.

    , & Eukaryotic ribosome biogenesis at a glance. J. Cell Sci. 126, 4815–4821 (2013).

  197. 197.

    & The function and synthesis of ribosomes. Nature Rev. Mol. Cell. Biol. 2, 514–520 (2001).

  198. 198.

    & U6 RNA biogenesis and disease association. Wiley Interdiscip. Rev. RNA 4, 581–592 (2013).

  199. 199.

    , & The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Rev. Mol. Cell. Biol. 11, 113–127 (2010).

  200. 200.

    & Eukaryotic stress granules: The ins and outs of translation. Mol. Cell 36, 932–941 (2009).

  201. 201.

    & P bodies and the control of mRNA translation and degradation. Mol. Cell 25, 635–646 (2007).

  202. 202.

    , & The highways and byways of mRNA decay. Nature Rev. Mol. Cell. Biol. 8, 113–126 (2007).

  203. 203.

    , & Biogenesis of small RNAs in animals. Nature Rev. Mol. Cell. Biol. 10, 126–139 (2009).

  204. 204.

    , & 7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription. Wiley Interdiscip. Rev. RNA 3, 92–103 (2011).

  205. 205.

    & Paraspeckles. Cold Spring Harb. Perspect. Biol. 2, a000687 (2010).

  206. 206.

    et al. LincRNA-p21 suppresses target mRNA translation. Mol. Cell 47, 648–655 (2012).

  207. 207.

    & RNA quality control in eukaryotes. Cell 131, 660–668 (2007).

  208. 208.

    , & RNA-quality control by the exosome. Nature Rev. Mol. Cell. Biol. 7, 529–539 (2006).

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Acknowledgements

The body map data were kindly provided by the Gene Expression Applications research group at Illumina. The authors thank P. Morozov, M. Carty, M. Brown, R. Kim and S. Lianoglou for discussions on the computational methods, as well as Z. Ozair, A. D. Haase and all laboratory members for comments on the manuscript. S.G. was supported by a Ph.D. fellowship from the Boehringer Ingelheim Fonds. M.H. is supported by the US National Institute of Arthritis and Musculoskeletal and Skin Diseases Intramural Research Program. T.T. is an Investigator of the Howard Hughes Medical Institute.

Author information

Affiliations

  1. Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, New York 10065, USA.

    • Stefanie Gerstberger
    •  & Thomas Tuschl
  2. Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, Maryland 20892, USA.

    • Markus Hafner

Authors

  1. Search for Stefanie Gerstberger in:

  2. Search for Markus Hafner in:

  3. Search for Thomas Tuschl in:

Competing interests

T.T. is a cofounder and scientific advisor to Alnylam Pharmaceuticals and a scientific advisor to Regulus Therapeutics. S.G. and M.H. declare no competing interests.

Corresponding author

Correspondence to Thomas Tuschl.

Supplementary information

Glossary

Ribonucleoprotein

(RNP). Protein (or proteins) complexed with RNA as an obligate binding partner.

RNA-binding proteins

(RBPs). Proteins involved in the maturation, stability, transport and degradation of cellular RNAs. RBPs directly bind to RNA or are integral parts of macromolecular protein complexes that bind to RNA.

Non-coding RNA

(ncRNA). An RNA that does not encode a protein. In this Analysis, ncRNA is also used to specifically group together all remaining ncRNAs that are not ribosomal RNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs or small Cajal body-specific RNAs.

RNA recognition elements

Short (rarely more than 4–6-nucleotide-long) sequence elements within RNA targets that are recognized and bound by RNA-binding proteins.

Crosslinking and immunoprecipitation followed by sequencing

(CLIP–seq). An experimental method to map the binding sites of RNA-binding proteins (RBPs) on RNA targets transcriptome-wide. RBPs are ultraviolet-crosslinked to RNA in vivo, followed by partial RNase treatment of cell lysates, immunoprecipitation of RBPs, recovery of covalently bound RNA, and small RNA cDNA library preparation for deep sequencing of crosslinked RNA segments.

RNA immunoprecipitation and sequencing

(RIP-seq). An experimental method to identify enrichment and targets of RNA-binding proteins (RBPs). RBPs are immunoprecipitated, and bound RNAs are library-prepared for deep sequencing.

Small Cajal body-specific RNAs

(scaRNAs). Small RNAs that have a similar structure and sequence to small nucleolar RNAs (snoRNAs), localize to the Cajal body and are involved in the methylation and pseudouridylation of snoRNAs.

RNA-binding domains

(RBDs). Structural protein domains that directly bind to RNA. In this Analysis, RBD is also used to include structural domains found exclusively in RNA-binding proteins that are able to transiently contact RNA during ribonucleoprotein assembly or disassembly.

Hidden Markov models

Statistical probability models that assume a Markov chain with unobserved (hidden) states. In protein domain predictions, HMMs are calculated from protein sequence alignments and compute the probability of a specific protein sequence.

Transcription factors

(TFs). Proteins that bind to specific DNA sequences at gene promoters, upstream and downstream elements, or within the gene body; they influence gene expression by enhancing or blocking transcription.

RPKM

(Reads per kilobase per million mapped reads). A measure for quantifying single-end read RNA-sequencing data per transcript or gene exon model; it normalizes the total number of mapped reads per transcript or gene exon model by the length of the transcript or gene exon model (in kilobases) and the library size (total number of reads mapped to the genome or transcriptome in million reads).

Small nuclear RNA

(snRNA). A type of short (~70–200-nucleotide) RNA found in the nucleus of eukaryotic cells. snRNAs associate with proteins of the spliceosome to form the spliceosomal core complexes.

Small nucleolar RNA

(snoRNA). A type of short (~50–200-nucleotide) RNA that is localized to the nucleolus and that guides methylation or pseudouridylation of ribosomal RNAs and small nuclear RNAs.

MicroRNA

(miRNA). A type of small (~21-nucleotide) non-coding RNA involved in post-transcriptional gene silencing. miRNAs form ribonucleoprotein complexes with Argonaute proteins to repress mRNA stability and protein expression by recruiting RNA deadenylation and degradation complexes to their RNA targets.

PIWI-interacting RNAs

(piRNAs). Small (~28-nucleotide) non-coding RNAs involved in post-transcriptional gene silencing that are expressed in the germ line; they form ribonucleoprotein complexes with PIWI proteins, and protect the genome from genomic instability by transcriptional and post-transcriptional repression of transposons.

Long ncRNAs

(lncRNAs). RNAs that do not encode proteins and are > 200 nucleotides long; they are found as structural components in nuclear and cytoplasmic ribonucleoprotein complexes and are transcribed by RNA polymerase II, similarly to mRNAs. Less abundant lncRNAs may influence the gene expression of neighbouring genes (in cis) at the transcriptional, post-transcriptional and translational levels.

Post-conception week

(PCW). A time measurement used to describe stages of human development in prenatal weeks. PCW records the time elapsed since the day of conception. Also commonly used is gestation week, which counts from the day of the last menstrual period. Assuming a normal 28-day menstrual cycle, PCW is 2 weeks less than gestation week.

3′ untranslated regions

(3′UTRs). 3′ ends of mRNAs, specifically the region between the stop codon and the poly(A) tail. 3′UTRs are targets of post-transcriptional regulation by many ribonucleoprotein and RNA-binding protein complexes, which determine their stability, translation and turnover.

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DOI

https://doi.org/10.1038/nrg3813

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