Skip to main content

Mechanisms of Post-transcriptional Gene Regulation

  • 972 Accesses

Abstract

Post-transcriptional control plays a pervasive role in the regulation of gene expression, with direct relevance to the proper function of endocrine systems. This chapter explores the mechanisms that control protein expression at the levels of translation and mRNA degradation. First, we provide an overview of the pathways and factors involved in these processes. Next, we discuss the cis and trans-acting factors that modulate the amount, timing, and location of protein production and that regulate the rates of mRNA degradation. To emphasize key concepts in post-transcriptional control, we present prime examples of signals and regulatory factors that control mRNAs. Among these, we explore RNA binding proteins and non-coding RNAs that specifically and potently influence mRNA fate.

Keywords

  • Gene regulation
  • RNA processing
  • Translation initiation and elongation
  • Translational control
  • Untranslated regions (UTRs)
  • RNA decay
  • Deadenylation
  • Decapping
  • Exoribonuclease
  • Endoribonuclease
  • RNA localization
  • RNA binding proteins
  • Non-coding RNA
  • Internal ribosome entry site (IRES)
  • MicroRNA
  • RNA induced silencing complex (RISC)
  • miRNA sponges
  • Competing endogenous RNAs (ceRNAs)
  • Pumilio and Fem-3 binding factor proteins (PUFs)
  • Nanos
  • Cytoplasmic poly-adenylation element binding protein (CPEB)
  • eIF4E binding protein (4EBP)
  • Poly-adenosine binding protein (PABP)

Note: Due to the space limitations and the broad nature of this chapter, we were unable to cite many important contributions, thus we apologize to colleagues whose work could not be highlighted.

This is a preview of subscription content, access via your institution.

Fig. 1.1
Fig. 1.2
Fig. 1.3
Fig. 1.4
Fig. 1.5

References

  • Abaza I, Gebauer F (2008) Trading translation with RNA-binding proteins. RNA 14:404–409

    CAS  Google Scholar 

  • Afonina ZA, Myasnikov AG, Shirokov VA, Klaholz BP, Spirin AS (2014) Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study. Nucleic Acids Res 42:9461–9469

    CAS  Google Scholar 

  • Aitken CE, Lorsch JR (2012) A mechanistic overview of translation initiation in eukaryotes. Nat Struct Mol Biol 19:568–576

    CAS  Google Scholar 

  • Akiri G, Nahari D, Finkelstein Y, Le SY, Elroy-Stein O, Levi BZ (1998) Regulation of vascular endothelial growth factor (VEGF) expression is mediated by internal initiation of translation and alternative initiation of transcription. Oncogene 17:227–236

    CAS  Google Scholar 

  • Andrei MA, Ingelfinger D, Heintzmann R, Achsel T, Rivera-Pomar R, Luhrmann R (2005) A role for eIF4E and eIF4E-transporter in targeting mRNPs to mammalian processing bodies. RNA 11:717–727

    CAS  Google Scholar 

  • Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M et al (2010) The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 34:883–923

    CAS  Google Scholar 

  • Arribas-Layton M, Wu D, Lykke-Andersen J, Song H (2013) Structural and functional control of the eukaryotic mRNA decapping machinery. Biochim Biophys Acta 1829:580–589

    CAS  Google Scholar 

  • Badis G, Saveanu C, Fromont-Racine M, Jacquier A (2004) Targeted mRNA degradation by deadenylation-independent decapping. Mol Cell 15:5–15

    CAS  Google Scholar 

  • Baird TD, Wek RC (2012) Eukaryotic initiation factor 2 phosphorylation and translational control in metabolism. Adv Nutr 3:307–321

    CAS  Google Scholar 

  • Bakheet T, Williams BR, Khabar KS (2006) ARED 3.0: the large and diverse AU-rich transcriptome. Nucleic Acids Res 34:D111–D114

    CAS  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    CAS  Google Scholar 

  • Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233

    CAS  Google Scholar 

  • Batista PJ, Chang HY (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell 152:1298–1307

    CAS  Google Scholar 

  • Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC (2007) Mammalian mirtron genes. Mol Cell 28:328–336

    CAS  Google Scholar 

  • Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S et al (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306:2242–2246

    CAS  Google Scholar 

  • Blewett NH, Goldstrohm AC (2012a) An eIF4E-binding protein promotes mRNA decapping and is required for PUF repression. Mol Cell Biol

    Google Scholar 

  • Blewett NH, Goldstrohm AC (2012b) A eukaryotic translation initiation factor 4E-binding protein promotes mRNA decapping and is required for PUF repression. Mol Cell Biol 32:4181–4194

    CAS  Google Scholar 

  • Boeck R, Tarun S Jr, Rieger M, Deardorff JA, Muller-Auer S, Sachs AB (1996) The yeast Pan2 protein is required for poly(A)-binding protein-stimulated poly(A)-nuclease activity. J Biol Chem 271:432–438

    CAS  Google Scholar 

  • Boisvert FM, van Koningsbruggen S, Navascues J, Lamond AI (2007) The multifunctional nucleolus. Nat Rev Mol Cell Biol 8:574–585

    CAS  Google Scholar 

  • Borman AM, Michel YM, Kean KM (2000) Biochemical characterisation of cap-poly(A) synergy in rabbit reticulocyte lysates: the eIF4G-PABP interaction increases the functional affinity of eIF4E for the capped mRNA 5′-end. Nucleic Acids Res 28:4068–4075

    CAS  Google Scholar 

  • Brooks SA, Blackshear PJ (2013) Tristetraprolin (TTP): interactions with mRNA and proteins, and current thoughts on mechanisms of action. Biochim Biophys Acta 1829:666–679

    CAS  Google Scholar 

  • Brown CE, Tarun SZ Jr, Boeck R, Sachs AB (1996) PAN3 encodes a subunit of the Pab1p-dependent poly(A) nuclease in Saccharomyces cerevisiae. Mol Cell Biol 16:5744–5753

    CAS  Google Scholar 

  • Buxbaum AR, Haimovich G, Singer RH (2015) In the right place at the right time: visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 16:95–109

    CAS  Google Scholar 

  • Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A (2015) Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol 16:20

    Google Scholar 

  • Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C et al (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491:454–457

    CAS  Google Scholar 

  • Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655

    CAS  Google Scholar 

  • Cech TR, Steitz JA (2014) The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157:77–94

    CAS  Google Scholar 

  • Charlesworth A, Meijer HA, de Moor CH (2013) Specificity factors in cytoplasmic polyadenylation. Wiley Interdiscip Rev RNA 4:437–461

    CAS  Google Scholar 

  • Chen CY, Gherzi R, Ong SE, Chan EL, Raijmakers R, Pruijn GJ, Stoecklin G, Moroni C, Mann M, Karin M (2001) AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107:451–464

    CAS  Google Scholar 

  • Chen N, Walsh MA, Liu Y, Parker R, Song H (2005) Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. J Mol Biol 347:707–718

    CAS  Google Scholar 

  • Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G et al (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149–1154

    CAS  Google Scholar 

  • Cho PF, Poulin F, Cho-Park YA, Cho-Park IB, Chicoine JD, Lasko P, Sonenberg N (2005) A new paradigm for translational control: inhibition via 5′-3′ mRNA tethering by bicoid and the eIF4E cognate 4EHP. Cell 121:411–423

    CAS  Google Scholar 

  • Cho PF, Gamberi C, Cho-Park YA, Cho-Park IB, Lasko P, Sonenberg N (2006) Cap-dependent translational inhibition establishes two opposing morphogen gradients in Drosophila embryos. Curr Biol 16:2035–2041

    CAS  Google Scholar 

  • Cho H, Park OH, Park J, Ryu I, Kim J, Ko J, Kim YK (2015) Glucocorticoid receptor interacts with PNRC2 in a ligand-dependent manner to recruit UPF1 for rapid mRNA degradation. Proc Natl Acad Sci U S A 112:E1540–E1549

    CAS  Google Scholar 

  • Christie M, Boland A, Huntzinger E, Weichenrieder O, Izaurralde E (2013) Structure of the PAN3 pseudokinase reveals the basis for interactions with the PAN2 deadenylase and the GW182 proteins. Mol Cell 51:360–373

    CAS  Google Scholar 

  • Claycomb JM (2014) Ancient endo-siRNA pathways reveal new tricks. Curr Biol 24:R703–R715

    CAS  Google Scholar 

  • Collart MA (2003) Global control of gene expression in yeast by the Ccr4-not complex. Gene 313:1–16

    CAS  Google Scholar 

  • Craig AW, Haghighat A, Yu AT, Sonenberg N (1998) Interaction of polyadenylate-binding protein with the eIF4G homologue PAIP enhances translation. Nature 392:520–523

    CAS  Google Scholar 

  • Curtis D, Lehmann R, Zamore PD (1995) Translational regulation in development. Cell 81:171–178

    CAS  Google Scholar 

  • Das B, Butler JS, Sherman F (2003) Degradation of normal mRNA in the nucleus of Saccharomyces cerevisiae. Mol Cell Biol 23:5502–5515

    CAS  Google Scholar 

  • Dennis MD, Jefferson LS, Kimball SR (2012) Role of p70S6K1-mediated phosphorylation of eIF4B and PDCD4 proteins in the regulation of protein synthesis. J Biol Chem 287:42890–42899

    CAS  Google Scholar 

  • Dever TE, Green R (2012) The elongation, termination, and recycling phases of translation in eukaryotes. Cold Spring Harb Perspect Biol 4:a013706

    Google Scholar 

  • Diederichs S (2014) The four dimensions of noncoding RNA conservation. Trends Genet 30:121–123

    CAS  Google Scholar 

  • Ebert MS, Sharp PA (2010) Emerging roles for natural microRNA sponges. Curr Biol 20:R858–R861

    CAS  Google Scholar 

  • Elkon R, Ugalde AP, Agami R (2013) Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet 14:496–506

    CAS  Google Scholar 

  • Esau C, Kang X, Peralta E, Hanson E, Marcusson EG, Ravichandran LV, Sun Y, Koo S, Perera RJ, Jain R et al (2004) MicroRNA-143 regulates adipocyte differentiation. J Biol Chem 279:52361–52365

    CAS  Google Scholar 

  • Fenger-Gron M, Fillman C, Norrild B, Lykke-Andersen J (2005) Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol Cell 20:905–915

    CAS  Google Scholar 

  • Fernandez IS, Bai XC, Murshudov G, Scheres SH, Ramakrishnan V (2014) Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome. Cell 157:823–831

    CAS  Google Scholar 

  • Fischer N, Weis K (2002) The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1. EMBO J 21:2788–2797

    CAS  Google Scholar 

  • Franks TM, Singh G, Lykke-Andersen J (2010) Upf1 ATPase-dependent mRNP disassembly is required for completion of nonsense- mediated mRNA decay. Cell 143:938–950

    CAS  Google Scholar 

  • Fraser CS, Doudna JA (2007) Structural and mechanistic insights into hepatitis C viral translation initiation. Nat Rev Microbiol 5:29–38

    CAS  Google Scholar 

  • Freedman JE, Tanriverdi K (2013) Defining miRNA targets: balancing simplicity with complexity. Circulation 127:2075–2077

    Google Scholar 

  • Fromont-Racine M, Bertrand E, Pictet R, Grange T (1993) A highly sensitive method for mapping the 5′ termini of mRNAs. Nucleic Acids Res 21:1683–1684

    CAS  Google Scholar 

  • Fu XD, Ares M Jr (2014) Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15:689–701

    CAS  Google Scholar 

  • Fukao A, Mishima Y, Takizawa N, Oka S, Imataka H, Pelletier J, Sonenberg N, Thoma C, Fujiwara T (2014) MicroRNAs trigger dissociation of eIF4AI and eIF4AII from target mRNAs in humans. Mol Cell 56:79–89

    CAS  Google Scholar 

  • Fukaya T, Iwakawa HO, Tomari Y (2014) MicroRNAs block assembly of eIF4F translation initiation complex in Drosophila. Mol Cell 56:67–78

    CAS  Google Scholar 

  • Gaddam D, Stevens N, Hollien J (2013) Comparison of mRNA localization and regulation during endoplasmic reticulum stress in Drosophila cells. Mol Biol Cell 24:14–20

    CAS  Google Scholar 

  • Gallie DR (1991) The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency. Genes Dev 5:2108–2116

    CAS  Google Scholar 

  • Gao M, Fritz DT, Ford LP, Wilusz J (2000) Interaction between a poly(A)-specific ribonuclease and the 5′ cap influences mRNA deadenylation rates in vitro. Mol Cell 5:479–488

    CAS  Google Scholar 

  • Gao M, Wilusz CJ, Peltz SW, Wilusz J (2001) A novel mRNA-decapping activity in HeLa cytoplasmic extracts is regulated by AU-rich elements. EMBO J 20:1134–1143

    CAS  Google Scholar 

  • Garneau NL, Wilusz J, Wilusz CJ (2007) The highways and byways of mRNA decay. Nat Rev Mol Cell Biol 8:113–126

    CAS  Google Scholar 

  • Geisler S, Coller J (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 14:699–712

    CAS  Google Scholar 

  • Gerstberger S, Hafner M, Tuschl T (2014) A census of human RNA-binding proteins. Nat Rev Genet 15:829–845

    CAS  Google Scholar 

  • Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108

    CAS  Google Scholar 

  • Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, Lee S, Xu J, Kittler EL, Zapp ML, Weng Z et al (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320:1077–1081

    CAS  Google Scholar 

  • Ghosh S, Jacobson A (2010) RNA decay modulates gene expression and controls its fidelity. Wiley Interdiscip Rev RNA 1:351–361

    CAS  Google Scholar 

  • Goldstrohm AC, Wickens M (2008) Multifunctional deadenylase complexes diversify mRNA control. Nat Rev Mol Cell Biol 9:337–344

    CAS  Google Scholar 

  • Goldstrohm AC, Hook BA, Seay DJ, Wickens M (2006) PUF proteins bind Pop2p to regulate messenger RNAs. Nat Struct Mol Biol 13:533–539

    CAS  Google Scholar 

  • Goldstrohm AC, Seay DJ, Hook BA, Wickens M (2007) PUF protein-mediated deadenylation is catalyzed by Ccr4p. J Biol Chem 282:109–114

    CAS  Google Scholar 

  • Gong C, Maquat LE (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470:284–288

    CAS  Google Scholar 

  • Gray NK, Wickens M (1998) Control of translation initiation in animals. Annu Rev Cell Dev Biol 14:399–458

    CAS  Google Scholar 

  • Green CB, Besharse JC (1996) Identification of a novel vertebrate circadian clock-regulated gene encoding the protein nocturnin. Proc Natl Acad Sci U S A 93:14884–14888

    CAS  Google Scholar 

  • Green CB, Douris N, Kojima S, Strayer CA, Fogerty J, Lourim D, Keller SR, Besharse JC (2007) Loss of nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity. Proc Natl Acad Sci U S A 104:9888–9893

    CAS  Google Scholar 

  • Groisman I, Huang YS, Mendez R, Cao Q, Theurkauf W, Richter JD (2000) CPEB, maskin, and cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division. Cell 103:435–447

    CAS  Google Scholar 

  • Groisman I, Jung MY, Sarkissian M, Cao Q, Richter JD (2002) Translational control of the embryonic cell cycle. Cell 109:473–483

    CAS  Google Scholar 

  • Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509–524

    CAS  Google Scholar 

  • Han D, Lerner AG, Vande Walle L, Upton JP, Xu W, Hagen A, Backes BJ, Oakes SA, Papa FR (2009a) IRE1alpha kinase activation modes control alternate endoribonuclease outputs to determine divergent cell fates. Cell 138:562–575

    CAS  Google Scholar 

  • Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, Kim VN (2009b) Posttranscriptional crossregulation between Drosha and DGCR8. Cell 136:75–84

    CAS  Google Scholar 

  • Harigaya Y, Jones BN, Muhlrad D, Gross JD, Parker R (2010) Identification and analysis of the interaction between Edc3 and Dcp2 in Saccharomyces cerevisiae. Mol Cell Biol 30:1446–1456

    CAS  Google Scholar 

  • He L (2010) Posttranscriptional regulation of PTEN dosage by noncoding RNAs. Sci Signal 3:pe39

    Google Scholar 

  • Hellen CU, Sarnow P (2001) Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev 15:1593–1612

    CAS  Google Scholar 

  • Heo I, Ha M, Lim J, Yoon MJ, Park JE, Kwon SC, Chang H, Kim VN (2012) Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell 151:521–532

    CAS  Google Scholar 

  • Hinnebusch AG (2014) The scanning mechanism of eukaryotic translation initiation. Annu Rev Biochem 83:779–812

    CAS  Google Scholar 

  • Hollien J, Lin JH, Li H, Stevens N, Walter P, Weissman JS (2009) Regulated Ire1-dependent decay of messenger RNAs in mammalian cells. J Cell Biol 186:323–331

    CAS  Google Scholar 

  • Hudson WH, Pickard MR, de Vera IM, Kuiper EG, Mourtada-Maarabouni M, Conn GL, Kojetin DJ, Williams GT, Ortlund EA (2014) Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate. Nat Commun 5:5395

    CAS  Google Scholar 

  • Huez I, Creancier L, Audigier S, Gensac MC, Prats AC, Prats H (1998) Two independent internal ribosome entry sites are involved in translation initiation of vascular endothelial growth factor mRNA. Mol Cell Biol 18:6178–6190

    CAS  Google Scholar 

  • Huntzinger E, Kuzuoglu-Ozturk D, Braun JE, Eulalio A, Wohlbold L, Izaurralde E (2013) The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets. Nucleic Acids Res 41:978–994

    CAS  Google Scholar 

  • Ibba M, Soll D (2000) Aminoacyl-tRNA synthesis. Annu Rev Biochem 69:617–650

    CAS  Google Scholar 

  • Igreja C, Izaurralde E (2011) CUP promotes deadenylation and inhibits decapping of mRNA targets. Genes Dev 25:1955–1967

    CAS  Google Scholar 

  • Inge-Vechtomov S, Zhouravleva G, Philippe M (2003) Eukaryotic release factors (eRFs) history. Biol Cell 95:195–209

    CAS  Google Scholar 

  • Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15:205–213

    CAS  Google Scholar 

  • Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789–802

    CAS  Google Scholar 

  • Ishmael FT, Fang X, Houser KR, Pearce K, Abdelmohsen K, Zhan M, Gorospe M, Stellato C (2011) The human glucocorticoid receptor as an RNA-binding protein: global analysis of glucocorticoid receptor-associated transcripts and identification of a target RNA motif. J Immunol 186:1189–1198

    CAS  Google Scholar 

  • Ivshina M, Lasko P, Richter JD (2014) Cytoplasmic polyadenylation element binding proteins in development, health, and disease. Annu Rev Cell Dev Biol 30:393–415

    CAS  Google Scholar 

  • Jackson RJ, Hellen CU, Pestova TV (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11:113–127

    CAS  Google Scholar 

  • Jackson RJ, Hellen CU, Pestova TV (2012) Termination and post-termination events in eukaryotic translation. Adv Protein Chem Struct Biol 86:45–93

    CAS  Google Scholar 

  • Jha S, Komar AA (2011) Birth, life and death of nascent polypeptide chains. Biotechnol J 6:623–640

    CAS  Google Scholar 

  • Jonas S, Izaurralde E (2013) The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Genes Dev 27:2628–2641

    CAS  Google Scholar 

  • Jonas S, Izaurralde E (2015) Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet 16:421–433

    CAS  Google Scholar 

  • Jonas S, Christie M, Peter D, Bhandari D, Loh B, Huntzinger E, Weichenrieder O, Izaurralde E (2014) An asymmetric PAN3 dimer recruits a single PAN2 exonuclease to mediate mRNA deadenylation and decay. Nat Struct Mol Biol 21:599–608

    CAS  Google Scholar 

  • Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G et al (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 14:331–342

    CAS  Google Scholar 

  • Kawahara H, Imai T, Imataka H, Tsujimoto M, Matsumoto K, Okano H (2008) Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP. J Cell Biol 181:639–653

    CAS  Google Scholar 

  • Kawamata T, Seitz H, Tomari Y (2009) Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat Struct Mol Biol 16:953–960

    CAS  Google Scholar 

  • Khaleghpour K, Svitkin YV, Craig AW, DeMaria CT, Deo RC, Burley SK, Sonenberg N (2001) Translational repression by a novel partner of human poly(A) binding protein, Paip2. Mol Cell 7:205–216

    CAS  Google Scholar 

  • Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209–216

    CAS  Google Scholar 

  • Kim JH, Richter JD (2006) Opposing polymerase-deadenylase activities regulate cytoplasmic polyadenylation. Mol Cell 24:173–183

    CAS  Google Scholar 

  • Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP (2010) Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3:ra8

    Google Scholar 

  • Knoll M, Lodish HF, Sun L (2015) Long non-coding RNAs as regulators of the endocrine system. Nat Rev Endocrinol 11:151–160

    CAS  Google Scholar 

  • Kong J, Lasko P (2012) Translational control in cellular and developmental processes. Nat Rev Genet 13:383–394

    CAS  Google Scholar 

  • Korobeinikova AV, Garber MB, Gongadze GM (2012) Ribosomal proteins: structure, function, and evolution. Biochemistry (Mosc) 77:562–574

    CAS  Google Scholar 

  • Kozak M (1987) An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 15:8125–8148

    CAS  Google Scholar 

  • Krichevsky AM, King KS, Donahue CP, Khrapko K, Kosik KS (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9:1274–1281

    CAS  Google Scholar 

  • Kuhn U, Wahle E (2004) Structure and function of poly(A) binding proteins. Biochim Biophys Acta 1678:67–84

    CAS  Google Scholar 

  • Kuzuoglu-Ozturk D, Huntzinger E, Schmidt S, Izaurralde E (2012) The Caenorhabditis elegans GW182 protein AIN-1 interacts with PAB-1 and subunits of the PAN2-PAN3 and CCR4-NOT deadenylase complexes. Nucleic Acids Res 40:5651–5665

    Google Scholar 

  • Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858

    CAS  Google Scholar 

  • Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862

    CAS  Google Scholar 

  • Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S et al (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415–419

    CAS  Google Scholar 

  • Lemaire PA, Anderson E, Lary J, Cole JL (2008) Mechanism of PKR activation by dsRNA. J Mol Biol 381:351–360

    CAS  Google Scholar 

  • Leppek K, Schott J, Reitter S, Poetz F, Hammond MC, Stoecklin G (2013) Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs. Cell 153:869–881

    CAS  Google Scholar 

  • Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20

    CAS  Google Scholar 

  • Li Y, Kiledjian M (2010) Regulation of mRNA decapping. Wiley Interdiscip Rev RNA 1:253–265

    Google Scholar 

  • Li Y, Lu J, Han Y, Fan X, Ding SW (2013) RNA interference functions as an antiviral immunity mechanism in mammals. Science 342:231–234

    CAS  Google Scholar 

  • Liang J, Saad Y, Lei T, Wang J, Qi D, Yang Q, Kolattukudy PE, Fu M (2010) MCP-induced protein 1 deubiquitinates TRAF proteins and negatively regulates JNK and NF-kappaB signaling. J Exp Med 207:2959–2973

    CAS  Google Scholar 

  • Ling SH, Qamra R, Song H (2011) Structural and functional insights into eukaryotic mRNA decapping. Wiley Interdiscip Rev RNA 2:193–208

    CAS  Google Scholar 

  • Liu H, Kiledjian M (2005) Scavenger decapping activity facilitates 5′ to 3′ mRNA decay. Mol Cell Biol 25:9764–9772

    CAS  Google Scholar 

  • Liu B, Qian SB (2014) Translational reprogramming in cellular stress response. Wiley Interdiscip Rev RNA 5:301–315

    CAS  Google Scholar 

  • Liu Q, Greimann JC, Lima CD (2006) Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127:1223–1237

    CAS  Google Scholar 

  • Londin E, Loher P, Telonis AG, Quann K, Clark P, Jing Y, Hatzimichael E, Kirino Y, Honda S, Lally M et al (2015) Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc Natl Acad Sci U S A 112:E1106–E1115

    CAS  Google Scholar 

  • Luo W, Johnson AW, Bentley DL (2006) The role of Rat1 in coupling mRNA 3′-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev 20:954–965

    CAS  Google Scholar 

  • Lykke-Andersen J, Wagner E (2005) Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1. Genes Dev 19:351–361

    CAS  Google Scholar 

  • Ma XM, Blenis J (2009) Molecular mechanisms of mTOR-mediated translational control. Nat Rev Mol Cell Biol 10:307–318

    Google Scholar 

  • MacRae IJ, Zhou K, Doudna JA (2007) Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol 14:934–940

    CAS  Google Scholar 

  • Martineau Y, Derry MC, Wang X, Yanagiya A, Berlanga JJ, Shyu AB, Imataka H, Gehring K, Sonenberg N (2008) Poly(A)-binding protein-interacting protein 1 binds to eukaryotic translation initiation factor 3 to stimulate translation. Mol Cell Biol 28:6658–6667

    CAS  Google Scholar 

  • Martinez J, Ren YG, Thuresson AC, Hellman U, Astrom J, Virtanen A (2000) A 54-kDa fragment of the Poly(A)-specific ribonuclease is an oligomeric, processive, and cap-interacting Poly(A)-specific 3′ exonuclease. J Biol Chem 275:24222–24230

    CAS  Google Scholar 

  • Marzluff WF, Wagner EJ, Duronio RJ (2008) Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet 9:843–854

    CAS  Google Scholar 

  • Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H et al (2009) Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature 458:1185–1190

    CAS  Google Scholar 

  • Mattick JS (2004) RNA regulation: a new genetics? Nature reviews. Genetics 5:316–323

    CAS  Google Scholar 

  • Maurel M, Chevet E, Tavernier J, Gerlo S (2014) Getting RIDD of RNA: IRE1 in cell fate regulation. Trends Biochem Sci 39:245–254

    CAS  Google Scholar 

  • Meister G (2013) Argonaute proteins: functional insights and emerging roles. Nat Rev Genet 14:447–459

    CAS  Google Scholar 

  • Meyuhas O, Kahan T (2015) The race to decipher the top secrets of TOP mRNAs. Biochim Biophys Acta 1849:801–811

    CAS  Google Scholar 

  • Michel YM, Poncet D, Piron M, Kean KM, Borman AM (2000) Cap-Poly(A) synergy in mammalian cell-free extracts. Investigation of the requirements for poly(A)-mediated stimulation of translation initiation. J Biol Chem 275:32268–32276

    CAS  Google Scholar 

  • Micklem DR (1995) mRNA localisation during development. Dev Biol 172:377–395

    CAS  Google Scholar 

  • Mignone F, Gissi C, Liuni S, Pesole G (2002) Untranslated regions of mRNAs. Genome Biol 3:REVIEWS0004

    Google Scholar 

  • Miki TS, Grosshans H (2013) The multifunctional RNase XRN2. Biochem Soc Trans 41:825–830

    CAS  Google Scholar 

  • Miller DL, Dibbens JA, Damert A, Risau W, Vadas MA, Goodall GJ (1998) The vascular endothelial growth factor mRNA contains an internal ribosome entry site. FEBS Lett 434:417–420

    CAS  Google Scholar 

  • Moraes KC, Wilusz CJ, Wilusz J (2006) CUG-BP binds to RNA substrates and recruits PARN deadenylase. RNA 12:1084–1091

    CAS  Google Scholar 

  • Muckenthaler M, Gray NK, Hentze MW (1998) IRP-1 binding to ferritin mRNA prevents the recruitment of the small ribosomal subunit by the cap-binding complex eIF4F. Mol Cell 2:383–388

    CAS  Google Scholar 

  • Mukherjee C, Patil DP, Kennedy BA, Bakthavachalu B, Bundschuh R, Schoenberg DR (2012) Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. Cell Rep 2:674–684

    CAS  Google Scholar 

  • Nagarajan VK, Jones CI, Newbury SF, Green PJ (2013) XRN 5′→3′ exoribonucleases: structure, mechanisms and functions. Biochim Biophys Acta 1829:590–603

    CAS  Google Scholar 

  • Nakagawa S, Niimura Y, Gojobori T, Tanaka H, Miura K (2008) Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nucleic Acids Res 36:861–871

    CAS  Google Scholar 

  • Nakamura A, Sato K, Hanyu-Nakamura K (2004) Drosophila cup is an eIF4E binding protein that associates with Bruno and regulates oskar mRNA translation in oogenesis. Dev Cell 6:69–78

    CAS  Google Scholar 

  • Nechama M, Peng Y, Bell O, Briata P, Gherzi R, Schoenberg DR, Naveh-Many T (2009) KSRP-PMR1-exosome association determines parathyroid hormone mRNA levels and stability in transfected cells. BMC Cell Biol 10:70

    Google Scholar 

  • Nelson MR, Leidal AM, Smibert CA (2004) Drosophila cup is an eIF4E-binding protein that functions in Smaug-mediated translational repression. EMBO J 23:150–159

    CAS  Google Scholar 

  • Ng CK, Shboul M, Taverniti V, Bonnard C, Lee H, Eskin A, Nelson SF, Al-Raqad M, Altawalbeh S, Seraphin B et al (2015) Loss of the scavenger mRNA decapping enzyme DCPS causes syndromic intellectual disability with neuromuscular defects. Hum Mol Genet 24:3163–3171

    CAS  Google Scholar 

  • Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130:89–100

    CAS  Google Scholar 

  • Ostareck DH, Ostareck-Lederer A, Shatsky IN, Hentze MW (2001) Lipoxygenase mRNA silencing in erythroid differentiation: the 3′UTR regulatory complex controls 60S ribosomal subunit joining. Cell 104:281–290

    CAS  Google Scholar 

  • Park E, Maquat LE (2013) Staufen-mediated mRNA decay. Wiley Interdiscip Rev RNA 4:423–435

    CAS  Google Scholar 

  • Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P et al (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408:86–89

    CAS  Google Scholar 

  • Pastori RL, Moskaitis JE, Buzek SW, Schoenberg DR (1991a) Coordinate estrogen-regulated instability of serum protein-coding messenger RNAs in Xenopus laevis. Mol Endocrinol 5:461–468

    CAS  Google Scholar 

  • Pastori RL, Moskaitis JE, Schoenberg DR (1991b) Estrogen-induced ribonuclease activity in Xenopus liver. Biochemistry 30:10490–10498

    CAS  Google Scholar 

  • Pechmann S, Frydman J (2013) Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nat Struct Mol Biol 20:237–243

    CAS  Google Scholar 

  • Peters L, Meister G (2007) Argonaute proteins: mediators of RNA silencing. Mol Cell 26:611–623

    CAS  Google Scholar 

  • Pfaff J, Hennig J, Herzog F, Aebersold R, Sattler M, Niessing D, Meister G (2013) Structural features of Argonaute-GW182 protein interactions. Proc Natl Acad Sci U S A 110:E3770–E3779

    CAS  Google Scholar 

  • Piccirillo C, Khanna R, Kiledjian M (2003) Functional characterization of the mammalian mRNA decapping enzyme hDcp2. RNA 9:1138–1147

    CAS  Google Scholar 

  • Poliseno L, Pandolfi PP (2015) PTEN ceRNA networks in human cancer. Methods 77–78:41–50

    Google Scholar 

  • Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465:1033–1038

    CAS  Google Scholar 

  • Popp MW, Maquat LE (2013) Organizing principles of mammalian nonsense-mediated mRNA decay. Annu Rev Genet 47:139–165

    CAS  Google Scholar 

  • Popp MW, Maquat LE (2014) The dharma of nonsense-mediated mRNA decay in mammalian cells. Mol Cells 37:1–8

    Google Scholar 

  • Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer S, Tuschl T, Rajewsky N, Rorsman P et al (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432:226–230

    CAS  Google Scholar 

  • Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR et al (2015) Codon optimality is a major determinant of mRNA stability. Cell 160:1111–1124

    CAS  Google Scholar 

  • Quax TE, Claassens NJ, Soll D, van der Oost J (2015) Codon bias as a means to fine-tune gene expression. Mol Cell 59:149–161

    CAS  Google Scholar 

  • Reis FP, Pobre V, Silva IJ, Malecki M, Arraiano CM (2013) The RNase II/RNB family of exoribonucleases: putting the ‘Dis’ in disease. Wiley Interdiscip Rev RNA 4:607–615

    Google Scholar 

  • Rendl LM, Bieman MA, Vari HK, Smibert CA (2012) The eIF4E-binding protein Eap1p functions in Vts1p-mediated transcript decay. PLoS One 7, e47121

    CAS  Google Scholar 

  • Riis B, Rattan SI, Clark BF, Merrick WC (1990) Eukaryotic protein elongation factors. Trends Biochem Sci 15:420–424

    Google Scholar 

  • Rom E, Kim HC, Gingras AC, Marcotrigiano J, Favre D, Olsen H, Burley SK, Sonenberg N (1998) Cloning and characterization of 4EHP, a novel mammalian eIF4E-related cap-binding protein. J Biol Chem 273:13104–13109

    CAS  Google Scholar 

  • Roy G, De Crescenzo G, Khaleghpour K, Kahvejian A, O’Connor-McCourt M, Sonenberg N (2002) Paip1 interacts with poly(A) binding protein through two independent binding motifs. Mol Cell Biol 22:3769–3782

    CAS  Google Scholar 

  • Sandler H, Kreth J, Timmers HT, Stoecklin G (2011) Not1 mediates recruitment of the deadenylase Caf1 to mRNAs targeted for degradation by tristetraprolin. Nucleic Acids Res 39:4373–4386

    CAS  Google Scholar 

  • Sarkissian M, Mendez R, Richter JD (2004) Progesterone and insulin stimulation of CPEB-dependent polyadenylation is regulated by Aurora A and glycogen synthase kinase-3. Genes Dev 18:48–61

    CAS  Google Scholar 

  • Sasikumar AN, Perez WB, Kinzy TG (2012) The many roles of the eukaryotic elongation factor 1 complex. Wiley Interdiscip Rev RNA 3:543–555

    CAS  Google Scholar 

  • Schafer IB, Rode M, Bonneau F, Schussler S, Conti E (2014) The structure of the Pan2-Pan3 core complex reveals cross-talk between deadenylase and pseudokinase. Nat Struct Mol Biol 21:591–598

    Google Scholar 

  • Schmid M, Jensen TH (2008) Quality control of mRNP in the nucleus. Chromosoma 117:419–429

    CAS  Google Scholar 

  • Schoenberg DR, Maquat LE (2012) Regulation of cytoplasmic mRNA decay. Nat Rev Genet 13:246–259

    CAS  Google Scholar 

  • Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2011) Global quantification of mammalian gene expression control. Nature 473:337–342

    Google Scholar 

  • She M, Decker CJ, Chen N, Tumati S, Parker R, Song H (2006) Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe. Nat Struct Mol Biol 13:63–70

    CAS  Google Scholar 

  • She M, Decker CJ, Svergun DI, Round A, Chen N, Muhlrad D, Parker R, Song H (2008) Structural basis of dcp2 recognition and activation by dcp1. Mol Cell 29:337–349

    CAS  Google Scholar 

  • Shirai YT, Suzuki T, Morita M, Takahashi A, Yamamoto T (2014) Multifunctional roles of the mammalian CCR4-NOT complex in physiological phenomena. Front Genet 5:286

    Google Scholar 

  • Siddiqui N, Mangus DA, Chang TC, Palermino JM, Shyu AB, Gehring K (2007) Poly(A) nuclease interacts with the C-terminal domain of polyadenylate-binding protein domain from poly(A)-binding protein. J Biol Chem 282:25067–25075

    CAS  Google Scholar 

  • Sinturel F, Brechemier-Baey D, Kiledjian M, Condon C, Benard L (2012) Activation of 5′-3′ exoribonuclease Xrn1 by cofactor Dcs1 is essential for mitochondrial function in yeast. Proc Natl Acad Sci U S A 109:8264–8269

    CAS  Google Scholar 

  • Slayter HS, Warner JR, Rich A, Hall CE (1963) The visualization of polyribosomal structure. J Mol Biol 7:652–657

    CAS  Google Scholar 

  • Sonenberg N, Hinnebusch AG (2009) Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136:731–745

    CAS  Google Scholar 

  • Song MG, Bail S, Kiledjian M (2013) Multiple Nudix family proteins possess mRNA decapping activity. RNA 19:390–399

    CAS  Google Scholar 

  • Stebbins-Boaz B, Cao Q, de Moor CH, Mendez R, Richter JD (1999) Maskin is a CPEB-associated factor that transiently interacts with elF-4E. Mol Cell 4:1017–1027

    CAS  Google Scholar 

  • Tarrant D, von der Haar T (2014) Synonymous codons, ribosome speed, and eukaryotic gene expression regulation. Cell Mol Life Sci 71:4195–4206

    CAS  Google Scholar 

  • Tavares MR, Pavan IC, Amaral CL, Meneguello L, Luchessi AD, Simabuco FM (2015) The S6K protein family in health and disease. Life Sci 131:1–10

    CAS  Google Scholar 

  • Tay Y, Rinn J, Pandolfi PP (2014) The multilayered complexity of ceRNA crosstalk and competition. Nature 505:344–352

    CAS  Google Scholar 

  • Tharun S, Parker R (2001) Targeting an mRNA for decapping: displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs. Mol Cell 8:1075–1083

    CAS  Google Scholar 

  • Thornton JE, Chang HM, Piskounova E, Gregory RI (2012) Lin28-mediated control of let-7 microRNA expression by alternative TUTases Zcchc11 (TUT4) and Zcchc6 (TUT7). RNA 18:1875–1885

    CAS  Google Scholar 

  • Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA et al (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39:925–938

    CAS  Google Scholar 

  • Tucker M, Valencia-Sanchez MA, Staples RR, Chen J, Denis CL, Parker R (2001) The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104:377–386

    CAS  Google Scholar 

  • Tucker M, Staples RR, Valencia-Sanchez MA, Muhlrad D, Parker R (2002) Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. EMBO J 21:1427–1436

    CAS  Google Scholar 

  • Uchida N, Hoshino S, Katada T (2004) Identification of a human cytoplasmic poly(A) nuclease complex stimulated by poly(A)-binding protein. J Biol Chem 279:1383–1391

    CAS  Google Scholar 

  • Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46

    CAS  Google Scholar 

  • Van Etten J, Schagat TL, Hrit J, Weidmann CA, Brumbaugh J, Coon JJ, Goldstrohm AC (2012) Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J Biol Chem 287:36370–36383

    Google Scholar 

  • Vlasova-St Louis I, Bohjanen PR (2011) Coordinate regulation of mRNA decay networks by GU-rich elements and CELF1. Curr Opin Genet Dev 21:444–451

    CAS  Google Scholar 

  • Wang, Z, Jiao X, Carr-Schmid A, Kiledjian M (2002) The hDcp2 protein is a mammalian decapping enzyme. Proceedings of the National Academy of Sciences USA 99(20):12663–12668

    Google Scholar 

  • Wang X, He C (2014) Dynamic RNA modifications in posttranscriptional regulation. Mol Cell 56:5–12

    CAS  Google Scholar 

  • Wang M, Pestov DG (2011) 5′-end surveillance by Xrn2 acts as a shared mechanism for mammalian pre-rRNA maturation and decay. Nucleic Acids Res 39:1811–1822

    Google Scholar 

  • Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P, Ding SW (2006) RNA interference directs innate immunity against viruses in adult Drosophila. Science 312:452–454

    CAS  Google Scholar 

  • Warner JR, Knopf PM, Rich A (1963) A multiple ribosomal structure in protein synthesis. Proc Natl Acad Sci U S A 49:122–129

    CAS  Google Scholar 

  • Weidmann CA, Raynard NA, Blewett NH, Van Etten J, Goldstrohm AC (2014) The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation. RNA 20:1298–1319

    CAS  Google Scholar 

  • Wells SE, Hillner PE, Vale RD, Sachs AB (1998) Circularization of mRNA by eukaryotic translation initiation factors. Mol Cell 2:135–140

    CAS  Google Scholar 

  • Wickramasinghe VO, Laskey RA (2015) Control of mammalian gene expression by selective mRNA export. Nat Rev Mol Cell Biol 16:431–442

    CAS  Google Scholar 

  • Wilson DN, Doudna Cate JH (2012) The structure and function of the eukaryotic ribosome. Cold Spring Harb Perspect Biol 4

    Google Scholar 

  • Wilson T, Treisman R (1988) Removal of poly(A) and consequent degradation of c-fos mRNA facilitated by 3′ AU-rich sequences. Nature 336:396–399

    CAS  Google Scholar 

  • Wolf J, Valkov E, Allen MD, Meineke B, Gordiyenko Y, McLaughlin SH, Olsen TM, Robinson CV, Bycroft M, Stewart M et al (2014) Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation. EMBO J 33:1514–1526

    CAS  Google Scholar 

  • Yamashita A, Chang TC, Yamashita Y, Zhu W, Zhong Z, Chen CY, Shyu AB (2005) Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nat Struct Mol Biol 12:1054–1063

    CAS  Google Scholar 

  • Yang N, Kazazian HH Jr (2006) L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol 13:763–771

    CAS  Google Scholar 

  • Yoda M, Kawamata T, Paroo Z, Ye X, Iwasaki S, Liu Q, Tomari Y (2010) ATP-dependent human RISC assembly pathways. Nat Struct Mol Biol 17:17–23

    CAS  Google Scholar 

  • Yu JH, Yang WH, Gulick T, Bloch KD, Bloch DB (2005) Ge-1 is a central component of the mammalian cytoplasmic mRNA processing body. RNA 11:1795–1802

    CAS  Google Scholar 

  • Yusupova G, Yusupov M (2014) High-resolution structure of the eukaryotic 80S ribosome. Annu Rev Biochem 83:467–486

    CAS  Google Scholar 

  • Zekri L, Kuzuoglu-Ozturk D, Izaurralde E (2013) GW182 proteins cause PABP dissociation from silenced miRNA targets in the absence of deadenylation. EMBO J 32:1052–1065

    CAS  Google Scholar 

  • Zeng Y, Cullen BR (2003) Sequence requirements for micro RNA processing and function in human cells. RNA 9:112–123

    CAS  Google Scholar 

Download references

Acknowledgments

We thank Brian Alzua, who provided proofreading and comments on this chapter. This research was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM105707. R.A. was supported by the Michigan Predoctoral Training Program in Genetics through NIH National Research Service Award 5T32GM007544. J.B. was supported by the Michigan Predoctoral Training Program in Cellular Biotechnology through NIH National Research Service Award 5T32GM008353. E.A. was supported by the Michigan Predoctoral Training Program in Chemistry and Biology Interface through NIH National Research Service Award 2T32GM008597. A.C.G. was supported by a Research Scholar Grant, RSG-13-080-01-RMC, from the American Cancer Society.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Aaron C. Goldstrohm .

Editor information

Editors and Affiliations

Rights and permissions

Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 2.5 International License (http://creativecommons.org/licenses/by-nc/2.5/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

The images or other third party material in this chapter are included in the chapter's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

Reprints and Permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Arvola, R., Abshire, E., Bohn, J., Goldstrohm, A.C. (2016). Mechanisms of Post-transcriptional Gene Regulation. In: Menon, PhD, K., Goldstrohm, PhD, A. (eds) Post-transcriptional Mechanisms in Endocrine Regulation. Springer, Cham. https://doi.org/10.1007/978-3-319-25124-0_1

Download citation