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Is Transcription the Dominant Force During Dynamic Changes in Gene Expression?

  • Martin Turner
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 780)

Abstract

Dynamic changes in gene expression punctuate lymphocyte development and are a characteristic of lymphocyte activation. A prevailing view has been that these changes are driven by DNA transcription factors, which are the dominant force in gene expression. Accumulating evidence is challenging this DNA centric view and has highlighted the prevalence and dynamic nature of RNA handling mechanisms. Alternative splicing and differential polyadenylation appear to be more widespread than first thought. Changes in mRNA decay rates also affect the abundance of transcripts and this mechanism may contribute significantly to gene expression. Additional RNA handling mechanisms that control the intracellular localization of mRNA and association with translating ribosomes are also important. Thus, gene expression is regulated through the coordination of transcriptional and post-transcriptional mechanisms. Developing a more “RNA centric” view of gene expression will allow a more systematic understanding of how gene expression and cell function are integrated.

Keywords

mRNA Decay Translational Control CD154 mRNA Stress Granule Nucleosome Occupancy 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

I thank all of my colleagues for their contributions to our work on post-transcriptional control. Work in the author’s laboratory is supported by a Senior Non-clinical Fellowship by the Medical Research Council and by the Biotechnology and Biological Sciences Research Council.

References

  1. 1.
    Merritt C, Rasoloson D, Ko D, Seydoux G (2008) 3′ UTRs are the primary regulators of gene expression in the C. elegans germline. Curr Biol 18:1476–1482PubMedCrossRefGoogle Scholar
  2. 2.
    Garcia-Martinez J, Aranda A, Perez-Ortin JE (2004) Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell 15:303–313PubMedCrossRefGoogle Scholar
  3. 3.
    Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 99:5860–5865PubMedCrossRefGoogle Scholar
  4. 4.
    Yang E, van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell JE Jr (2003) Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res 13:1863–1872PubMedCrossRefGoogle Scholar
  5. 5.
    Raghavan A, Ogilvie RL, Reilly C, Abelson ML, Raghavan S, Vasdewani J, Krathwohl M, Bohjanen PR (2002) Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res 30:5529–5538PubMedCrossRefGoogle Scholar
  6. 6.
    Cheadle C, Fan J, Cho-Chung YS, Werner T, Ray J, Do L, Gorospe M, Becker KG (2005) Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability. BMC Genomics 6:75PubMedCrossRefGoogle Scholar
  7. 7.
    Lam LT, Pickeral OK, Peng AC, Rosenwald A, Hurt EM, Giltnane JM, Averett LM, Zhao H, Davis RE, Sathyamoorthy M, Wahl LM, Harris ED, Mikovits JA, Monks AP, Hollingshead MG, Sausville EA, Staudt LM (2001) Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol. Genome Biol 2:RESEARCH0041PubMedCrossRefGoogle Scholar
  8. 8.
    Friedel CC, Dolken L, Ruzsics Z, Koszinowski UH, Zimmer R (2009) Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res 37:e115PubMedCrossRefGoogle Scholar
  9. 9.
    Dolken L, Ruzsics Z, Radle B, Friedel CC, Zimmer R, Mages J, Hoffmann R, Dickinson P, Forster T, Ghazal P, Koszinowski UH (2008) High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14:1959–1972PubMedCrossRefGoogle Scholar
  10. 10.
    Friedel CC, Dolken L (2009) Metabolic tagging and purification of nascent RNA: implications for transcriptomics. Mol Biosyst 5:1271–1278PubMedCrossRefGoogle Scholar
  11. 11.
    Keene JD (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8:533–543PubMedCrossRefGoogle Scholar
  12. 12.
    Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720–1730PubMedGoogle Scholar
  13. 13.
    Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R (2002) Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 1:323–333PubMedCrossRefGoogle Scholar
  14. 14.
    Serikawa KA, Xu XL, MacKay VL, Law GL, Zong Q, Zhao LP, Bumgarner R, Morris DR (2003) The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae. Mol Cell Proteomics 2:191–204PubMedCrossRefGoogle Scholar
  15. 15.
    Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE (2004) Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol Cell Proteomics 3:960–969PubMedCrossRefGoogle Scholar
  16. 16.
    Lu P, Vogel C, Wang R, Yao X, Marcotte EM (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25:117–124PubMedCrossRefGoogle Scholar
  17. 17.
    Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma’ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR (2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 462:358–362PubMedCrossRefGoogle Scholar
  18. 18.
    Swanson BJ, Murakami M, Mitchell TC, Kappler J, Marrack P (2002) RANTES production by memory phenotype T cells is controlled by a posttranscriptional, TCR-dependent process. Immunity 17:605–615PubMedCrossRefGoogle Scholar
  19. 19.
    Li W, Sofi MH, Yeh N, Sehra S, McCarthy BP, Patel DR, Brutkiewicz RR, Kaplan MH, Chang CH (2007) Thymic selection pathway regulates the effector function of CD4 T cells. J Exp Med 204:2145–2157PubMedCrossRefGoogle Scholar
  20. 20.
    Stetson DB, Mohrs M, Reinhardt RL, Baron JL, Wang ZE, Gapin L, Kronenberg M, Locksley RM (2003) Constitutive cytokine mRNAs mark natural killer (NK) and NK T cells poised for rapid effector function. J Exp Med 198:1069–1076PubMedCrossRefGoogle Scholar
  21. 21.
    Scheu S, Stetson DB, Reinhardt RL, Leber JH, Mohrs M, Locksley RM (2006) Activation of the integrated stress response during T helper cell differentiation. Nat Immunol 7:644–651PubMedCrossRefGoogle Scholar
  22. 22.
    Mavropoulos A, Sully G, Cope AP, Clark AR (2005) Stabilization of IFN-gamma mRNA by MAPK p38 in IL-12- and IL-18-stimulated human NK cells. Blood 105:282–288PubMedCrossRefGoogle Scholar
  23. 23.
    Anderson P, Kedersha N (2009) RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nat Rev Mol Cell Biol 10:430–436PubMedCrossRefGoogle Scholar
  24. 24.
    Kedersha NL, Gupta M, Li W, Miller I, Anderson P (1999) RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2 alpha to the assembly of mammalian stress granules. J Cell Biol 147:1431–1442PubMedCrossRefGoogle Scholar
  25. 25.
    Fasken MB, Corbett AH (2009) Mechanisms of nuclear mRNA quality control. RNA Biol 6:237–241PubMedCrossRefGoogle Scholar
  26. 26.
    Wu H, Xu H, Miraglia LJ, Crooke ST (2000) Human RNase III is a 160-kDa protein involved in preribosomal RNA processing. J Biol Chem 275:36957–36965PubMedCrossRefGoogle Scholar
  27. 27.
    Oberdoerffer S, Moita LF, Neems D, Freitas RP, Hacohen N, Rao A (2008) Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL. Science 321:686–691PubMedCrossRefGoogle Scholar
  28. 28.
    Wu Z, Jia X, de la Cruz L, Su XC, Marzolf B, Troisch P, Zak D, Hamilton A, Whittle B, Yu D, Sheahan D, Bertram E, Aderem A, Otting G, Goodnow CC, Hoyne GF (2008) Memory T cell RNA rearrangement programmed by heterogeneous nuclear ribonucleoprotein hnRNPLL. Immunity 29:863–875PubMedCrossRefGoogle Scholar
  29. 29.
    Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476PubMedCrossRefGoogle Scholar
  30. 30.
    Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O’Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956–960PubMedCrossRefGoogle Scholar
  31. 31.
    Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413–1415PubMedCrossRefGoogle Scholar
  32. 32.
    Castle JC, Zhang C, Shah JK, Kulkarni AV, Kalsotra A, Cooper TA, Johnson JM (2008) Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 40:1416–1425PubMedCrossRefGoogle Scholar
  33. 33.
    Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887–898PubMedCrossRefGoogle Scholar
  34. 34.
    Spies N, Nielsen CB, Padgett RA, Burge CB (2009) Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36:245–254PubMedCrossRefGoogle Scholar
  35. 35.
    Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T (2010) Regulation of alternative splicing by histone modifications. Science 327:996–1000PubMedCrossRefGoogle Scholar
  36. 36.
    Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320:1643–1647PubMedCrossRefGoogle Scholar
  37. 37.
    Mayr C, Bartel DP (2009) Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138:673–684PubMedCrossRefGoogle Scholar
  38. 38.
    Mazumder B, Seshadri V, Fox PL (2003) Translational control by the 3′-UTR: the ends specify the means. Trends Biochem Sci 28:91–98PubMedCrossRefGoogle Scholar
  39. 39.
    Mignone F, Gissi C, Liuni S, Pesole G (2002) Untranslated regions of mRNAs. Genome Biol 3:REVIEWS0004PubMedCrossRefGoogle Scholar
  40. 40.
    Orom UA, Nielsen FC, Lund AH (2008) MicroRNA-10a binds the 5′UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30:460–471PubMedCrossRefGoogle Scholar
  41. 41.
    Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science 318:1931–1934PubMedCrossRefGoogle Scholar
  42. 42.
    Bakheet T, Williams BR, Khabar KS (2006) ARED 3.0: the large and diverse AU-rich transcriptome. Nucleic Acids Res 34:D111–D114PubMedCrossRefGoogle Scholar
  43. 43.
    Espel E (2005) The role of the AU-rich elements of mRNAs in controlling translation. Semin Cell Dev Biol 16:59–67PubMedCrossRefGoogle Scholar
  44. 44.
    Shaw G, Kamen R (1986) A conserved AU sequence from the 3′ untranslated region of GM-CSF mRNA mediates selective mRNA degradation. Cell 46:659–667PubMedCrossRefGoogle Scholar
  45. 45.
    Schuler GD, Cole MD (1988) GM-CSF and oncogene mRNA stabilities are independently regulated in trans in a mouse monocytic tumor. Cell 55:1115–1122PubMedCrossRefGoogle Scholar
  46. 46.
    Keene JD (2001) Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 98:7018–7024PubMedCrossRefGoogle Scholar
  47. 47.
    Galante PA, Sandhu D, de Sousa AR, Gradassi M, Slager N, Vogel C, de Souza SJ, Penalva LO (2009) A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: identification of potential players in tumor formation. RNA Biol 6:426–433PubMedCrossRefGoogle Scholar
  48. 48.
    Yamamoto H, Tsukahara K, Kanaoka Y, Jinno S, Okayama H (1999) Isolation of a mammalian homologue of a fission yeast differentiation regulator. Mol Cell Biol 19:3829–3841PubMedGoogle Scholar
  49. 49.
    Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares M Jr, Black DL (2007) A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21:1636–1652PubMedCrossRefGoogle Scholar
  50. 50.
    Spellman R, Llorian M, Smith CW (2007) Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol Cell 27:420–434PubMedCrossRefGoogle Scholar
  51. 51.
    Besse F, Lopez de Quinto S, Marchand V, Trucco A, Ephrussi A (2009) Drosophila PTB promotes formation of high-order RNP particles and represses oskar translation. Genes Dev 23:195–207PubMedCrossRefGoogle Scholar
  52. 52.
    Galban S, Kuwano Y, Pullmann R Jr, Martindale JL, Kim HH, Lal A, Abdelmohsen K, Yang X, Dang Y, Liu JO, Lewis SM, Holcik M, Gorospe M (2008) RNA-binding proteins HuR and PTB promote the translation of hypoxia-inducible factor 1alpha. Mol Cell Biol 28:93–107PubMedCrossRefGoogle Scholar
  53. 53.
    Kosinski PA, Laughlin J, Singh K, Covey LR (2003) A complex containing polypyrimidine tract-binding protein is involved in regulating the stability of CD40 ligand (CD154) mRNA. J Immunol 170:979–988PubMedGoogle Scholar
  54. 54.
    Vavassori S, Shi Y, Chen CC, Ron Y, Covey LR (2009) In vivo post-transcriptional regulation of CD154 in mouse CD4+ T cells. Eur J Immunol 39:2224–2232PubMedCrossRefGoogle Scholar
  55. 55.
    Porter JF, Vavassori S, Covey LR (2008) A polypyrimidine tract-binding protein-dependent pathway of mRNA stability initiates with CpG activation of primary B cells. J Immunol 181:3336–3345PubMedGoogle Scholar
  56. 56.
    Kedde M, Agami R (2008) Interplay between microRNAs and RNA-binding proteins determines developmental processes. Cell Cycle 7:899–903PubMedCrossRefGoogle Scholar
  57. 57.
    Bhattacharyya SN, Habermacher R, Martine U, Closs EI, Filipowicz W (2006) Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125:1111–1124PubMedCrossRefGoogle Scholar
  58. 58.
    Dumitru CD, Ceci JD, Tsatsanis C, Kontoyiannis D, Stamatakis K, Lin JH, Patriotis C, Jenkins NA, Copeland NG, Kollias G, Tsichlis PN (2000) TNF-alpha induction by LPS is regulated posttranscriptionally via a Tpl2/ERK-dependent pathway. Cell 103:1071–1083PubMedCrossRefGoogle Scholar
  59. 59.
    Mahtani KR, Brook M, Dean JL, Sully G, Saklatvala J, Clark AR (2001) Mitogen-activated protein kinase p38 controls the expression and posttranslational modification of tristetraprolin, a regulator of tumor necrosis factor alpha mRNA stability. Mol Cell Biol 21:6461–6469PubMedCrossRefGoogle Scholar
  60. 60.
    Tudor C, Marchese FP, Hitti E, Aubareda A, Rawlinson L, Gaestel M, Blackshear PJ, Clark AR, Saklatvala J, Dean JL (2009) The p38 MAPK pathway inhibits tristetraprolin-directed decay of interleukin-10 and pro-inflammatory mediator mRNAs in murine macrophages. FEBS Lett 583:1933–1938PubMedCrossRefGoogle Scholar
  61. 61.
    Brook M, Tchen CR, Santalucia T, McIlrath J, Arthur JS, Saklatvala J, Clark AR (2006) Posttranslational regulation of tristetraprolin subcellular localization and protein stability by p38 mitogen-activated protein kinase and extracellular signal-regulated kinase pathways. Mol Cell Biol 26:2408–2418PubMedCrossRefGoogle Scholar
  62. 62.
    Hitti E, Iakovleva T, Brook M, Deppenmeier S, Gruber AD, Radzioch D, Clark AR, Blackshear PJ, Kotlyarov A, Gaestel M (2006) Mitogen-activated protein kinase-activated protein kinase 2 regulates tumor necrosis factor mRNA stability and translation mainly by altering tristetraprolin expression, stability, and binding to adenine/uridine-rich element. Mol Cell Biol 26:2399–2407PubMedCrossRefGoogle Scholar
  63. 63.
    Maitra S, Chou CF, Luber CA, Lee KY, Mann M, Chen CY (2008) The AU-rich element mRNA decay-promoting activity of BRF1 is regulated by mitogen-activated protein kinase-activated protein kinase 2. RNA 14:950–959PubMedCrossRefGoogle Scholar
  64. 64.
    Schmidlin M, Lu M, Leuenberger SA, Stoecklin G, Mallaun M, Gross B, Gherzi R, Hess D, Hemmings BA, Moroni C (2004) The ARE-dependent mRNA-destabilizing activity of BRF1 is regulated by protein kinase B. EMBO J 23:4760–4769PubMedCrossRefGoogle Scholar
  65. 65.
    Benjamin D, Schmidlin M, Min L, Gross B, Moroni C (2006) BRF1 protein turnover and mRNA decay activity are regulated by protein kinase B at the same phosphorylation sites. Mol Cell Biol 26:9497–9507PubMedCrossRefGoogle Scholar
  66. 66.
    Taylor GA, Carballo E, Lee DM, Lai WS, Thompson MJ, Patel DD, Schenkman DI, Gilkeson GS, Broxmeyer HE, Haynes BF, Blackshear PJ (1996) A pathogenetic role for TNF alpha in the syndrome of cachexia, arthritis, and auto-immunity resulting from tristetraprolin (TTP) deficiency. Immunity 4:445–454PubMedCrossRefGoogle Scholar
  67. 67.
    Carballo E, Lai WS, Blackshear PJ (1998) Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin. Science 281:1001–1005PubMedCrossRefGoogle Scholar
  68. 68.
    Lai WS, Carballo E, Strum JR, Kennington EA, Phillips RS, Blackshear PJ (1999) Evidence that tristetraprolin binds to AU-rich elements and promotes the deadenylation and destabilization of tumor necrosis factor alpha mRNA. Mol Cell Biol 19:4311–4323PubMedGoogle Scholar
  69. 69.
    Kontoyiannis D, Pasparakis M, Pizarro TT, Cominelli F, Kollias G (1999) Impaired on/off regulation of TNF biosynthesis in mice lacking TNF AU-rich elements: implications for joint and gut-associated immunopathologies. Immunity 10:387–398PubMedCrossRefGoogle Scholar
  70. 70.
    Stoecklin G, Tenenbaum SA, Mayo T, Chittur SV, George AD, Baroni TE, Blackshear PJ, Anderson P (2008) Genome-wide analysis identifies interleukin-10 mRNA as target of tristetraprolin. J Biol Chem 283:11689–11699PubMedCrossRefGoogle Scholar
  71. 71.
    Emmons J, Townley-Tilson WH, Deleault KM, Skinner SJ, Gross RH, Whitfield ML, Brooks SA (2008) Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation. RNA 14:888–902PubMedCrossRefGoogle Scholar
  72. 72.
    Stoecklin G, Colombi M, Raineri I, Leuenberger S, Mallaun M, Schmidlin M, Gross B, Lu M, Kitamura T, Moroni C (2002) Functional cloning of BRF1, a regulator of ARE-dependent mRNA turnover. EMBO J 21:4709–4718PubMedCrossRefGoogle Scholar
  73. 73.
    Ning ZQ, Norton JD, Li J, Murphy JJ (1996) Distinct mechanisms for rescue from apoptosis in Ramos human B cells by signaling through CD40 and interleukin-4 receptor: role for inhibition of an early response gene, Berg36. Eur J Immunol 26:2356–2563PubMedCrossRefGoogle Scholar
  74. 74.
    Stumpo DJ, Byrd NA, Phillips RS, Ghosh S, Maronpot RR, Castranio T, Meyers EN, Mishina Y, Blackshear PJ (2004) Chorioallantoic fusion defects and embryonic lethality resulting from disruption of Zfp36L1, a gene encoding a CCCH tandem zinc finger protein of the tristetraprolin family. Mol Cell Biol 24:6445–6455PubMedCrossRefGoogle Scholar
  75. 75.
    Bell SE, Sanchez MJ, Spasic-Boskovic O, Santalucia T, Gambardella L, Burton GJ, Murphy JJ, Norton JD, Clark AR, Turner M (2006) The RNA binding protein Zfp36l1 is required for normal vascularisation and post-transcriptionally regulates VEGF expression. Dev Dyn 235:3144–3155PubMedCrossRefGoogle Scholar
  76. 76.
    Ciais D, Cherradi N, Bailly S, Grenier E, Berra E, Pouyssegur J, Lamarre J, Feige JJ (2004) Destabilization of vascular endothelial growth factor mRNA by the zinc-finger protein TIS11b. Oncogene 23:8673–8680PubMedCrossRefGoogle Scholar
  77. 77.
    Prouteau M, Daugeron MC, Seraphin B (2008) Regulation of ARE transcript 3′ end processing by the yeast Cth2 mRNA decay factor. EMBO J 27:2966–2976PubMedCrossRefGoogle Scholar
  78. 78.
    Ramos SB, Stumpo DJ, Kennington EA, Phillips RS, Bock CB, Ribeiro-Neto F, Blackshear PJ (2004) The CCCH tandem zinc-finger protein Zfp36l2 is crucial for female fertility and early embryonic development. Development 131:4883–4893PubMedCrossRefGoogle Scholar
  79. 79.
    Stumpo DJ, Broxmeyer HE, Ward T, Cooper S, Hangoc G, Chung YJ, Shelley WC, Richfield EK, Ray MK, Yoder MC, Aplan PD, Blackshear PJ (2009) Targeted disruption of Zfp36l2, encoding a CCCH tandem zinc finger RNA-binding protein, results in defective hematopoiesis. Blood 114:2401–2410PubMedCrossRefGoogle Scholar
  80. 80.
    Hodson DJ, Janas ML, Galloway A, Andrews S, Li C, Pannell R, Siebel CW, MacDonald HR, Grutz G, Turner M (2010) Deletion of the RNA-binding proteins TIS11b and TIS11d leads to perturbed thymic development and T-lymphoblastic leukaemia. Nat Immunol 11:717–724 Google Scholar
  81. 81.
    Lecuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, Krause HM (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131:174–187PubMedCrossRefGoogle Scholar
  82. 82.
    Holt CE, Bullock SL (2009) Subcellular mRNA localization in animal cells and why it matters. Science 326:1212–1216PubMedCrossRefGoogle Scholar
  83. 83.
    Franks TM, Lykke-Andersen J (2007) TTP and BRF proteins nucleate processing body formation to silence mRNAs with AU-rich elements. Genes Dev 21:719–735PubMedCrossRefGoogle Scholar
  84. 84.
    Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, Gharakhani J, Julicher F, Hyman AA (2009) Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324:1729–1732PubMedCrossRefGoogle Scholar
  85. 85.
    Wang Z, Tollervey J, Briese M, Turner D, Ule J (2009) CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods 48:287–293PubMedCrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Laboratory of Lymphocyte Signaling and DevelopmentThe Babraham InstituteCambridgeUK

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