Transcriptional priming of cytoplasmic post-transcriptional regulation

Transcription

Volumn 2, Issue 6, 2011, Pages 258-262

  Tirosh, Itay ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Coupling; mRNA degradation; Nuclear cytoplasmic shuttling; Post transcriptional regulation; Transcription

Indexed keywords

MESSENGER RNA; RNA BINDING PROTEIN; RNA POLYMERASE II; UNTRANSLATED RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHROMATIN STRUCTURE; COMPLEX FORMATION; GENE CONTROL; GENE EXPRESSION REGULATION; GENETIC DAMAGE; GENETIC TRANSCRIPTION; HUMAN; NONHUMAN; PROTEIN DEFECT; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; REGULATORY RNA SEQUENCE; RNA CONFORMATION; RNA DEGRADATION; RNA PROCESSING; RNA SPLICING; RNA TRANSLATION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION; TRANSCRIPTIONAL PRIMING;

EID: 84855168518     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.2.6.18608     Document Type: Article

References (28)

1. Hagiwara M, Nojima T. Cross-talks between transcription and post-transcriptional events within a 'mRNA factory'. J Biochem 2007; 142:11-5; PMID:17567655; http://dx.doi.org/10.1093/jb/mvm123.
2. Shen Z, St-Denis A, Chartrand P. Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud. Genes Dev 2010; 24:1914-26; PMID:20713510; http://dx.doi.org/10.1101/gad.1937510.
3. Giorgi C, Moore MJ. The nuclear nurture and cytoplasmic nature of localized mRNPs. Semin Cell Dev Biol 2007; 18:186-93; PMID:17459736; http://dx.doi.org/10.1016/j.semcdb.2007.01.002.
4. Goler-Baron V, Selitrennik M, Barkai O, Haimovich G, Lotan R, Choder M. Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes. Genes Dev 2008; 22:2022-7; PMID:18676807; http://dx.doi.org/10.1101/gad.473608.
5. Harel-Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M. RNA Polymerase II Subunits Link Transcription and mRNA Decay to Translation. Cell 2010; 143:552-63; PMID:21074047; http://dx.doi.org/10.1016/j.cell.2010.10.033.
6. Shalem O, Groisman B, Choder M, Dahan O, Pilpel Y. Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA PolII. PLoS Genet 2011; 7:1002273; PMID:21931566; http://dx.doi.org/10.1371/journal.pgen.1002273.
7. Dori-Bachash M, Shema E, Tirosh I. Coupled evolution of transcription and mRNA degradation. PLoS Biol 2011; 9:1001106; PMID:21811398; http://dx.doi.org/10.1371/journal.pbio.1001106.
8. Kerr SC, Azzouz N, Fuchs SM, Collart MA, Strahl BD, Corbett AH, et al. The Ccr4-Not complex interacts with the mRNA export machinery. PLoS ONE 2011; 6:18302; PMID:21464899; http://dx.doi.org/10.1371/journal.pone.0018302.
9. Costa FF. Non-coding RNAs: Meet thy masters. Bioessays 2010; 32:599-608; PMID:20544733; http://dx.doi.org/10.1002/bies.200900112.
10. Egloff S, Murphy S. Cracking the RNA polymerase II CTD code. Trends Genet 2008; 24:280-8; PMID:18457900; http://dx.doi.org/10.1016/j.tig.2008.03.008.
11. Casolari JM, Brown CR, Komili S, West J, Hieronymus H, Silver PA. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 2004; 117:427-39; PMID:15137937; http://dx.doi.org/10.1016/S0092-8674(04)00448-9.
12. Katahira J, Yoneda Y. Roles of the TREX complex in nuclear export of mRNA. RNA Biol 2009; 6:149-52; PMID:19229134; http://dx.doi.org/10.4161/rna.6.2.8046.
13. Pinto PA, Henriques T, Freitas MO, Martins T, Domingues RG, Wyrzykowska PS, et al. RNA polymerase II kinetics in polo polyadenylation signal selection. EMBO J 2011; 30:2431-44; PMID:21602789; http://dx.doi.org/10.1038/emboj.2011.156.
14. Di Giammartino DC, Nishida K, Manley JL. Mechanisms and Consequences of Alternative Polyadenylation. Mol Cell 2011; 43:853-66; PMID:21925375; http://dx.doi.org/10.1016/j.molcel. 2011.08.017.
15. Pal S, Gupta R, Kim H, Wickramasinghe P, Baubet V, Showe LC, et al. Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development. Genome Res 2011; 21:1260-72; PMID:21712398; http://dx.doi.org/10.1101/gr.120535.111.
16. Ji Z, Luo W, Li W, Hoque M, Pan Z, Zhao Y, et al. Transcriptional activity regulates alternative cleavage and polyadenylation. Mol Syst Biol 2011; 7:534; PMID:21952137; http://dx.doi.org/10.1038/msb.2011.69.
17. Hundley HA, Bass BL. ADAR editing in double-stranded UTRs and other noncoding RNA sequences. Trends Biochem Sci 2010; 35:377-83; PMID:20382028; http://dx.doi.org/10.1016/j.tibs.2010.02.008.
18. Laurencikiene J, Kallman AM, Fong N, Bentley DL, Ohman M. RNA editing and alternative splicing: the importance of co-transcriptional coordination. EMBO Rep 2006; 7:303-7; PMID:16440002.
19. Scadden AD. The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nat Struct Mol Biol 2005; 12:489-96; PMID:15895094; http://dx.doi.org/10.1038/nsmb936.
20. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, et al. Widespread RNA and DNA sequence differences in the human transcriptome. Science 2011; 333:53-8; PMID:21596952; http://dx.doi.org/10.1126/science.1207018.
21. He C. Grand challenge commentary: RNA epigenetics? Nat Chem Biol 2010; 6:863-5; PMID:21079590; http://dx.doi.org/10.1038/nchembio.482.
22. Elkon R, Zlotorynski E, Zeller KI, Agami R. Major role for mRNA stability in shaping the kinetics of gene induction. BMC Genomics 2010; 11:259; PMID:20409322; http://dx.doi.org/10.1186/1471-2164-11-259.
23. Wurtmann EJ, Wolin SL. RNA under attack: cellular handling of RNA damage. Crit Rev Biochem Mol Biol 2009; 44:34-49; PMID:19089684; http://dx.doi.org/10.1080/10409230802594043.
24. Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008; 134:341-52; PMID:18662548; http://dx.doi.org/10.1016/j.cell.2008.05.042.
25. Choder M. mRNA imprinting: Additional level in the regulation of gene expression. Cell Logist 2011; 1:37-40; PMID:21686103; http://dx.doi.org/10.4161/cl.1.1.14465.
26. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol 2008; 6:255; PMID:18959479; http://dx.doi.org/10.1371/journal.pbio.0060255.
27. Sanford JR, Wang X, Mort M, Vanduyn N, Cooper DN, Mooney SD, et al. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res 2009; 19:381-94; PMID:19116412; http://dx.doi.org/10.1101/gr.082503.108.
28. Plotkin JB. Transcriptional regulation is only half the story. Mol Syst Biol 2010; 6:406; PMID:20739928; http://dx.doi.org/10.1038/msb.2010.63.