The super elongation complex family of RNA polymerase II elongation factors: Gene target specificity and transcriptional output

Molecular and Cellular Biology

Volumn 32, Issue 13, 2012, Pages 2608-2617

  Luo, Zhuojuan ^a   Lin, Chengqi ^a   Guest, Erin ^a   Garrett, Alexander S ^a   Mohaghegh, Nima ^a   Swanson, Selene ^a   Marshall, Stacy ^a   Florens, Laurence ^a   Washburn, Michael P ^a,b   Shilatifard, Ali ^a  

^a STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^b UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR; MESSENGER RNA; PROTEIN AF9; PROTEIN AFF2; PROTEIN AFF3; PROTEIN ENL; PROTEIN P TEFB; PROTEIN SEC L2; PROTEIN SEC L3; RNA POLYMERASE II; SUPER ELONGATION COMPLEX; UNCLASSIFIED DRUG;

ACUTE GRANULOCYTIC LEUKEMIA; ACUTE LYMPHOCYTIC LEUKEMIA; ANIMAL; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; ENZYME ACTIVITY; GENE; GENE EXPRESSION REGULATION; GENE INDUCTION; GENE OVEREXPRESSION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HSP70 GENE; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; ONCOGENE MYC; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE ANALYSIS; STRESS;

BASE SEQUENCE; CELL LINE; GENE EXPRESSION REGULATION; GENE KNOCKDOWN TECHNIQUES; GENES, MYC; HEK293 CELLS; HSP70 HEAT-SHOCK PROTEINS; HUMANS; JURKAT CELLS; LEUKEMIA; MULTIPROTEIN COMPLEXES; NUCLEAR PROTEINS; POSITIVE TRANSCRIPTIONAL ELONGATION FACTOR B; REPRESSOR PROTEINS; RNA POLYMERASE II; RNA, MESSENGER; RNA, NEOPLASM; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ELONGATION FACTORS;

METAZOA;

EID: 84864020768     PISSN: 02707306     EISSN: 10985549     Source Type: Journal    
DOI: 10.1128/MCB.00182-12     Document Type: Article

References (59)

1. Bitoun E, Davies KE. 2005. The robotic mouse: unravelling the function of AF4 in the cerebellum. Cerebellum 4:250-260.
2. Bitoun E, Oliver PL, Davies KE. 2007. The mixed-lineage leukemia fusion partner AF4 stimulates RNA polymerase II transcriptional elongation and mediates coordinated chromatin remodeling. Hum. Mol. Genet. 16:92-106.
3. Boettiger AN, Levine M. 2009. Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science 325:471-473.
4. Bres V, Yoh SM, Jones KA. 2008. The multi-tasking P-TEFb complex. Curr. Opin. Cell Biol. 20:334-340.
5. Bursen A, Moritz S, Gaussmann A, Dingermann T, Marschalek R. 2004. Interaction of AF4 wild-type and AF4.MLL fusion protein with SIAH proteins: indication for t(4;11) pathobiology? Oncogene 23:6237-6249.
6. Core LJ, Lis JT. 2008. Transcription regulation through promoterproximal pausing of RNA polymerase II. Science 319:1791-1792.
7. Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845-1848.
8. Dawson MA, et al. 2011. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature 478:529-533.
9. Delmore JE, et al. 2011. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146:904-917.
10. Eferl R, Wagner EF. 2003. AP-1: a double-edged sword in tumorigenesis. Nat. Rev. Cancer 3:859-868.
11. Eilers M, Eisenman RN. 2008. Myc's broad reach. Genes Dev. 22:2755-2766.
12. Fuda NJ, Ardehali MB, Lis JT. 2009. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461:186-192.
13. Gecz J, Gedeon AK, Sutherland GR, Mulley JC. 1996. Identification of the gene FMR2, associated with FRAXE mental retardation. Nat. Genet. 13:105-108.
14. Gerber DJ, et al. 2001. Hyperactivity, elevated dopaminergic transmission, and response to amphetamine in M1 muscarinic acetylcholine receptor- deficient mice. Proc. Natl. Acad. Sci. U.S.A. 98:15312-15317.
15. Gu Y, Shen Y, Gibbs RA, Nelson DL. 1996. Identification of FMR2, a novel gene associated with the FRAXE CCG repeat and CpG island. Nat. Genet. 13:109-113.
16. He N, et al. 2011. Human polymerase-associated factor complex (PAFc) connects the super elongation complex (SEC) to RNA polymerase II on chromatin. Proc. Natl. Acad. Sci. U.S.A. 108:E636-645.
17. He N, et al. 2010. HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. Mol. Cell 38:428-438.
18. He N, Zhou Q. 2011. New insights into the control of HIV-1 transcription: when Tat meets the 7SK snRNP and super elongation complex (SEC). J. Neuroimmune Pharmacol. 6:260-268.
19. Herdegen T, Leah JD. 1998. Inducible and constitutive transcription factors in the mammalian nervous system: control of gene expression by Jun, Fos and Krox, and CREB/ATF proteins. Brain Res. Brain Res. Rev. 28:370-490.
20. Jang MK, et al. 2005. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase IIdependent transcription. Mol. Cell 19:523-534.
21. Jones KA, Peterlin BM. 1994. Control of RNA initiation and elongation at the HIV-1 promoter. Annu. Rev. Biochem. 63:717-743.
22. Kapushesky M, et al. 2010. Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res. 38:D690-D698.
23. Kent WJ, et al. 2002. The human genome browser at UCSC. Genome Res. 12:996-1006.
24. Krumm A, Meulia T, Groudine M. 1993. Common mechanisms for the control of eukaryotic transcriptional elongation. Bioessays 15:659-665.
25. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
26. Lee TI, Johnstone SE, Young RA. 2006. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 1:729-748.
27. Lin C, et al. 2011. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes Dev. 25:1486-1498.
28. Lin C, et al. 2010. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Mol. Cell 37:429-437.
29. Lis JT, Mason P, Peng J, Price DH, Werner J. 2000. P-TEFb kinase recruitment and function at heat shock loci. Genes Dev. 14:792-803.
30. Ma C, Staudt LM. 1996. LAF-4 encodes a lymphoid nuclear protein with transactivation potential that is homologous to AF-4, the gene fused to MLL in t(4;11) leukemias. Blood 87:734-745.
31. Meyer N, Penn LZ. 2008. Reflecting on 25 years with MYC. Nat. Rev. Cancer 8:976-990.
32. Mohan M, et al. 2010. Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom). Genes Dev. 24: 574-589.
33. Mohan M, Lin C, Guest E, Shilatifard A. 2010. Licensed to elongate: a molecular mechanism for MLL-based leukaemogenesis. Nat. Rev. Cancer 10:721-728.
34. Mueller D, et al. 2009. Misguided transcriptional elongation causes mixed lineage leukemia. PLoS Biol. 7:e1000249. doi:10.1371/ journal.pbio.1000249.
35. Muse GW, et al. 2007. RNA polymerase is poised for activation across the genome. Nat. Genet. 39:1507-1511.
36. Nguyen VT, Kiss T, Michels AA, Bensaude O. 2001. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 414:322-325.
37. Peterlin BM, Price DH. 2006. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 23:297-305.
38. Rahl PB, et al. 2010. c-Myc regulates transcriptional pause release. Cell 141:432-445.
39. Rocks N, et al. 2008. ADAMTS-1 metalloproteinase promotes tumor development through the induction of a stromal reaction in vivo. Cancer Res. 68:9541-9550.
40. Shilatifard A, Conaway RC, Conaway JW. 2003. The RNA polymerase II elongation complex. Annu. Rev. Biochem. 72:693-715.
41. Shilatifard A, Lane WS, Jackson KW, Conaway RC, Conaway JW. 1996. AnRNApolymerase II elongation factor encoded by the human ELL gene. Science 271:1873-1876.
42. Sims RJ, III, Belotserkovskaya R, Reinberg D. 2004. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18:2437-2468.
43. Smith E, Lin C, Shilatifard A. 2011. The super elongation complex (SEC) and MLL in development and disease. Genes Dev. 25:661-672.
44. Sobhian B, et al. 2010. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP. Mol. Cell 38:439-451.
45. Spencer CA, Groudine M. 1990. Molecular analysis of the c-myc transcription elongation block. Implications for the generation of Burkitt's lymphoma. Ann. N. Y. Acad. Sci. 599:12-28.
46. Stahl EA, et al. 2010. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat. Genet. 42:508-514.
47. Takahashi H, et al. 2011. Human mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell 146:92-104.
48. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111.
49. Trapnell C, et al. 2010. Transcript assembly and quantification by RNASeq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511-515.
50. Wada T, et al. 1998. DSIF, a novel transcription elongation factor that regulatesRNApolymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12:343-356.
51. Workman JL, Kingston RE. 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:545-579.
52. Wu M, et al. 2008. Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS. Mol. Cell. Biol. 28: 7337-7344.
53. Yamaguchi Y, et al. 1999. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97: 41-51.
54. Yang Z, et al. 2005. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol. Cell 19:535-545.
55. Yang Z, Zhu Q, Luo K, Zhou Q. 2001. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 414: 317-322.
56. Yokoyama A, Lin M, Naresh A, Kitabayashi I, Cleary ML. 2010. A higher-order complex containing AF4 and ENL family proteins with P-TEFb facilitates oncogenic and physiologic MLL-dependent transcription. Cancer Cell 17:198-212.
57. Zeitlinger J, et al. 2007. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat. Genet. 39:1512-1516.
58. Zhang Y, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9:R137.
59. Zuber J, et al. 2011. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478:524-528.