Functional association of gdown1 with RNA polymerase II poised on human genes

Molecular Cell

Volumn 45, Issue 1, 2012, Pages 38-50

  Cheng, Bo ^a   Li, Tiandao ^a   Rahl, Peter B ^b   Adamson, Todd E ^a   Loudas, Nicholas B ^a   Guo, Jiannan ^a   Varzavand, Katayoun ^a   Cooper, Jeffrey J ^a   Hu, Xiaopeng ^c,d   Gnatt, Averell ^c   Young, Richard A ^b   Price, David H ^a  

^a UNIVERSITY OF IOWA   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^d SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; GDOWN1 PROTEIN; MESSENGER RNA; RNA POLYMERASE II; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ENZYME SYNTHESIS; FEMALE; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENOME; HUMAN; HUMAN CELL; PROTEIN FUNCTION; RNA TRANSLATION; TRANSCRIPTION REGULATION;

HELA CELLS; HUMANS; RNA POLYMERASE II; TRANSCRIPTION FACTORS, TFII; TRANSCRIPTION, GENETIC;

EID: 84862909057     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2011.10.022     Document Type: Article

References (46)

1. Adamson T.E., Price D.H. Cotranscriptional processing of Drosophila histone mRNAs. Mol. Cell. Biol. 2003, 23:4046-4055.
2. Adamson T.E., Shore S.M., Price D.H. Analysis of RNA polymerase II elongation invitro. Methods Enzymol. 2003, 371:264-275.
3. Adelman K., Marr M.T., Werner J., Saunders A., Ni Z., Andrulis E.D., Lis J.T. Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol. Cell 2005, 17:103-112.
4. Barski A., Cuddapah S., Cui K., Roh T.Y., Schones D.E., Wang Z., Wei G., Chepelev I., Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
5. Boettiger A.N., Levine M. Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science 2009, 325:471-473.
6. Byers S.A., Price J.P., Cooper J.J., Li Q., Price D.H. HEXIM2, a HEXIM1-related protein, regulates positive transcription elongation factor b through association with 7SK. J.Biol. Chem. 2005, 280:16360-16367.
7. Chao S.H., Price D.H. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription invivo. J.Biol. Chem. 2001, 276:31793-31799.
8. Cheng B., Price D.H. Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation. J.Biol. Chem. 2007, 282:21901-21912.
9. Cheng B., Price D.H. Analysis of factor interactions with RNA polymerase II elongation complexes using a new electrophoretic mobility shift assay. Nucleic Acids Res. 2008, 36:e135. 10.1093/nar/gkn630.
10. Cheng B., Price D.H. Isolation and functional analysis of RNA polymerase II elongation complexes. Methods 2009, 48:346-352.
11. Cheung A.C., Cramer P. Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature 2011, 471:249-253.
12. Core L.J., Waterfall J.J., Lis J.T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008, 322:1845-1848.
13. Gilchrist D.A., Nechaev S., Lee C., Ghosh S.K., Collins J.B., Li L., Gilmour D.S., Adelman K. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev. 2008, 22:1921-1933.
14. Guenther M.G., Levine S.S., Boyer L.A., Jaenisch R., Young R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007, 130:77-88.
15. Guo H., Price D.H. Mechanism of DmS-II-mediated pause suppression by Drosophila RNA polymerase II. J.Biol. Chem. 1993, 268:18762-18770.
16. Hendrix D.A., Hong J.W., Zeitlinger J., Rokhsar D.S., Levine M.S. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 2008, 105:7762-7767.
17. Hu X., Malik S., Negroiu C.C., Hubbard K., Velalar C.N., Hampton B., Grosu D., Catalano J., Roeder R.G., Gnatt A. A Mediator-responsive form of metazoan RNA polymerase II. Proc. Natl. Acad. Sci. USA 2006, 103:9506-9511.
18. Izban M.G., Luse D.S. SII-facilitated transcript cleavage in RNApolymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments. J.Biol. Chem. 1993, 268:12864-12873.
19. Jiang Y., Liu M., Spencer C.A., Price D.H. Involvement of transcription termination factor 2 in mitotic repression of transcription elongation. Mol. Cell 2004, 14:375-385.
20. Kagey M.H., Newman J.J., Bilodeau S., Zhan Y., Orlando D.A., van Berkum N.L., Ebmeier C.C., Goossens J., Rahl P.B., Levine S.S., et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010, 467:430-435.
21. Kettenberger H., Armache K.J., Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 2004, 16:955-965.
22. Kornberg R.D. The molecular basis of eukaryotic transcription. Proc. Natl. Acad. Sci. USA 2007, 104:12955-12961.
23. Lee T.I., Johnstone S.E., Young R.A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 2006, 1:729-748.
24. Lee C., Li X., Hechmer A., Eisen M., Biggin M.D., Venters B.J., Jiang C., Li J., Pugh B.F., Gilmour D.S. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol. Cell. Biol. 2008, 28:3290-3300.
25. Luse D.S., Spangler L.C., Ujvari A. Efficient and rapid nucleosome traversal by RNA polymerase II depends on a combination of transcript elongation factors. J.Biol. Chem. 2011, 286:6040-6048.
26. Malik S., Barrero M.J., Jones T. Identification of a regulator of transcription elongation as an accessory factor for the human Mediator coactivator. Proc. Natl. Acad. Sci. USA 2007, 104:6182-6187.
27. Marshall N.F., Price D.H. Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol. Cell. Biol. 1992, 12:2078-2090.
28. Marshall N.F., Price D.H. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J.Biol. Chem. 1995, 270:12335-12338.
29. Moteki S., Price D. Functional coupling of capping and transcription of mRNA. Mol. Cell 2002, 10:599-609.
30. Muse G.W., Gilchrist D.A., Nechaev S., Shah R., Parker J.S., Grissom S.F., Zeitlinger J., Adelman K. RNA polymerase is poised for activation across the genome. Nat. Genet. 2007, 39:1507-1511.
31. Nechaev S., Adelman K. Pol II waiting in the starting gates: regulating the transition from transcription initiation into productive elongation. Biochim. Biophys. Acta 2011, 1809:34-45.
32. Nechaev S., Fargo D.C., dos Santos G., Liu L., Gao Y., Adelman K. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 2010, 327:335-338.
33. Ni Z., Saunders A., Fuda N.J., Yao J., Suarez J.R., Webb W.W., Lis J.T. P-TEFb is critical for the maturation of RNA polymerase II into productive elongation invivo. Mol. Cell. Biol. 2008, 28:1161-1170.
34. Palangat M., Renner D.B., Price D.H., Landick R. A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS. Proc. Natl. Acad. Sci. USA 2005, 102:15036-15041.
35. Peng J., Liu M., Marion J., Zhu Y., Price D.H. RNA polymerase II elongation control. Cold Spring Harb. Symp. Quant. Biol. 1998, 63:365-370.
36. Peterlin B.M., Price D.H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 2006, 23:297-305.
37. Price D.H., Sluder A.E., Greenleaf A.L. Dynamic interaction between a Drosophila transcription factor and RNA polymerase II. Mol. Cell. Biol. 1989, 9:1465-1475.
38. Rahl P.B., Lin C.Y., Seila A.C., Flynn R.A., McCuine S., Burge C.B., Sharp P.A., Young R.A. c-Myc regulates transcriptional pause release. Cell 2010, 141:432-445.
39. Reines D. Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II. J.Biol. Chem. 1992, 267:3795-3800.
40. Renner D.B., Yamaguchi Y., Wada T., Handa H., Price D.H. Ahighly purified RNA polymerase II elongation control system. J.Biol. Chem. 2001, 276:42601-42609.
41. Roginski R.S., Mohan Raj B.K., Birditt B., Rowen L. The human GRINL1A gene defines a complex transcription unit, an unusual form of gene organization in eukaryotes. Genomics 2004, 84:265-276.
42. Romano G., Giordano A. Role of the cyclin-dependent kinase 9-related pathway in mammalian gene expression and human diseases. Cell Cycle 2008, 7:3664-3668.
43. Saunders A., Core L.J., Lis J.T. Breaking barriers to transcription elongation. Nat. Rev. Mol. Cell Biol. 2006, 7:557-567.
44. Seila A.C., Core L.J., Lis J.T., Sharp P.A. Divergent transcription: a new feature of active promoters. Cell Cycle 2009, 8:2557-2564.
45. Zeitlinger J., Stark A., Kellis M., Hong J.W., Nechaev S., Adelman K., Levine M., Young R.A. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat. Genet. 2007, 39:1512-1516.
46. Zhou Q., Yik J.H. The Yin and Yang of P-TEFb regulation: implications for human immunodeficiency virus gene expression and global control of cell growth and differentiation. Microbiol. Mol. Biol. Rev. 2006, 70:646-659.