Chromatin potentiates transcription

Proceedings of the National Academy of Sciences of the United States of America

Volumn 114, Issue 7, 2017, Pages 1536-1541

  Nagai, Shigeki ^a   Davis, Ralph E ^a   Mattei, Pierre Jean ^a   Eagen, Kyle Patrick ^a   Kornberg, Roger D ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

PHO5; RNA polymerase II; Saccharomyces cerevisiae

Indexed keywords

MEDIATOR COMPLEX; NAKED DNA; PHO4 GENE ACTIVATOR PROTEIN; PROTEIN; RNA POLYMERASE II; SWI/SNF RELATED MATRIX ASSOCIATED ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1; TISSUE FACTOR PATHWAY INHIBITOR; TRANSCRIPTION FACTOR II; TRANSCRIPTION FACTOR SAGA; UNCLASSIFIED DRUG; ACID PHOSPHATASE; CIRCULAR DNA; FUNGAL DNA; FUNGAL RNA; HISTONE; HISTONE H3 TRIMETHYL LYS4; MESSENGER RNA; MULTIPROTEIN COMPLEX; PHO5 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA TRANSCRIPTION; GENE; GENE ACTIVATION; GENE LOCUS; IN VIVO STUDY; LIMIT OF QUANTITATION; NONHUMAN; NUCLEOSOME; PHO5 GENE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TATA BOX; TRANSCRIPTION INITIATION SITE; YEAST; ACETYLATION; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; METHYLATION; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN PROCESSING; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

ACETYLATION; ACID PHOSPHATASE; BASE SEQUENCE; DNA, CIRCULAR; DNA, FUNGAL; GENE EXPRESSION REGULATION, FUNGAL; HISTONES; METHYLATION; MULTIPROTEIN COMPLEXES; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; PROTEIN PROCESSING, POST-TRANSLATIONAL; RNA, FUNGAL; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 85012960893     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1620312114     Document Type: Article

References (47)

1. Lorch Y, LaPointe JW, Kornberg RD (1987) Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49(2):203-210.
2. Han M, Grunstein M (1988) Nucleosome loss activates yeast downstream promoters in vivo. Cell 55(6):1137-1145.
3. Lemon B, Inouye C, King DS, Tjian R (2001) Selectivity of chromatin-remodelling cofactors for ligand-activated transcription. Nature 414(6866):924-928.
4. LeRoy G, Orphanides G, Lane WS, Reinberg D (1998) Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science 282(5395):1900-1904.
5. Mizuguchi G, Vassilev A, Tsukiyama T, Nakatani Y, Wu C (2001) ATP-dependent nucleosome remodeling and histone hyperacetylation synergistically facilitate transcription of chromatin. J Biol Chem 276(18):14773-14783.
6. Pavri R, et al. (2006) Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 125(4):703-717.
7. Carey M, Li B, Workman JL (2006) RSC exploits histone acetylation to abrogate the nucleosomal block to RNA polymerase II elongation. Mol Cell 24(3):481-487.
8. Orphanides G, LeRoy G, Chang CH, Luse DS, Reinberg D (1998) FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92(1):105-116.
9. Guermah M, Palhan VB, Tackett AJ, Chait BT, Roeder RG (2006) Synergistic functions of SII and p300 in productive activator-dependent transcription of chromatin templates. Cell 125(2):275-286.
10. Griesenbeck J, Boeger H, Strattan JS, Kornberg RD (2003) Affinity purification of specific chromatin segments from chromosomal loci in yeast. Mol Cell Biol 23(24):9275-9282.
11. Hamperl S, et al. (2014) Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic Acids Res 42(1):e2.
12. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD (2003) Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell 11(6):1587-1598.
13. Barbaric S, Reinke H, Hörz W (2003) Multiple mechanistically distinct functions of SAGA at the PHO5 promoter. Mol Cell Biol 23(10):3468-3476.
14. Musladin S, Krietenstein N, Korber P, Barbaric S (2014) The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening. Nucleic Acids Res 42(7):4270-4282.
15. Kuryan BG, et al. (2012) Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro. Proc Natl Acad Sci USA 109(6):1931-1936.
16. Phelan ML, Schnitzler GR, Kingston RE (2000) Octamer transfer and creation of stably remodeled nucleosomes by human SWI-SNF and its isolated ATPases. Mol Cell Biol 20(17):6380-6389.
17. Korber P, Barbaric S (2014) The yeast PHO5 promoter: From single locus to systems biology of a paradigm for gene regulation through chromatin. Nucleic Acids Res 42(17):10888-10902.
18. Rudolph H, Hinnen A (1987) The yeast PHO5 promoter: Phosphate-control elements and sequences mediating mRNA start-site selection. Proc Natl Acad Sci USA 84(5):1340-1344.
19. Brown CR, Mao C, Falkovskaia E, Law JK, Boeger H (2011) In vivo role for the chromatin-remodeling enzyme SWI/SNF in the removal of promoter nucleosomes by disassembly rather than sliding. J Biol Chem 286(47):40556-40565.
20. Laurent BC, Carlson M (1992) Yeast SNF2/SWI2, SNF5, and SNF6 proteins function coordinately with the gene-specific transcriptional activators GAL4 and Bicoid. Genes Dev 6(9):1707-1715.
21. Prather DM, Larschan E, Winston F (2005) Evidence that the elongation factor TFIIS plays a role in transcription initiation at GAL1 in Saccharomyces cerevisiae. Mol Cell Biol 25(7):2650-2659.
22. Hassan AH, et al. (2002) Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111(3):369-379.
23. Reinke H, Hörz W (2003) Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol Cell 11(6):1599-1607.
24. Small EC, Xi L, Wang JP, Widom J, Licht JD (2014) Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity. Proc Natl Acad Sci USA 111(24):E2462-E2471.
25. Bian C, et al. (2011) Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation. EMBO J 30(14):2829-2842.
26. Wang SS, Zhou BO, Zhou JQ (2011) Histone H3 lysine 4 hypermethylation prevents aberrant nucleosome remodeling at the PHO5 promoter. Mol Cell Biol 31(15):3171-3181.
27. Dudley AM, Rougeulle C, Winston F (1999) The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. Genes Dev 13(22):2940-2945.
28. Tse C, Sera T, Wolffe AP, Hansen JC (1998) Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol 18(8):4629-4638.
29. Shanle EK, et al. (2015) Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response. Genes Dev 29(17):1795-1800.
30. Lorch Y, Beve J, Gustafsson CM, Myers LC, Kornberg RD (2000) Mediator-nucleosome interaction. Mol Cell 6(1):197-201.
31. Liu Z, Myers LC (2012) Med5(Nut1) and Med17(Srb4) are direct targets of mediator histone H4 tail interactions. PLoS One 7(6):e38416.
32. Ramachandran S, Zentner GE, Henikoff S (2015) Asymmetric nucleosomes flank promoters in the budding yeast genome. Genome Res 25(3):381-390.
33. Martinez-Campa C, et al. (2004) Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1. Mol Cell 15(1):69-81.
34. Albert I, et al. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446(7135):572-576.
35. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29(9):e45.
36. Güldener U, Heck S, Fielder T, Beinhauer J, Hegemann JH (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 24(13):2519-2524.
37. Wu PY, Winston F (2002) Analysis of Spt7 function in the Saccharomyces cerevisiae SAGA coactivator complex. Mol Cell Biol 22(15):5367-5379.
38. Ghaemmaghami S, et al. (2003) Global analysis of protein expression in yeast. Nature 425(6959):737-741.
39. Hamperl S, et al. (2014) Purification of specific chromatin domains from single-copy gene loci in Saccharomyces cerevisiae. Methods Mol Biol 1094:329-341.
40. Longtine MS, et al. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14(10):953-961.
41. Murakami K, et al. (2013) Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex. J Biol Chem 288(9):6325-6332.
42. Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD (2012) Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc Natl Acad Sci USA 109(44):17931-17935.
43. Lorch Y, Kornberg RD (2004) Isolation and assay of the RSC chromatin-remodeling complex from Saccharomyces cerevisiae. Methods Enzymol 377:316-322.
44. O'Neill EM, Kaffman A, Jolly ER, O'Shea EK (1996) Regulation of PHO4 nuclear localization by the PHO80-PHO85 cyclin-CDK complex. Science 271(5246):209-212.
45. Brown CR, Mao C, Falkovskaia E, Jurica MS, Boeger H (2013) Linking stochastic fluctuations in chromatin structure and gene expression. PLoS Biol 11(8):e1001621.
46. Murakami K, et al. (2015) Uncoupling promoter opening from start-site scanning. Mol Cell 59(1):133-138.
47. Lorch Y, Zhang M, Kornberg RD (1999) Histone octamer transfer by a chromatin-remodeling complex. Cell 96(3):389-392.