Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Nov 1;72(3):594-600.e2.
doi: 10.1016/j.molcel.2018.09.030. Epub 2018 Oct 25.

Histone Acetylation Inhibits RSC and Stabilizes the +1 Nucleosome

Yahli Lorch  1 , Barbara Maier-Davis  2 , Roger D Kornberg  2
Affiliations

Histone Acetylation Inhibits RSC and Stabilizes the +1 Nucleosome

Yahli Lorch et al. Mol Cell. .

Abstract

The +1 nucleosome of yeast genes, within which reside transcription start sites, is characterized by histone acetylation, by the displacement of an H2A-H2B dimer, and by a persistent association with the RSC chromatin-remodeling complex. Here we demonstrate the interrelationship of these characteristics and the conversion of a nucleosome to the +1 state in vitro. Contrary to expectation, acetylation performs an inhibitory role, preventing the removal of a nucleosome by RSC. Inhibition is due to both enhanced RSC-histone interaction and diminished histone-chaperone interaction. Acetylation does not prevent all RSC activity, because stably bound RSC removes an H2A-H2B dimer on a timescale of seconds in an irreversible manner.

Keywords: NAP1; NuA4; SAGA; chromatin; chromatin-remodeling; transcription.

PubMed Disclaimer

Conflict of interest statement

DECLARATION OF INTERESTS

The authors declare no competing interests.

Figures

Figure 1.
Figure 1.. Inhibition of RSC Activity by SAGA and Acetyl-CoA
(A) Nucleosome disassembly (conversion to naked DNA) in reactions with RSC, NAP1, and ATP, in the presence (red squares) or absence (blue diamonds) of SAGA and acetyl-CoA. (B) Nucleosome disassembly in reactions with RSC, NAP1, and ATP, following preincubation of nucleosomes with (red squares) or without SAGA and acetyl-CoA, or preincubation of RSC with (x’s) or without (green triangles) RSC and ATP. (C) Nucleosome disassembly in reactions with RSC, NAP1, and ATP. Nucleosomes were treated with SAGA and acetyl-CoA (red squares, blue diamonds) or not (x’s, green triangles) and reisolated by gradient sedimentation before the experiment. Nucleosomes were preincubated for 30 min at 30 °C w ith 0.5 μg of HDAC6 (red squares, x’s) or not (blue diamonds, green triangles) before the addition of RSC and ATP.
Figure 2.
Figure 2.. Enhancement of RSC-Nucleosome Interaction by SAGA and Acetyl-CoA
Nucleosomes were treated with SAGA and acetyl-CoA (upper middle panel, plotted as red squares in lower panel) or not (upper right panel, plotted as blue diamonds in lower panel) and reisolated by gradient sedimentation. Electrophoretic mobility shift experiments were preformed by the same procedure as for nucleosome disassembly reactions, except with the concentrations of RSC indicated, no NAP1, incubation for 15 min, and no salmon sperm DNA added before electrophoresis. Optical densities were integrated over bands in PhosphorImager scans (brackets, upper panels) for calculations (lower panel). In a separate electrophoretic mobility shift experiment (upper left panel), SAGA (0.36 μg) or RSC (0.08 μg) were combined with untreated nucleosomes under the same conditions.
Figure 3.
Figure 3.. Effect of Acetylation on NAP1 Dependence of Nucleosome Disassembly by RSC
(A) Nucleosomes were treated with SAGA and acetyl-CoA (upper middle panel, red squares) or not (upper right panel, blue diamonds) and reisolated by gradient sedimentation. Disassembly reactions were performed with the concentrations of NAP1 indicated. Apparent first order rate constants (units of min−1, multiplied by −1) were determined from plots such as Fig. 1. Error bars represent standard deviations determined from three technical replicates. (B) Nucleosome disassembly as in Fig. 1, in the presence of H3 tail peptide (blue diamonds) or doubly acetylated H3 tail peptide (red squares). (C) Nucleosome disassembly as in Fig. 1, in the presence of H4 tail peptide (blue diamonds) or acetylated H4 tail peptide (red squares).
Figure 4.
Figure 4.. Conversion of Octamer to Hexamer Nucleosome
(A) Irreversible conversion of octamer to hexamer nucleosome (hexasome), unaffected by acetylation with SAGA and acetyl-CoA. Reactions were performed as for Fig. 1, except in the absence of NAP1, with incubation for 20 min at 30 °C with no RSC and no ATP (lanes 1, 6), with RSC only (lanes 2, 7), and with RSC and ATP (lanes 3, 8). To test reversibility, hexokinase (1.25 μg) and glucose (0.3 micromoles) were added after 10 min of incubation (lane 5), and to confirm that this treatment destroyed all ATP, hexokinase and glucose were added at the beginning and RSC only added after 10 min of incubation (lane 4). Reactions were performed with nucleosomes pretreated with SAGA and acetyl-CoA (lanes 6–8) or not (lanes 1–5). (B) Time course of conversion of octamer to hexasome by RSC and ATP. A reaction mixture identical to that in lane 3 in part (A) was incubated for 0, 20, 40, 60, and 120 sec, and optical densities were integrated over bands in PhosphorImager scans for nucleosomes and hexasomes.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Allard S, Utley RT, Savard J, Clarke A, Grant P, Brandl CJ, Pillus L, Workman JL, and Cote J (1999). NuA4, an essential transcription adaptor/histone H4 acetyltransferase complex containing Esa1p and the ATM-related cofactor Tra1p. EMBO J 18, 5108–5119. - PMC - PubMed
    1. Baptista T, Grunberg S, Minoungou N, Koster MJE, Timmers HTM, Hahn S, Devys D, and Tora L (2017). SAGA Is a General Cofactor for RNA Polymerase II Transcription. Mol Cell 68, 130–143 e135. - PMC - PubMed
    1. Belotserkovskaya R, Oh S, Bondarenko VA, Orphanides G, Studitsky VM, and Reinberg D (2003). FACT facilitates transcription-dependent nucleosome alteration. Science 301, 1090–1093. - PubMed
    1. Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides T, and Schreiber SL (2002). Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A 99, 8695–8700. - PMC - PubMed
    1. Bian C, Xu C, Ruan J, Lee KK, Burke TL, Tempel W, Barsyte D, Li J, Wu M, Zhou BO, et al. (2011). Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation. EMBO J 30, 2829–2842. - PMC - PubMed

Publication types

MeSH terms

LinkOut - more resources