Cell cycle-dependent changes in conformation and composition of nucleosomes containing human histone gene sequences

Sterner, Richard; Boffa, Lidia C.; Chen, Thelma A.; Allfrey, Vincent G.

doi:10.1093/nar/15.11.4375

Cited by 43 publications

(20 citation statements)

References 54 publications

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“…6 scription is accompanied by a selective loss of any histones from the nudeosome core. In agreement with earlier findings [14,15], the Hg-bound nucleosomes do not contain significant amounts of histone H1. Histone hypperuwt,vlution in the Hg-hound nucleosome.fractions.…”

Section: Structural Differences In Chromatographicully Sepurated Nuclsupporting

confidence: 93%

“…6), these results place the hyperacetylated forms of histone H4 in both classes of transcriptionally active chromatin subunits. This confirms earlier observations on the high levels of histone acetylation in the total Hg-bound nucleosome fractions of liver [14] and HeLa cells [15]. The link between hyperacetylation of the core histones and transcription is further strengthened by the observation that nucleosomes containing the transcribed a-D-globin DNA sequences of avian red cells are immunoprecipitated by antibodies specific for hyperacetylated histone H4 [37].…”

Section: Structural Differences In Chromatographicully Sepurated Nuclsupporting

confidence: 89%

“…It has been shown that the Hg-bound nucleosome fraction of HeLa cells contains nascent RNA fragments which remain with the nucleosoines during subsequent centrifugation in sucrose gradients [15]. To determine whether RNA-binding proteins on nascent transcripts play a role in the retention of transcriptionally active nucleosomes on the Hg-agarose column, comparisons were made of nucleosome fractionations in control and ribonuclease-treated S fractions.…”

Section: Structural Differences In Chromatographicully Sepurated Nuclmentioning

confidence: 99%

“…The technique of Hg-agarose affinity chromatography developed in this laboratory not only separates the nucleosomes of active and inactive genes [14-171; it also has been shown to reveal the timing and extent of gene expression [16, 181. The procedure fractionates the nucleosomes released during limited micrococcal nuclease digestion of isolated nuclei by chromatography on Hg-agarose columns. The modified nucleosomes of transcriptionally active DNA sequences are retained bv the column, while the compactly beaded in intact and permeabilized cells Eflects --nucleosomes of inactive genes, such as the pre-proenkephalin gene of rat liver 1141, or the a-globin gene of HeLa cells [15], are rejected. The bound nucleosomes are retained on the Hgagarose column for two reasons: (a) they become associated with thiol-containing non-histone proteins recruited to the transcribing DNA; (b) the unfolding of transcribed nucleosomes to uncover the previously shielded thiol groups of histone H3 molecules located at the center of the nucleosome core particle.…”

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Factors affecting nucleosome structure in transcriptionally active chromatin

Boffa

Walker

Chen

et al. 1990

European Journal of Biochemistry

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The nucleosomes of transcriptionally active genes can be separated from those of inactive genes by affinity chromatography on organomercury-agarose (Hg-agarose) columns. The basis for this separation is the difference in accessibility of the sulfhydryl groups of histone H3 and certain non-histone proteins in active and inactive chromatin. A new procedure distinguishing between different modes of binding of transcriptionally active nucleosomes to the Hg-agarose column has been applied to study several factors which might influence the binding reaction. Nucleosomes that bind to the column because of salt-labile associations with SH-reactive non-histone proteins, such as the high-mobility-group proteins, HMG-1 and HMG-2, were released by adding 0.5 M NaCl to the eluting buffer. The remaining nucleosomes, in which reactive histone H3 thiol groups can bind covalently to the organomercury, were then displaced from the column by 10 mM dithiothreitol. Both Hg-agarose-bound fractions contain the transcriptionally active DNA sequences of the cell, but inactive nucleosomes, such as those containing a-globin DNA, pass through the column. The histones of both Hg-agarose-bound fractions have significantly higher levels of acetylation than do histones of the unbound fraction, but the content of tri-and tetra-acetylated H3 and H4 is significantly higher in the nucleosomes with reactive H3 thiols.The rate of turnover of histone N-acetyl groups is also far greater in the Hg-agarose-bound nucleosomes than in the unbound nucleosomes. Although the overall levels of histone acetylation can be increased significantly by incubating HeLa cells in the presence of the deacetylase inhibitor, 5 mM sodium butyrate, this treatment has little if any effect on the total number of nucleosomes retained on the Hg-agarose column. However, the ability of Hgagarose chromatography to detect localized changes in chromatin structure is evidenced by an 11-fold increase in the Hg-agarose binding of nucleosomes containing the DNA of the butyrate-inducible alkaline phosphatase gene, compared to the Hg-agarose-bound nucleosomes of control cells. Although nascent RNA chains are present in the Hg-agarose-bound nucleosomes released by dithiothreitol, binding of the SH-reactive nucleosomes to the Hgagarose column is not dependent on the presence of proteins associated with nascent RNA chains, since binding does not decrease following removal of the nascent transcripts by ribonuclease treatment.The inhibition of RNA polymerase I1 by a-amanitin results in a loss of the affinity for Hg of nucleosomes containing c-myc and histone H4 gene sequences, but there is no corresponding loss of Hg affinity with nucleosomes containing 28s ribosomal DNA sequences, which are transcribed by amanitin-resistant RNA polymerase I.When RNA synthesis is inhibited by actinomycin D, which we find to intercalate preferentially into the DNA of transcriptionally active DNA sequences, there is no loss of Hg affinity of nucleosomes containing the histone H4 or c-myc DNA sequences. The result...

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Section: Structural Differences In Chromatographicully Sepurated Nuclsupporting

confidence: 93%

Section: Structural Differences In Chromatographicully Sepurated Nuclsupporting

confidence: 89%

Section: Structural Differences In Chromatographicully Sepurated Nuclmentioning

confidence: 99%

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confidence: 99%

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Factors affecting nucleosome structure in transcriptionally active chromatin

Boffa

Walker

Chen

et al. 1990

European Journal of Biochemistry

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“…These U-shaped particles are retained on Hg columns, in part because of accessibility of the single H3 thiol, and are enriched in acetylated histones and transcribed DNA sequences (55)(56)(57)(58). This H3 thiol (H3-C110) is in the center of the H3-H3 four-helix bundle that binds the two H3/H4 dimers into a tetramer (21).…”

Section: Unfolding or Disassembling Nucleosome Coresmentioning

confidence: 99%

Alteration of Nucleosome Structure as a Mechanism of Transcriptional Regulation

Workman

Kingston

1998

Annu. Rev. Biochem.

1,066

778

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The nucleosome, which is the primary building block of chromatin, is not a static structure: It can adopt alternative conformations. Changes in solution conditions or changes in histone acetylation state cause nucleosomes and nucleosomal arrays to behave with altered biophysical properties. Distinct subpopulations of nucleosomes isolated from cells have chromatographic properties and nuclease sensitivity different from those of bulk nucleosomes. Recently, proteins that were initially identified as necessary for transcriptional regulation have been shown to alter nucleosomal structure. These proteins are found in three types of multiprotein complexes that can acetylate nucleosomes, deacetylate nucleosomes, or alter nucleosome structure in an ATP-dependent manner. The direct modification of nucleosome structure by these complexes is likely to play a central role in appropriate regulation of eukaryotic genes. CONTENTS

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Elevation of large‐T antigen production by sodium butyrate treatment of SV40‐transformed WI‐38 fibroblasts

1992

J of Cellular Biochemistry

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The effects of sodium butyrate on simian virus 40 early gene expression were determined in SV40-transformed human embryonic lung fibroblasts (SVWI-38). Northern blot analysis and nuclear run-off transcription studies revealed that treatment of cells with millimolar concentrations of sodium butyrate (2.5 to 10 mM) resulted in increased levels of SV40 early gene transcripts, with a concomitant increase in their corresponding proteins (large-T and small-t antigens). Although sodium butyrate treatment enhanced the expression of the early genes, it was associated with a reduction in cell growth and total protein synthesis, as measured by cell number and incorporation of 3H-leucine into macromolecules, respectively. Immunoprecipitation of 35S-labelled cellular proteins with anti-p53 and anti-T antibodies revealed that the level of the cellular protein, p53, declined markedly in the presence of sodium butyrate. Furthermore, in control cells only 30% of the p53 was complexed with large-T antigen, whereas in butyrate-treated cells all the p53 was complexed with large-T antigen. The increased early gene expression was not due to altered methylation patterns, gene amplification, or rearrangement of the integrated SV40 genome. Sodium butyrate treatment did, however, result in the appearance of a new nuclear protein which bound specifically to a SV40 promoter fragment containing large-T antigen binding sites I and II.

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Cell cycle-dependent changes in conformation and composition of nucleosomes containing human histone gene sequences

Cited by 43 publications

References 54 publications

Factors affecting nucleosome structure in transcriptionally active chromatin

Factors affecting nucleosome structure in transcriptionally active chromatin

Alteration of Nucleosome Structure as a Mechanism of Transcriptional Regulation

Elevation of large‐T antigen production by sodium butyrate treatment of SV40‐transformed WI‐38 fibroblasts

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