Histone Acetylation and Deacetylation

Zhang, Kangling; Williams, Katherine E.; Huang, Lan; Yau, Peter; Siino, Joseph S.; Bradbury, E. Morton; Jones, Patrick R.; Minch, Michael J.; Burlingame, Alma L.

doi:10.1074/mcp.m200031-mcp200

Cited by 154 publications

(73 citation statements)

References 44 publications

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“…The distribution of species located in LC-MS fraction 6 corresponded in mass to post-translationally modified histone H4 isoforms ( Figure 3A). H4 has been shown to be predominantly dimethylated at K20 and acetylated at K16, K12, K8 and K5 in human cells [47][48][49][50]. All the masses observed for H4 isoforms were 42 Da higher than their theoretical masses, consistent with N-terminal acetylation of H4 [51].…”

Section: Core Histone Profilesmentioning

confidence: 70%

“…Due to isobaric nature of three methyl groups and one acetyl group (both add 42 Da), the species at 11,320 Da could also be due to N-Ac + TriMe and / or N-Ac + DiMe + Me and / or NAc + 3Me, and the species at 11,334 Da could be due to N-Ac + TriMe + Me and / or N-Ac + DiMe + 2Me and / or N-Ac + 2DiMe and / or N-Ac + 4Me. Previous reports that used peptide mass mapping and tandem mass spectrometry favor the assignments of 11,306 Da as N-Ac + K20DiMe, 11,348/9 Da as N-Ac + K16Ac + K20DiMe and 11390/1 Da as NAc + K16Ac + K12Ac + K20DiMe [47,48].…”

Section: Core Histone Profilesmentioning

confidence: 93%

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Liquid chromatography mass spectrometry profiling of histones

Jacob

Amunugama

et al. 2007

Journal of Chromatography B

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Here we describe the use of reverse-phase liquid chromatography mass spectrometry (RP-LC-MS) to simultaneously characterize variants and post-translationally modified isoforms for each histone. The analysis of intact proteins significantly reduces the time of sample preparation and simplifies data interpretation. LC-MS analysis and peptide mass mapping have previously been applied to identify histone proteins and to characterize their post-translational modifications. However, these studies provided limited characterization of both linker histones and core histones. The current LC-MS analysis allows for the simultaneous observation of all histone PTMs and variants (both replacement and bulk histones) without further enrichment, which will be valuable in comparative studies. Protein identities were verified by the analysis of histone H2A species using RPLC fractionation, AU-PAGE separation and nano-LC-MS/MS.

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Section: Core Histone Profilesmentioning

confidence: 70%

Section: Core Histone Profilesmentioning

confidence: 93%

Liquid chromatography mass spectrometry profiling of histones

Jacob

Amunugama

et al. 2007

Journal of Chromatography B

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“…Since acetylation of histone H4 in the nucleus is proposed to occur at K16 first, then at K12, K8, and K5 [14], the simultaneous acetylation of K5 and K8 indicates a typical state of histone H4 hyperacetylation [14]. Indeed, BET proteins preferentially bind to the K5/K8-diacetylated H4 tail peptides mimicking hyperacetylated H4 in vitro [12,13].…”

Section: Introductionmentioning

confidence: 99%

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

Handoko¹,

Kaczkowski²,

Hon³

et al. 2018

Epigenetics

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The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed, suggesting that recruitment of BRD2 does not influence global histone H4 hyperacetylation levels. This finding supports a model in which recruitment of BET proteins via histone H4 hyperacetylation is predominant over hyperacetylation of histone H4 by BET protein-associated acetyltransferases. In addition, we found that a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and -independent manner.

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“…For example, antibodies, which are specific to one modification, can detect single-site modifications (e.g. mArg-3), the abundance of which in some cell types may be below the detection limit of MS. "Bottom-up MS" allows the detection of combinations of modifications only when they reside on the same peptide (15). The use of peptide mass fingerprinting relies on mass accuracy instead of fragmentation for PTM detection (16).…”

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confidence: 99%

Combinatorial Modification of Human Histone H4 Quantitated by Two-dimensional Liquid Chromatography Coupled with Top Down Mass Spectrometry

Pesavento

Bullock

LeDuc

et al. 2008

Journal of Biological Chemistry

179

184

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Quantitative proteomics has focused heavily on correlating protein abundances, ratios, and dynamics by developing methods that are protein expression-centric (e.g. isotope coded affinity tag, isobaric tag for relative and absolute quantification, etc.). These methods effectively detect changes in protein abundance but fail to provide a comprehensive perspective of the diversity of proteins such as histones, which are regulated by post-translational modifications. Here, we report the characterization of modified forms of HeLa cell histone H4 with a dynamic range >10 4 using a strictly Top Down mass spectrometric approach coupled with two dimensions of liquid chromatography. This enhanced dynamic range enabled the precise characterization and quantitation of 42 forms uniquely modified by combinations of methylation and acetylation, including those with trimethylated Lys-20, monomethylated Arg-3, and the novel dimethylated Arg-3 (each <1% of all H4 forms). Quantitative analyses revealed distinct trends in acetylation site occupancy depending on Lys-20 methylation state. Because both modifications are dynamically regulated through the cell cycle, we simultaneously investigated acetylation and methylation kinetics through three cell cycle phases and used these data to statistically assess the robustness of our quantitative analysis. This work represents the most comprehensive analysis of histone H4 forms present in human cells reported to date.Histones are a class of proteins around which DNA is wrapped and packaged inside a eukaryotic nucleus. Two molecules of each core histone H2A, H2B, H3, and H4 together with ϳ146 bp of DNA form the fundamental unit of chromatin called the nucleosome. These proteins are heavily modified, with combinations of these enzymatic modifications thought to form a "histone code" orchestrating epigenetic processes such as long-term gene silencing and gene activation (1), higher level chromatin packaging (2), and DNA repair mechanisms (3). All of these activities change with relation to the cell cycle, a sequence of events during which a cell commits to DNA replication (G 1 ), replicates its DNA (S), prepares for mitosis (G 2 ), and undergoes cell division (M) (4). Histone synthesis and deposition are largely coupled to DNA replication during S phase (5). As a cell doubles its nuclear DNA, there is a concomitant doubling of the content of histones and nucleosomes. Even though antibodies have been used to track single modifications, the fate of preexisting histone modifications and the acquisition of new histone modifications during the cell cycle is not well understood because this approach is unable to distinguish previously modified forms from newly modified ones (6 -8). However, an epigenetic mechanism presumably exists to faithfully transmit patterns of histone modification and chromatin structure to ensure normal cellular function over successive generations (9).Dynamic changes in the PTMs 4 affecting the N-terminal tails of the core histones, which comprise ϳ25-30% of their individual...

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Histone Acetylation and Deacetylation

Cited by 154 publications

References 44 publications

Liquid chromatography mass spectrometry profiling of histones

Liquid chromatography mass spectrometry profiling of histones

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

Combinatorial Modification of Human Histone H4 Quantitated by Two-dimensional Liquid Chromatography Coupled with Top Down Mass Spectrometry

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