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Mnase-seq for six histone mutants and two wild-types in S. cerevisiae

ABSTRACT: Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown. Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance. This regulatory functional map of the core histones led to novel findings. First, the residues specific to each histone family tend to be more influential than those commonly found among different histones. Second, unlike histone acetylations, H3K4 trimethylation does not appear to be prerequisite for gene activation. Third, H3Q5 has been newly identified for its putative interactions with many chromatin regulators for transcription control. Lastly, the nucleosome lateral surface seems to play a key role through interactions with the surrounding DNA. Remarkably, we discovered a novel role for H3K56 in chromatin dynamics. The deletion of this residue, but not the alteration of acetylation states, caused a genome-wide decrease in nucleosome mobility and stabilized nucleosome positioning near transcription start and end sites. Occupying the DNA entry/exit site, H3K56 is thought to modulate nucleosome sliding along DNA. Taken together, genomics approaches such as microarray and deep sequencing prove valuable for mapping the function of histone residues. SUBMITTER_CITATION: Global Mapping of the Regulatory Interactions of Histone Residues, Epigenomics Keystone Symposium, January 21th (2012).

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE29026 | GEO | 2012/12/05

SECONDARY ACCESSION(S): PRJNA142829

REPOSITORIES: GEO

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Gene expression changes upon the mutation of individual residues of histone H3 and H4

Project description:Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown. Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance. This regulatory functional map of the core histones led to novel findings. First, the residues specific to each histone family tend to be more influential than those commonly found among different histones. Second, unlike histone acetylations, H3K4 trimethylation does not appear to be prerequisite for gene activation. Third, H3Q5 has been newly identified for its putative interactions with many chromatin regulators for transcription control. Lastly, the nucleosome lateral surface seems to play a key role through interactions with the surrounding DNA. Remarkably, we discovered a novel role for H3K56 in chromatin dynamics. The deletion of this residue, but not the alteration of acetylation states, caused a genome-wide decrease in nucleosome mobility and stabilized nucleosome positioning near transcription start and end sites. Occupying the DNA entry/exit site, H3K56 is thought to modulate nucleosome sliding along DNA. Taken together, genomics approaches such as microarray and deep sequencing prove valuable for mapping the function of histone residues. SUBMITTER_CITATION: Global Mapping of the Regulatory Interactions of Histone Residues, Epigenomics Keystone Symposium, January 21th (2012).

2012-12-05 | GSE29059 | GEO

Mnase-seq for six histone mutants and two wild-types in S. cerevisiae

Project description:Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown. Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance. This regulatory functional map of the core histones led to novel findings. First, the residues specific to each histone family tend to be more influential than those commonly found among different histones. Second, unlike histone acetylations, H3K4 trimethylation does not appear to be prerequisite for gene activation. Third, H3Q5 has been newly identified for its putative interactions with many chromatin regulators for transcription control. Lastly, the nucleosome lateral surface seems to play a key role through interactions with the surrounding DNA. Remarkably, we discovered a novel role for H3K56 in chromatin dynamics. The deletion of this residue, but not the alteration of acetylation states, caused a genome-wide decrease in nucleosome mobility and stabilized nucleosome positioning near transcription start and end sites. Occupying the DNA entry/exit site, H3K56 is thought to modulate nucleosome sliding along DNA. Taken together, genomics approaches such as microarray and deep sequencing prove valuable for mapping the function of histone residues. Performing Mnase-seq for six histone mutants and two wild-types in Saccharomyces cerevisiae

2012-12-05 | E-GEOD-29026 | biostudies-arrayexpress

Gene expression changes upon the mutation of individual residues of histone H3 and H4

Project description:Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown. Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance. This regulatory functional map of the core histones led to novel findings. First, the residues specific to each histone family tend to be more influential than those commonly found among different histones. Second, unlike histone acetylations, H3K4 trimethylation does not appear to be prerequisite for gene activation. Third, H3Q5 has been newly identified for its putative interactions with many chromatin regulators for transcription control. Lastly, the nucleosome lateral surface seems to play a key role through interactions with the surrounding DNA. Remarkably, we discovered a novel role for H3K56 in chromatin dynamics. The deletion of this residue, but not the alteration of acetylation states, caused a genome-wide decrease in nucleosome mobility and stabilized nucleosome positioning near transcription start and end sites. Occupying the DNA entry/exit site, H3K56 is thought to modulate nucleosome sliding along DNA. Taken together, genomics approaches such as microarray and deep sequencing prove valuable for mapping the function of histone residues. Microarray analysis was performed for 123 histone mutants and four wild-types as two reaplications of H3 and H4 of Saccharomyces ceravisiae.

2012-12-05 | E-GEOD-29059 | biostudies-arrayexpress

A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT

Project description:Nucleosome assembly in vivo requires assembly factors, such as histone chaperones, to bind to histones and mediate their deposition onto DNA. In yeast, the essential histone chaperone FACT (FAcilitates Chromatin Transcription) functions in nucleosome assembly and H2A-H2B deposition during transcription elongation and DNA replication. Recent studies have identified candidate histone residues that mediate FACT binding to histones, but it is not known which histone residues are important for FACT to deposit histones onto DNA during nucleosome assembly. In this study, we report that the histone H2B repression (HBR) domain within the H2B N-terminal tail is important for histone deposition by FACT. Deletion of the HBR domain causes significant defects in histone occupancy in the yeast genome, particularly at HBR-repressed genes, and a pronounced increase in H2A-H2B dimers that remain bound to FACT in vivo. Moreover, the HBR domain is required for purified FACT to efficiently assemble recombinant nucleosomes in vitro. We propose that the interaction between the highly basic HBR domain and DNA plays an important role in stabilizing the nascent nucleosome during the process of histone H2A-H2B deposition by FACT. 6 samples, 2 inputs and 4 ChIP samples for histone H2B (2 for wild-type and 2 for an H2B â30-37 mutant)

2016-08-10 | E-GEOD-80831 | biostudies-arrayexpress

Histone H3 lysine 56 acetylation is required for formation of normal levels of meiotic DNA breaks in S. cerevisiae

Project description:Genomic profiling of (1) histone H3K56 acetylation and (2) meiotic DSBs flanked by replication protein A (RPA). The major goal was to reveal the genome-wide distribution DSBs when the H3K56 residue was mutated to alanine (H3K56A).

2019-12-25 | GSE37487 | GEO

A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT

2016-08-10 | GSE80831 | GEO

Probing nucleosome function: A highly versatile library of synthetic histone H3 and H4 mutants

Project description:The structural integrity of the nucleosome is central to regulation of DNA metabolism and transcription. We describe a library of 486 systematic histone H3 and H4 substitution and deletion mutants in Saccharomyces cerevisiae that probe the contribution of each residue to nucleosome function and can be episomal or genomically integrated. We tagged each mutant histone gene with unique molecular barcodes, facilitating identification of mutant pools through barcode amplification, labeling, and microarray hybridization. We probed fitness contributions of each residue to chemical perturbagens of chromosome integrity and transcription, mapping global patterns of chemical sensitivities and requirements for three forms of transcriptional silencing onto the nucleosome surface. Lethal mutants were surprisingly rare and of distinct types; one set of mutations mapped precisely to the DNA interaction surface. The barcode microarrays were useful for scoring complex phenotypes such as competitive fitness in a chemostat, proficiency of DNA repair, and synthetic genetic interactions. Keywords: genetic modification These nine datasets characterize a microarray platform repurposed for profiling a barcoded comprehensive library of synthetic histone mutants. The first two datasets establish the wide dynamic range and high sensitivity and specificity of data from this platform. The other seven datasets demonstrate the usefulness of this technology for scoring subtle and complex phenotypes of the histone H3 and H4 alleles in this library.

2008-09-18 | E-GEOD-10860 | biostudies-arrayexpress

Direct Nucleosome Binding of Borealin Secures Chromosome Association of the Chromosomal Passenger Complex

Project description:CPC-NCP complexes were crosslinked using EDC and analysed by mass spectrometry. The results showed Borealin is critical for nucleosome binding made extensive contacts with NCPs, whereas Survivin interactions are mostly limited to the BIR domain and the H3 N-terminal tail as expected. Mapping the crosslinks onto the three dimensional structures of NCP and CPC suggests a model where the localisation module of the CPC together with a highly basic N-terminal tail of Borealin docks onto the acidic patch formed by H2A and H2B, a surface commonly involved in nucleosome recognition. This interaction may orient the Survivin BIR domain to facilitate binding of histone H3 tail phosphorylated at Thr3. Notably, Borealin loop residues trace along the DNA-histone interface implying its major contribution to nucleosome binding involves both protein-histone and possibly protein-DNA contacts.

2019-09-30 | PXD012882 | Pride

Probing nucleosome function: A highly versatile library of synthetic histone H3 and H4 mutants

2008-09-19 | GSE10860 | GEO

Structural basis of H2A.Z recognition and H4K20 methylation by SUV420H2

Project description:DNA replication ensures the accurate transmission of genetic information during cell cycle. The interaction between histone methyltransferase SUV420H1 and histone variant H2A.Z plays a critical role in the licensing of early replication origins. However, the mechanism by which SUV420H1 preferentially recognizes H2A.Z-nucleosome and deposits H4 lysine 20 dimethylation (H4K20me2) on DNA replication origins remains elusive. Here, we determined the cryo-EM structures of SUV420H1 bound to H2A.Z-nucleosome or H2A-nucleosome. Our structures show that the SUV420H1 catalytic domain (CD) directly interacts with histone H4 and nucleosomal DNA, whereas a SUV420H1 arginine-rich motif (ARM) anchors to the acidic patch of the nucleosome. The N-terminal aminal acid residues of H4 (Aa 1-24) forms a lasso-shaped structure sandwiched between SUV420H1 CD and nucleosome. The lasso-shaped structure stabilizes the SUV420H1-nucleosome interaction and precisely projects the H4 K20 residue into the SUV420H1 catalytic center. Further analyses revealed a crucial role of SUV420H1 KR-loop (aminal acid residues 214-223), which spatially lies closely to H2A.Z specific residues D97/S98, in dictating the preference for H2A.Z-nucleosome. SUV420H1 K219A/R220A mutations reduced the activity of SUV420H1 for H4K20me2 modification, the preference of SUV420H1 for H2A.Z-nucleosome, and the efficiency of DNA replication initiation. Collectively, our findings elucidate how SUV420H1 preferentially recognizes H2A.Z-nucleosome to deposit H4K20me2 modification and shed light on therapeutic strategies targeting the DNA replication initiation.

2023-12-04 | GSE210197 | GEO

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