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Association of Taf14 with acetylated histone H3 directs the DNA damage response and gene transcription

ABSTRACT: We sequenced mRNA from triplicate log-phase cultures of BY4741 (WT) transformed with pRS313-HA3-SSN6 and taf14D transformed with pRS313-HA3-SSN6 (empty vector), full-length pRS313-TAF14-HA3-SSN6, or pRS313-taf14W81A-HA3-SSN6 cultured in synthetic complete media lacking histidine.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE71768 | GEO | 2015/09/09

SECONDARY ACCESSION(S): PRJNA292038

REPOSITORIES: GEO

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Association of Taf14 with acetylated histone H3 directs the DNA damage response and gene transcription

Project description:We sequenced mRNA from triplicate log-phase cultures of BY4741 (WT) transformed with pRS313-HA3-SSN6 and taf14D transformed with pRS313-HA3-SSN6 (empty vector), full-length pRS313-TAF14-HA3-SSN6, or pRS313-taf14W81A-HA3-SSN6 cultured in synthetic complete media lacking histidine. Examination of changes in gene expression when the YEATS domain of Taf14 is mutated so it cannot bind acetyl-H3.

2015-09-09 | E-GEOD-71768 | biostudies-arrayexpress

Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response.

Project description:The YEATS domain, found in a number of chromatin-associated proteins, has recently been shown to have the capacity to bind histone lysine acetylation. Here, we show that the YEATS domain of Taf14, a member of key transcriptional and chromatin-modifying complexes in yeast, is a selective reader of histone H3 Lys9 acetylation (H3K9ac). Structural analysis reveals that acetylated Lys9 is sandwiched in an aromatic cage formed by F62 and W81. Disruption of this binding in cells impairs gene transcription and the DNA damage response. Our findings establish a highly conserved acetyllysine reader function for the YEATS domain protein family and highlight the significance of this interaction for Taf14.

| S-EPMC4573853 | biostudies-literature

Ssn6 Overexpression

Project description:We have performed a genome wide expression profile study of the essential transcriptional co-repressor protein Ssn6 in Schizosaccharomyces pombe. Ssn6 affected targets were identified by over expression of Ssn6 protein in a WT strain. A WT strain holding a plasmid expressing Ssn6 (pDUAL-Ssn6) was compared against the expression in a WT with the empty plasmid (pDUAL-EMPTY) strain. Keywords: Overexpression/WT

2006-11-15 | GSE4502 | GEO

Transcription profiling of Pichia pastoris strain GS115 transformed with the empty vector pGAPHIS or consitutively overproducing the activated form of S. cerevisiae Hac1

Project description:Strain GS115 transformed with the empty vector pGAPHIS (a histidine prototrophic isogenic strain of GS115) was compared to Strain GS115 HAC1, constitutively overproducing the activated form of S. cerevisiae Hac1

2008-09-23 | E-MEXP-1616 | biostudies-arrayexpress

Association of reading disabilities with regions marked by acetylated H3 histones in KIAA0319.

Project description:Reading disabilities (RDs) have been associated with chromosome 6p with recent studies pointing to two genes, DCDC2 and KIAA0319. In this study, markers across the 6p region were tested for association with RD. Our strongest findings were for association with markers in KIAA0319, although with the opposite alleles compared with a previous study. We also found association with markers in VMP, but not with DCDC2. Current evidence indicates that differential regulation of KIAA0319 and DCDC2 contributes to RD, thus we used chromatin immunoprecipitation coupled with genomic tiling arrays (ChIP-chip) to map acetylated histones, a molecular marker for regulatory elements, across a 500 kb genomic region covering the RD locus on 6p. This approach identified several regions marked by acetylated histones that mapped near associated markers, including intron 7 of DCDC2 and the 5' region of KIAA0319. The latter is located within the 70 kb region previously associated with differential expression of KIAA0319. Interestingly, five markers associated with RD in independent studies were also located within the 2.7 kb acetylated region, and six additional associated markers, including the most significant one in this study, were located within a 22 kb haplotype block that encompassed this region. Our data indicates that this putative regulatory region is a likely site of genetic variation contributing to RD in our sample, further narrowing the candidate region.

| S-EPMC5381965 | biostudies-literature

Map1p overexpression versus control cells microarrays

Project description:BY4741 cells bearing plasmid pBG1805-Map1 (MAP1 with a galactose inducible promotor) or the empty plasmid pBG1805 (=control).

2010-12-06 | GSE21850 | GEO

Project description:Agrobacterium-transformed yeast BY4741 whole genome sequencing

| PRJNA834975 | ENA

H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation.

Project description:Methylation of histone H3 lysine 4 (H3K4me) is an evolutionarily conserved modification whose role in the regulation of gene expression has been extensively studied. In contrast, the function of H3K4 acetylation (H3K4ac) has received little attention because of a lack of tools to separate its function from that of H3K4me. Here we show that, in addition to being methylated, H3K4 is also acetylated in budding yeast. Genetic studies reveal that the histone acetyltransferases (HATs) Gcn5 and Rtt109 contribute to H3K4 acetylation in vivo. Whilst removal of H3K4ac from euchromatin mainly requires the histone deacetylase (HDAC) Hst1, Sir2 is needed for H3K4 deacetylation in heterochomatin. Using genome-wide chromatin immunoprecipitation (ChIP), we show that H3K4ac is enriched at promoters of actively transcribed genes and located just upstream of H3K4 tri-methylation (H3K4me3), a pattern that has been conserved in human cells. We find that the Set1-containing complex (COMPASS), which promotes H3K4me2 and -me3, also serves to limit the abundance of H3K4ac at gene promoters. In addition, we identify a group of genes that have high levels of H3K4ac in their promoters and are inadequately expressed in H3-K4R, but not in set1? mutant strains, suggesting that H3K4ac plays a positive role in transcription. Our results reveal a novel regulatory feature of promoter-proximal chromatin, involving mutually exclusive histone modifications of the same histone residue (H3K4ac and H3K4me).

| S-EPMC3069113 | biostudies-literature

Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14.

Project description:The coordination of chromatin remodeling with chromatin modification is a central topic in gene regulation. The yeast chromatin remodeling complex RSC bears multiple bromodomains, motifs for acetyl-lysine and histone tail interaction. Here, we identify and characterize Rsc4 and show that it bears tandem essential bromodomains. Conditional rsc4 bromodomain mutations were isolated, and were lethal in combination with gcn5Delta, whereas combinations with esa1 grew well. Replacements involving Lys14 of histone H3 (the main target of Gcn5), but not other H3 or H4 lysine residues, also conferred severe growth defects to rsc4 mutant strains. Importantly, wild-type Rsc4 bound an H3 tail peptide acetylated at Lys14, whereas a bromodomain mutant derivative did not. Loss of particular histone deacetylases suppressed rsc4 bromodomain mutations, suggesting that Rsc4 promotes gene activation. Furthermore, rsc4 mutants displayed defects in the activation of genes involved in nicotinic acid biosynthesis, cell wall integrity, and other pathways. Taken together, Rsc4 bears essential tandem bromodomains that rely on H3 Lys14 acetylation to assist RSC complex for gene activation.

| S-EPMC381415 | biostudies-literature

IDH1 and Glioma knockdown idh1

Project description:This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies (ST000199) This specific experiment is a pilot study to compare the metabolism of cells transformed using empty vector against cells transformed with vector carrying short hairpin RNA (shRNA) targeted to silence isocitrate dehydrogenase-1 (IDH1) gene.

2014-06-11 | ST000276 | MetabolomicsWorkbench

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