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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide map of HBO1 in cancer derived human cell line

ABSTRACT: We used ChIP-seq technology in order to map chromatin binding sites of the HBO1 MYST complex in the RKO cell line. We obtained a significant enrichment of the HBO1 signal right after TSS regions of genes and also In the proximal promoter region, with no signal on TSS. This enrichment also correlates with gene expression level. HBO1 signal in RKO cell line.

ORGANISM(S): Homo sapiens

SUBMITTER: Eric Paquet

PROVIDER: E-GEOD-33007 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Conserved molecular interactions within the HBO1 acetyltransferase complexes regulate cell proliferation.

Avvakumov Nikita N Lalonde Marie-Eve ME Saksouk Nehmé N Paquet Eric E Glass Karen C KC Landry Anne-Julie AJ Doyon Yannick Y Cayrou Christelle C Robitaille Geneviève A GA Richard Darren E DE Yang Xiang-Jiao XJ Kutateladze Tatiana G TG Côté Jacques J

Molecular and cellular biology 20111205 3

Acetyltransferase complexes of the MYST family with distinct substrate specificities and functions maintain a conserved association with different ING tumor suppressor proteins. ING complexes containing the HBO1 acetylase are a major source of histone H3 and H4 acetylation in vivo and play critical roles in gene regulation and DNA replication. Here, our molecular dissection of HBO1/ING complexes unravels the protein domains required for their assembly and function. Multiple PHD finger domains pr ...[more]

PMID: 22144582

Similar Datasets

Genome-wide map of HBO1 in cancer derived human cell line

Project description:We used ChIP-seq technology in order to map chromatin binding sites of the HBO1 MYST complex in the RKO cell line. We obtained a significant enrichment of the HBO1 signal right after TSS regions of genes and also In the proximal promoter region, with no signal on TSS. This enrichment also correlates with gene expression level.

2012-03-15 | GSE33007 | GEO

ChIP-seq of MYST acetyltransferases

Project description:Histone acetyltransferases (HAT) assemble into multisubunit complexes in order to target distinct lysine residues on nucleosomal histones. Here, we characterize native HAT complexes assembled by the BRPF-family of scaffold proteins. Their PHD-ZnKnuckle-PHD domain is essential for binding chromatin and restricted to unmethylated H3K4, a specificity that is reversed by the associated ING subunit. Native BRPF1 complexes can contain either MOZ/MORF or HBO1 as catalytic acetyltransferase subunit. Interestingly, while the previously reported HBO1 complexes containing JADE scaffold proteins target histone H4, the HBO1-BRPF1 complex acetylates only H3 in chromatin. We mapped a small region at the N-terminus of scaffold proteins responsible for histone tail selection on chromatin. Thus, alternate choice of subunits associated with HBO1 can switch its specificity from H4 to H3 tails, highlighting a crucial new role of associated subunits within HAT complexes, previously thought to be intrinsic to the catalytic subunit. Genome-wide mapping of MYST acetyltransferases subunits and H3K4me3 histone mark in RKO cells.

2013-10-09 | E-GEOD-47190 | biostudies-arrayexpress

ChIP-seq of MYST acetyltransferases in RKO cell line

Project description:Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells. Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells.

2016-02-05 | E-GEOD-63722 | biostudies-arrayexpress

Conserved molecular interactions within MYST-ING acetyltransferase complexes that regulate cell proliferation

Project description:This SuperSeries is composed of the following subset Series: GSE33007: Genome-wide map of HBO1 in cancer derived human cell line GSE33220: Effects of the JADE-HBO1 complex on gene expression Refer to individual Series

2012-03-15 | E-GEOD-33221 | biostudies-arrayexpress

Jade1 ChIP-chip on ENCODE Tiling array

Project description:Several MYST-family histone acetyltransferase (HAT) enzymes associate with specific ING tumor suppressor proteins. ING complexes containing the HBO1 HAT protein are the major source of histone H4 acetylation in vivo and have been shown to play critical roles in gene regulation and DNA replication. Here, we present a molecular dissection of HBO1/ING HAT complexes that unravels the protein domains required for complex assembly and function. A distinctive characteristic of ING HAT complexes is the presence of multiple PHD finger domains in different subunits. Biochemical and functional analysis of these domains indicate that they interact with histone H3 N-terminal tail region but with different specificity towards the methylation status of lysine 4. They play essential and intricate role in regulating binding to chromatin and substrate specificity. This is achieved in part through expression of subunit isoforms controlling which PHD fingers are present in the complex. Importantly, localization analysis on the human genome indicate that HBO1 complexes are enriched throughout the coding region of genes, supporting a role in transcription elongation. These results also underline the importance and versatility of PHD finger domains in regulating chromatin association and trans-histone acetylation specificity within a single protein complex. ChIP-chip of FLAG-JADE1 +/- doxorubicin treatment in Hela cells

2010-05-14 | E-GEOD-14309 | biostudies-arrayexpress

ChIP-seq of MYST acetyltransferases in RKO cell line

Project description:Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells.

2016-02-05 | GSE63722 | GEO

NUP98-HBO1-induced gene signature in human CB CD34+ cells

Project description:Chronic myelomonocytic leukemia (CMML) is an incurable hematopoietic stem cell malignancy. We identified a novel NUP98-HBO1 fusion from a patient with CMML. HBO1, a histone acetyltransferase (HAT) which belongs to the MYST family, is the first NUP98 fusion partner encodes HAT. To determine the effect of the NUP98-HBO1 fusion on downstream target gene regulation, we performed gene expression array analysis of NUP98-HBO1-transduced human cord blood (CB) CD34+ cells.

2019-03-13 | GSE112909 | GEO

Genome-wide maps of chromatin state in early erythroid precursors versus later, more differentiated erythroblasts.

Project description:Here we globally analyzed mRNA and epigenetic changes in both early erythroid progenitors and late erythroblasts. Concomitant with gene induction there was an increase in RNA Pol II binding and activation marks near the transcriptional start site (TSS) and the elongation mark H3K79me2 (but not H3K36me3),both near the TSS and along the full gene length. In contrast, most repressed genes became depleted of elongation marks. We also found that relative changes in histone modification levels--in particular, H3K79me2 and H4K16ac-- most predictive of gene expression patterns. Our data suggests that in terminal erythropoiesis both transcriptional initiation and elongation contribute to induction of erythroid genes; in contrast, gene repression is mainly mediated by inhibition of Pol II elongation. Our data provides a comprehensive map of the epigenome during terminal erythroid differentiation. Examination of 7 different histone modifications and Pol II binding in 2 cell types.

2011-08-23 | E-GEOD-27893 | biostudies-arrayexpress

POLIISER5 and POLIISER2 ChIP-Seq in mutant RNAi LID Drosophila Melanogaster

Project description:LID is a histone demethylase acting on H3K4me3, a mark related to transcription and found near the transcription start sites (TSS) of the genes. We analyzed where POLIISER5 and POLIISER2 are localized in LID RNAi mutants. 1 sample for POLIISER5 with an input control, and 1 sample for POLIISER2 with an input control.

2012-09-04 | E-GEOD-40599 | biostudies-arrayexpress

Genome-wide ChIP sequencing of NUCKS

Project description:NUCKS has a DNA binding domain at C-terminal region. We found that NUCKS has important roles in regulating glucose homeostasis. To get an unbiased handle on the plausible mechanism(s) of NUCKS action, we performed a genome-wide Chromatin Immunoprecipitation (ChIP)-sequencing for NUCKS in primary hepatocytes. We successfully mapped 25mln reads to the mm9 genome and detected NUCKS binding at 10203 sites, 60% of which were located in the proximity of a Transcription Start Sites (TSS). The peaks of NUCKS occupancy were often broad with some around 1Kb, suggesting that multiple NUCKS molecules could bind cooperatively to the same genomic loci. This study provides information of NUCKS binding sites in Mus musculus genome. Examination of NUCKS binding in mouse primary hepatocytes by Chromatin immunoprecipitation followed by deep sequencing.

2014-06-12 | E-GEOD-58100 | biostudies-arrayexpress

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