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Transcriptome of HEK293 cells stably knockdown for the BAHD1 gene with a shRNA

ABSTRACT: Comparison of gene expression profile of HEK293 cells stably expressing a shRNA control (SilX-CT) or a shRNA against BAHD1 (SilX-BAHD1) We used microarrays to identify the repertoire of genes differentially expressed upon knockdown of the chromatin repressor BAHD1 in human HEK293 cells.

ORGANISM(S): Homo sapiens

SUBMITTER: Emanuele Libertini

PROVIDER: E-GEOD-53284 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome.

Libertini Emanuele E Lebreton Alice A Lakisic Goran G Dillies Marie-Agnès MA Beck Stephan S Coppée Jean-Yves JY Cossart Pascale P Bierne Hélène H

Frontiers in genetics 20151201

BAH domain-containing protein 1 (BAHD1) is involved in heterochromatin formation and gene repression in human cells. BAHD1 also localizes to the inactive X chromosome (Xi), but the functional significance of this targeting is unknown. So far, research on this protein has been hampered by its low endogenous abundance and its role in epigenetic regulation remains poorly explored. In this work, we used whole-genome bisulfite sequencing (BS-seq) to compare the DNA methylation profile of HEK293 cells ...[more]

PMID: 26648976

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Transcriptome of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

Project description:Comparison of gene expression profile of HEK293-CT cells and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1) We used micrarrays to identify the repertoire of genes differentially expressed upon overexpression of the chromatin repressor BAHD1 in HEK293 cells.

2015-12-11 | E-GEOD-51863 | biostudies-arrayexpress

Methylated DNA immunoprecipitation-sequencing of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

Project description:we report the partial methylome (CG-rich regions) of HEK293 cells and HEK293 cells over-expressing the BAHD1 gene (HEK-BAHD1) We used MEDIP-seq to identify genomic regions differentially methylated upon overexpression of the chromatin repressor BAHD1 in HEK293 cells.

2015-12-11 | E-GEOD-51864 | biostudies-arrayexpress

whole-genome bisulfite sequencing (BS-seq) of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

Project description:Comparison of methylome of HEK293-CT cells and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1) We used BS-seq to identify genomic regions differentially methylated upon overexpression of the chromatin repressor BAHD1 in HEK293 cells.

2015-12-11 | E-GEOD-51867 | biostudies-arrayexpress

Transcriptome expression profile of primary mouse embryonic fibroblasts (MEFs) from BAHD1+/+ (WT) and BAHD1-/- (KO) mice

Project description:Comparisons of gene expression profiles of BAHD1-KO MEFs to those of wild-type MEFs (sampled at embryonic day E13.5). We used DNA microarrays to identify the repertoire of genes differentially expressed by ablation of the BAHD1 gene in mouse embryonic fibroblasts.

2016-03-15 | E-GEOD-73816 | biostudies-arrayexpress

HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-11 | E-GEOD-51868 | biostudies-arrayexpress

Chromatin immunoprecipitation-sequencing of HEK293 cells (HEK293-HPT-blue) and HEK293 cells stably over-expressing the BAHD1 gene (HEK293-HPT-BAHD1)

Project description:We report the genomic occupancy of the BAHD1 protein in HEK293 cells over-expressing the BAHD1 gene (HEK293-HPT-BAHD1) We used Native ChIP-seq to identify DNA regions bound to BAHD1 (native ChIP involves use of native chromatin before precipitation of immune complexes, without formaldehyde crosslinking of proteins with nucleic acids)

2015-12-11 | E-GEOD-53372 | biostudies-arrayexpress

Transcriptome expression profile of placental tissue from BAHD1+/+ (WT) and BAHD1-/- (KO) mice at embryonic day E18.5

Project description:Comparisons of placenta gene expression profiles of BAHD1-KO mice to those of wild-type littermate mice. We used DNA microarrays to identify the repertoire of genes differentially expressed by ablation of the BAHD1 gene in the placenta at embryonic day E18.5

2016-03-15 | E-GEOD-53375 | biostudies-arrayexpress

Transcriptome expression profile of embryonic liver and placenta tissue from BAHD1+/+ (WT) and BAHD1-/- (KO) mice at embryonic day E16.5

Project description:Comparisons of embryonic liver and placenta gene expression profiles of BAHD1-KO mice to those of wild-type littermate mice We used DNA microarrays to identify the repertoire of genes differentially expressed by ablation of the BAHD1 gene in embryos.

2016-03-15 | E-GEOD-53442 | biostudies-arrayexpress

Transcriptome of HEK293 cells stably knockdown for the BAHD1 gene with a shRNA

Project description:Comparison of gene expression profile of HEK293 cells stably expressing a shRNA control (SilX-CT) or a shRNA against BAHD1 (SilX-BAHD1)

2015-12-11 | GSE53284 | GEO

siRNA profiling of human HEK293 cells knocked down for BAHD1

Project description:Gene silencing via heterochromatin formation plays a major role in cell differentiation and maintenance of homeostasis. Here, we report the identification and characterization of a novel heterochromatinization factor in vertebrates, Bromo Adjacent Homology Domain-containing protein 1 (BAHD1). BAHD1 interacts with HP1, MBD1, HDAC5 and with several transcription factors. Through electron and immunofluorescence microscopy studies, we show that BAHD1 overexpression directs HP1 to specific nuclear sites and promotes formation of large heterochromatic domains, which lack acetyl histone H3 and are enriched in H3 trimethylated at lysine 27. Furthermore, ectopically expressed BAHD1 colocalizes with the heterochromatic X inactive chromosome. As highlighted by whole genome microarray analysis of BAHD1 knock down cells, BAHD1 represses several proliferation and survival genes and in particular, the insulin-like growth factor II gene (IGF2). BAHD1 specifically binds the CpG-rich P3 promoter of IGF2. This region contains DNA binding sequences for the transcription factor SP1, with which BAHD1 co-immunoprecipitates. Collectively, these findings provide evidence that BAHD1 acts as a silencer by recruiting proteins that coordinate heterochromatin assembly at specific sites in the genome. We used microarrays to identify BAHD1 gene targets. We compared the transcriptome profile of BAHD1 depleted cells with siRNA to that of cells treated with control siRNA. Experiment Overall Design: Six samples were analysed, including three biological replicates of control cells and three biological replicates of BAHD1 KD cells.

2009-08-07 | E-GEOD-16097 | biostudies-arrayexpress

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