Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

76 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeted chromatin profiling reveals novel enhancers in Ig heavy and light chain loci.

ABSTRACT: Chip-chip from pro-B cells from Rag1KO mice for H3K27ac and RNA Pol II Identification of novel enhancers from Ig heavy and light chain loci Rag1KO pro-B epigenetic landscape at Ig heavy and light chain loci

ORGANISM(S): Mus musculus

SUBMITTER: Eugene Oltz

PROVIDER: E-GEOD-53766 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci.

Predeus Alexander V AV Gopalakrishnan Suhasni S Huang Yue Y Tang Jun J Feeney Ann J AJ Oltz Eugene M EM Artyomov Maxim N MN

Journal of immunology (Baltimore, Md. : 1950) 20131218 3

The assembly and expression of mouse Ag receptor genes are controlled by a collection of cis-acting regulatory elements, including transcriptional promoters and enhancers. Although many powerful enhancers have been identified for Ig (Ig) and TCR (Tcr) loci, it remained unclear whether additional regulatory elements remain undiscovered. In this study, we use chromatin profiling of pro-B cells to define 38 epigenetic states in mouse Ag receptor loci, each of which reflects a distinct regulatory po ...[more]

PMID: 24353267

Similar Datasets

A Unifying Model for Molecular Determinants of the Pre-selection VÎ² Repertoire [ChIP-chip]

Project description:Chip-chip from pro-T(DN) cells from Rag1KO mice for H3K27ac, P300 and FAIRE The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified VÎ² usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DÎ²JÎ² targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of VÎ²usage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DÎ²JÎ²clusters. Rag1KO DN epigenetic landscape at Tcrb

2013-08-14 | E-GEOD-42851 | biostudies-arrayexpress

Chip-chip from HCT116 cells with p400 antibody

Project description:The chromatin remodeller p400 has oncogenic properties that promote early steps of colon cancer. Chromatin immunoprecipitation (ChIP) of p400 together with chromatin profiling by ChIP-on-chip analysis demonstrated that p400 directly binds the chromatin at promoters of p400 target genes. Study of p400 binding on promoters of HCT116 cells

2013-11-22 | E-GEOD-45614 | biostudies-arrayexpress

p400 binding and Tip60/p400 gene expression regulation in HCT116 cells

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

2013-11-22 | E-GEOD-45616 | biostudies-arrayexpress

Chip-chip from WI-38 human fibroblast with Argonaute antibody

Project description:In humans, there are four Ago proteins (Ago1–4) and AGO1- and 2 were previously implicated in TGS induced by exogenous siRNAs and microRNAs (miRs) directed against gene promoter transcripts via promotion of changes in histone covalent modifications and DNA methylation. Not-with-standing, many mechanistic details of this process remain poorly defined in human cells, and very little is known about the identity of possible endogenous signals, which may drive this process in human cells. Given the evolutionary conserved role of siRNAs and AGO proteins in TGS and heterochromatin formation, we set out to analyse their possible involvement in senesence-associated repression of E2F target genes. To determine, in an unbiased manner, which genes might be under the control of AGO proteins we perfomed genome-wide promoter profiling in senescent and presenescent control WI38 primary fibroblasts applying “ChIP-on-chip” technology using 4 an anti-pan-AGO antibody. DNA from matched genomic inputs and chromatin immunoprecipitation (ChIP) samples were purified, amplified by PCR, and labeled either with Cy3 or Cy5 fluorophores. The labeled DNA from input and ChIP fractions were then combined and hybridised to human promoter arrays containing ~59,000 promoters. determination of AGO binding sites in WI-38 pre-senescent human fibroblast and in senescent human fibroblast

2011-11-30 | E-GEOD-33998 | biostudies-arrayexpress

Chip-chip from Hepatocellular carcinoma (HCC) specimens with H3K4me3

Project description:Epigenetic changes commonly occur in hepatocellular carcinoma (HCC) and are associated with aberrant gene expression. Recently, we demonstrated the pivotal role of abnormal H3K4me3 methylation, which is catalyzed by the menin/MLL, a TrxG family, in HCC development. Meanwhile, there is clear evidence that increasing global levels of H3K27me3 are activated in human primary HCC. To further elucidate the functional relatedness of the active H3K4me3 and repressive H3K27me3 histone remodeling in HCC, we performed H3K4me3 and H3K27me3 ChIP-on-chip screen using three HCC specimens and their adjacent tissues. Comparison of ChIP-on-chip results between tumor(C) and adjacent tissues(N) from three HCC specimens with H3K4me3

2013-11-08 | E-GEOD-52190 | biostudies-arrayexpress

Chip-chip from HepG2 cells with EZH2, SUZ12 and H3K27me3

Project description:Polycomb group (PcG) proteins including EZH2, SUZ12 and so on, which specifically catalyze trimethylation of histone 3 lysine 27 (H3K27me3), and methylated H3K27 can be recognized by other specific binding proteins to compress chromatin structure, leading to the transcriptional repression of the target genes. To completely understand the epigenetic profile and molecular network of PcG in HCC, we performed ChIP-on-chip screens with EZH2, SUZ12 and H3K27me3 antibodies in HepG2 cells. Comparison of ChIP-on-chip results from EZH2, SUZ12 and H3K27me3.

2013-11-13 | E-GEOD-52300 | biostudies-arrayexpress

Chip-chip from Hepatocellular carcinoma (HCC) specimens with H3K27me3

Project description:Epigenetic changes commonly occur in hepatocellular carcinoma (HCC) and are associated with aberrant gene expression. Recently, we demonstrated the pivotal role of abnormal H3K4me3 methylation, which is catalyzed by the menin/MLL, a TrxG family, in HCC development. Meanwhile, there is clear evidence that increasing global levels of H3K27me3 are activated in human primary HCC. To further elucidate the functional relatedness of the repressive H3K27me3 and active H3K4me3 histone remodeling in HCC, we performed H3K27me3 and H3K4me3 ChIP-on-chip screen using three HCC specimens and their adjacent tissues. Comparison of ChIP-on-chip results between tumor(C) and adjacent tissues(N) from three HCC specimens with H3K27me3

2013-11-13 | E-GEOD-52301 | biostudies-arrayexpress

A Unifying Model for Molecular Determinants of the Pre-selection Vb Repertoire

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

2013-08-14 | E-GEOD-49234 | biostudies-arrayexpress

Chip-chip from pro-B cells with H3K4me3, H3K4me2 and H3K9ac

Project description:The transcription factor Pax5 represses B-lineage-inappropriate genes and activates B-cell-specific genes in B-lymphocytes. Here we have identified 170 novel Pax5-activated genes. Conditional mutagenesis demonstrated that the Pax5-regulated genes require continuous Pax5 activity for normal expression in pro-B and mature B cells. Expression of half of the Pax5-activated genes is either absent or significantly reduced upon Pax5 loss in plasma cells. Direct Pax5 target genes were identified based on their protein synthesis-independent activation by a Pax5-estrogen receptor fusion protein. Chromatin immunoprecipitation (ChIP) of Pax5 together with chromatin profiling by ChIP-on-chip analysis demonstrated that Pax5 directly activates the chromatin at promoters or putative enhancers of Pax5 target genes. The novel Pax5-activated genes code for key regulatory and structural proteins involved in B cell signaling, adhesion, migration, antigen presentation and germinal center B cell formation, thus revealing a complex regulatory network, which is activated by Pax5 to control B cell development and function. Keywords: Chip-chip, cell type comparison comparison of Pax5-/-Rag2-/- vs Rag2-/- pro-B cells

2010-05-20 | E-GEOD-15145 | biostudies-arrayexpress

Chip-chip from pro-B cells with H3K4me3, H3K4me2 and H3K9ac

2007-08-23 | E-GEOD-8472 | biostudies-arrayexpress