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RNA-SEQ on resting (R) and stimulated (S) B cells from several IgH 3'RR mutant models

ABSTRACT: We evaluated by RNA-seq obveral transcripts in B cells (resting and activated for 2 days with LPS) sorted from several KO mice models devoid of portion or all the IgH 3' Regulatory Region

ORGANISM(S): Mus musculus

PROVIDER: GSE76217 | GEO | 2016/03/02

SECONDARY ACCESSION(S): PRJNA306658

REPOSITORIES: GEO

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RNA-SEQ on resting (R) and stimulated (S) B cells from several IgH 3'RR mutant models

Project description:We evaluated by RNA-seq obveral transcripts in B cells (resting and activated for 2 days with LPS) sorted from several KO mice models devoid of portion or all the IgH 3' Regulatory Region One RNA-seq point was realized per condition (resting or stimulated) and per genotype. Each point corresponds to a pool of equivalent number of B cells sorted from 4 animals

2016-03-02 | E-GEOD-76217 | biostudies-arrayexpress

HDAC inhibitors and IgH locus transcription. Mini 3'RR and IgH locus transcription

Project description:Numerous B-cell lymphomas feature translocations linking oncogenes with the IgH locus and epigenetic drugs such as histone deacetylase inhibitors (HDACi) have been approved to treat some of them. In this study we investigated IgH locus transcription in B-cell splenocytes stimulated with LPS and the HDACi SAHA. B-cell development is spatially and temporally regulated with the 3'RR enhancer of the IgH locus as a conductor. 3'RR is composed of 4 enhancer elements with a palindromic structure of great significance. We investigated the role of this palindrome with KOKI mice where the 30Kb structure of the 3'RR has been deleted of its palindromic structure.

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5C Chromatin interactions in the Igh locus in resting splenic B cells

Project description:5C Chromatin interactions in the Igh locus in resting splenic B cells

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HDAC inhibitors and IgH locus transcription. Mini 3'RR and IgH locus transcription

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5C Chromatin interactions in the Igh locus in resting splenic B cells

Project description:These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme. The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. The cells are then lysed and chromatin is digested with the Hind III restriction enzyme. The digested fragments are ligated under dilute conditions to promote intra-molecular ligation. A genome-wide interaction library of ligation products corresponding to all possible chromatin interactions is produced by this method. In 5C assays, over 12,000 potential ligation products specific to the Igh locus are detected by PCR using multiplexed primer pairs. Here we focused on the 3’ end of the Igh locus to evaluate the status of the constant region domain of the locus in LPS+IL4 activated splenic B cells. We observe that the configuration of the 3’ end of the Igh locus spanning the CH region genes assumes a developmental stage specific configuration in B lineage B cells. We find that the interaction frequency and activation state of the 3’ enhancer increases as B cells mature.

2021-11-23 | GSE183574 | GEO

Transcriptome analysis of B cell lymphomas in several c-myc Igh transgenic mice

Project description:Investigation of B cell lymphomas (IgM+ IgD+) located in various places (lung, mesenteric lymph nodes,…) of three different c-myc Igh transgenic mice. Insertion of c-myc in 5' to Emu (cr), in 5' to Cmu with Emu deletion (hv), and in Calpha (co).

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Expression data for resting and activated B and T cells

Project description:The IgH locus encodes for part of the antibody exposed by B cells and is important for the immune system. In B cells, one allele produces protein, the other must remain silenced. It was proposed that both alleles reside in different nuclear compartments and that this is important to maintain mono-allelic productivity. Here we challenge this concept. We provide detailed genome-wide contact maps, which show that IgH adopts different nuclear locations in immune versus other cells but also demonstrate that in B cells both alleles reside in the same environment. Nuclear positioning is therefore not important to maintain allelic exclusion. We did a gene expression analysis on resting (Day 0) and in vitro activated (Day 4) B and T cells in triplicate Splenic B cells and T cells were separately isolated from spleen, using magnetic activated cell sorting, and activated in vitro for 4 days

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