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Genome wide analysis of gene expression in LPS stimulated splenic B cell.

ABSTRACT: Analysis of class switch recombination, maturation or differenciation of B cells at gene expression levels. The hypothesis tested in the present study was that TLR signaling in B cells plays an pivotal role for class switch, maturation and differenciation.

ORGANISM(S): Mus musculus

PROVIDER: GSE57837 | GEO | 2014/08/14

SECONDARY ACCESSION(S): PRJNA248214

REPOSITORIES: GEO

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Genome wide analysis of gene expression in LPS stimulated splenic B cell.

Project description:Analysis of class switch recombination, maturation or differenciation of B cells at gene expression levels. The hypothesis tested in the present study was that TLR signaling in B cells plays an pivotal role for class switch, maturation and differenciation. Total RNA obtained from cultured splenic B cells. Gene expression compared between control and cKO B cells.

2014-08-14 | E-GEOD-57837 | biostudies-arrayexpress

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Project description:Programmed mutagenesis of the immunoglobulin locus of B-lymphocytes during class switch recombination and somatic hypermutation requires RNA polymerase II (RNA polII) transcription complex dependent targeting of the DNA mutator, Activation Induced cytidine Deaminase (AID). AID deaminates cytidine residues on substrate sequences in the immunoglobulin (Ig) locus via a transcription-dependent mechanism and this activity is stimulated by the RNA polII stalling co-factor Spt5 and the eleven-subunit cellular non-coding RNA 3’-5’ exonucleolytic processing complex, RNA exosome. The mechanism by which the RNA exosome recognizes immunoglobulin locus RNA substrates to stimulate AID DNA deamination activity on its in vivo substrate sequences is an important question. Here we report that E3-ubiquitin ligase Nedd4 destabilizes AID-associated RNA polII by a ubiquitination event leading to generation of 3’-end free RNA exosome RNA substrates at the Ig locus and other AID target sequences genome-wide. Using highthrough-out RNA sequencing technology, we find that lack of Nedd4 activity in B cells leads to accumulation of RNA exosome substrates at AID target genes. Moreover, we find that Nedd4-deficient B cells are inefficient in undergoing class switch recombination. Taken together, our study links non-coding RNA processing following RNA polymerase II pausing with regulation of the mutator AID protein. Our study also identifies Nedd4 as a regulator of non-coding RNA that are generated by stalled RNA polII genome-wide. Splenic B cells from Nedd4+/+ and Nedd4-/- B cells fetal liver chimeric mice were were stimulated in culture for IgG1 CSR. Total RNA was isolated and evaluated with whole genome RNA-seq

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