The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development [ChIP-seq]

The establishment of proper epigenomic landscape is essential during B lymphocyte development in order to acquire a correct B cell identity at each cellular differentiation stage. We previously identified HDAC7 as a critical regulator of early B cell development. Its absence indeed led to the aberrant activation of inappropriate lineage genes, a reduction of proliferation and an increase in cell apoptosis. More recently, we have demonstrated that HDAC7 loss in infant pro-B-ALL associates with poor prognosis. Here we shed light into the HDAC7-mediated molecular mechanisms during early B cell development. HDAC7 deficiency drives not only the expression of inappropriate lineage genes, but also global chromatin de-condensation and deregulation of epigenetic regulators of DNA methylation and potential damaging elements. Specifically, HDAC7 absence induces the expression of TET2, which promotes DNA 5-hydroxymethylation and aberrant gene activation. HDAC7 deficiency also results in the uncontrolled expression of microRNAs and non-coding elements such as LINE-1 transposable elements. These findings are relevant for the mechanistic explanation of why HDAC7 is affected in multiple B-related hematological malignancies. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27ac and H3K27me3 in murine pro-B lymphocytes. Overall design: Cells were extracted from bone marrow (femur and tibia of both hind legs) of Hdac7+/- and Hdac7fl/- mice. Cells were stained and sorted as pro-B cells (IgM-,CD19+,B220+, CD43+). Pro-B lymphocytes from HDAC7 deficient and control mice were fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer. DNA sequencing libraries were prepared using the TRUESEQ ChIP kit (Illumina). Libraries were sequenced using HiSeqX 150+150PE platform from Magrogene Inc.Two duplicates per condition were processed.