The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development [ATAC-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. Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed in murine pro-B and pre-B lymphocytes. 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+) and pre-B cells (IgM-,CD19+,B220+, CD43-). Fresh whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina). DNA libraries were prepared as described in Buenrostro et al., 2015 and were sequenced using HiSeqX 150+150PE platform from Magrogene Inc. Two duplicates per condition were processed.