Abstract
The transcriptional functions of the class I histone deacetylases (HDACs) HDAC1 and HDAC2 are mainly viewed as both repressive and redundant based on murine knockout studies, but they may have additional independent roles and their physiological functions in human cells are not as clearly defined. To address the individual epigenomic functions of HDAC2, here we utilized CRISPR-Cas9 to disrupt HDAC2 in human cells. We find that while HDAC2 null cells exhibited signs of cross-regulation between HDAC1 and HDAC2, specific epigenomic phenotypes were still apparent using RNA-seq and ChIP assays. We identified specific targets of HDAC2 repression, and defined a novel class of genes that are actively expressed in a partially HDAC2-dependent manner. While HDAC2 was required for the recruitment of HDAC1 to repressed HDAC2-gene targets, HDAC2 was dispensable for HDAC1 binding to HDAC2-activated targets, supporting the notion of distinct classes of targets. Both active and repressed classes of gene targets demonstrated enhanced histone acetylation and methylation in HDAC2-null cells. Binding of the HDAC1/2-associated SIN3A corepressor was altered at most HDAC2-targets, but without a clear pattern. Overall, our study defines two classes of HDAC2 targets in human cells, with a dependence of HDAC1 on HDAC2 at one class of targets, and distinguishes unique functions for HDAC2.
Highlights
Epigenetic regulation of gene expression is mediated by chromatin modifying complexes that orchestrate transcriptional activation or repression
Net histone acetylation within chromatin regions is mediated by the interplay of histone acetyl transferases (HATs), which mediate the acetylation of lysines on histones to generally promote a transcriptionally active chromatin state, and the histone deacetylases (HDACs), which catalyze the removal of acetyl groups that is largely thought to induce a more repressive
CRISPR-Cas9 targeting of HDAC2 generates clonal lines that have disrupted HDAC2, and altered HDAC3, but not HDAC1 protein levels
Summary
Epigenetic regulation of gene expression is mediated by chromatin modifying complexes that orchestrate transcriptional activation or repression. Lacking known target specificity themselves, HDAC1 and HDAC2 together function as the catalytic core of three major co-repressor complexes: SIN3A/B, NuRD (nucleosome remodeling and deacetylation), and CoREST (co-repressor for element-1 silencing transcription factor) [3,4,5,6]. These HDAC1 and HDAC2-containing co-repressor complexes are recruited by specific transcription factors through DNA recognition motifs that bring HDACs to specific nucleosomal domains where they can act on histone substrates [7]. One of the best examples of this HDAC-HAT dynamic is the antagonism between MYC-MAX dimer recruitment of HATs to many of the same Ebox containing regions targeted by MXD-MAX repressive dimers that recruit SIN3-HDAC1-HDAC2 complexes [8]
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