Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells [Atad2_ES_ChIPseq2_MG2]

Although the conserved AAA ATPase – bromodomain factor, ATAD2, has been described as a transcriptional co-activator upregulated in many cancers, its function remains poorly understood. Here, using a combination of ChIP-seq, ChIP-proteomics and RNA-seq experiments in embryonic stem cells, we found that Atad2 is an abundant nucleosome-bound protein present on active genes, associated with chromatin remodelling, DNA replication and DNA repair factors. A structural analysis of its bromodomain and subsequent investigations demonstrate that histone acetylation guides ATAD2 to chromatin, resulting in an overall increase of chromatin accessibility and histone dynamics, which is required for the proper activity of the highly expressed gene fraction of the genome. While in exponentially growing cells Atad2 appears dispensable for cell growth, in differentiating ES cells, Atad2 becomes critical in sustaining specific gene expression programs, controlling proliferation and differentiation. Altogether, this work defines Atad2’s function as a facilitator of general chromatin-templated activities such as transcription. Chromatin immunoprecipitation of Atad2-TAP tag following tandem affinity purification (TAP) protocol in 46C ES wild type cells (control) and in Atad2-TAP tag expressing ES cells. Cross-linked sheared chromatin fragments underwent two rounds of ChIP. After the first ChIP, using an anti-Flag antibody, Atad2-bound fragments were released with an excess of Flag peptides and were then used for a second round of ChIP using an anti-Ha antibody.