Gene expression regulation by the Chromodomain Helicase DNA-binding protein 9 (CHD9) chromatin remodeler is dispensable for murine development

Purpose: Chromodomain helicase DNA-binding (CHD) chromatin remodelers regulate transcription and DNA repair. Chd1-8 show upon germline disruption pronounced, often developmental lethal phenotypes. Here we show that contrary to Chd1-8 disruption, Chd9–/– animals are viable, fertile and display no developmental defects or disease predisposition. Germline deletion of Chd9 only moderately affects gene expression in tissues and derived cells, whereas acute depletion in human cancer cells elicits more robust changes suggesting that CHD9 is a highly context-dependent chromatin regulator that, surprisingly, is dispensable for mouse development. Methods: The role of CHD9 in gene expression regulation during murine development and lymphomagenesis, as well as in human cancer cell lines was explored by RNA-seq analysis. Embryonic (E15) brain and liver were isolated from littermates and snap-frozen. Mouse embryonic fibroblasts (MEFs) were isolated from the Chd9+/-x Chd9+/- cross at day 13.5 post coitum and cultured using standard methods. Three wild-type control and four Chd9 knockout derived fibroblast lines were used. Embryonic stem cells (ESC) were derived from the Chd9+/-x Chd9+/- cross as described before (Huijbers IJ, et al, 2015). Three wild-type control and three Chd9 knockout derived ESC lines were used. For all the experiments early passage MEFs and ESCs were used. Enlarged lymph nodes from three moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen. Human SNB19 and K562 cells bearing doxycycline-inducible short hairpin RNAs (shRNA) targeting CHD9 were induced with 1ug/ml doxycycline for 48 hours, harvested, and pellet was snap-frozen. Total RNA was extracted, prepared using TruSeq protocol, and standard sample preparation protocols and RNA-seq was performed on a Hiseq2000 machine (Illumina) at the NKI Genomics Core Facility. Results: Sequencing data were aligned to mm9 (MEFs, ESCs), mm10 (E15 brain and liver; Emu-Myc lymphomas), hg37 (K562 and SNB19 cells) using TopHat (v2.1.0 using bowtie 1.1.0). and number of reads per gene were measured with HTSeq count (v0.5.3). Statistical analysis of the differential expression of genes were performed using DESeq2. Results were considered statistically significant at an adjusted p?