Abstract Chromodomain helicase DNA-binding (CHD) chromatin remodelers regulate transcription and DNA repair. They govern cell-fate decisions during embryonic development and are often deregulated in human pathologies. 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. Introduction Normal organismal development requires accurate transcriptional control. This is achieved by myriad of transcription factors and chromatin regulators that act in concert to control expression of the right genes at the right time. Chromodomain helicase DNA-binding enzymes belong to the superfamily of chromatin remodelers that control nucleosomal structure and phasing to regulate gene expression and DNA repair. They contain hallmark amino-terminal double chromodomains and central SNF2 helicase-like ATPase domains, allowing nucleosome recognition and remodeling [[38]1]. Different accessory domains facilitate these actions [[39]1]. The CHD enzymes have limited DNA-specificity and rely on specific histone modifications and transcription factors for recruitment to target loci [[40]2]. Based on their constituent domains, they are classified into three subfamilies: subfamily I (CHD1 and CHD2), subfamily II (CHD3, CHD4 and CHD5) and subfamily III (CHD6, CHD7, CHD8 and CHD9). In addition to the hallmark domains, members of the subfamily III contain SANT–like and tandem brahma kismet domains (BRK), implicated in DNA [[41]3] and CTCF [[42]4] binding, respectively. These enzymes are homologs of Drosophila Kismet (KIS-L), a Trithorax family protein that counteracts gene repression by Polycomb group proteins during development [[43]5]. It regulates early stages of RNA Polymerase II elongation [[44]6] and is involved in key developmental signaling pathways [[45]7]. Importantly, kismet loss-of-function causes specific segmentation defects and homeotic transformation [[46]8] resulting in lethality. Most of these functions have been conserved in the mammalian homologs. Subfamily III members are found in both promoter and enhancer regions, regulating different stages of RNA Polymerase I and II transcription [[47]2,[48]9]. Subfamily III members have limited DNA affinity [[49]10], and their recruitment to target loci is mediated through interaction with methylated histone tails [[50]9,[51]11] and transcription factors [[52]2]. Despite their high sequence similarity, these enzymes display different substrate specificities and remodeling activities in vitro [[53]9,[54]10]. CHD enzymes appear to have non-redundant functions in murine embryonic development [[55]12]. Chd7 knockout animals survive up to embryonic day 10.5 (E10.5) [[56]13], whereas homozygous deletion of Chd8 is embryonic lethal at E5.5–7.5 due to widespread p53-mediated apoptosis [[57]14]. These enzymes act in a dose-dependent manner and mice heterozygous for Chd7 or Chd8 faithfully recapitulate features of human CHARGE syndrome [[58]15] and autism spectrum disorders (ASD) [[59]16], respectively. Subfamily III enzymes are often deregulated or mutated in human cancers. In aggressive breast cancers, CHD7 amplification and overexpression correlates with poor prognosis. In contrast, heterozygous loss of CHD9 is observed in 55% of breast cancer patients [[60]17]. Low expression is also associated with poor prognosis in colorectal cancer [[61]18]. In addition, a number of studies reported frequent mutations in human cancers: CHD6 in bladder cancer [[62]19], CHD7 in medulloblastoma [[63]20,[64]21], whereas CHD8 harbors mutations in many cancer types [[65]22]. CHD9 (also known as PRIC320 and CReMM) is the least characterized member of the subfamily. It was identified as transcriptional regulator in rat liver [[66]23] and mesenchymal stem cells [[67]24]. Biochemical studies revealed CHD9 interaction with H3K4me2/3, H3K9me2/3 and H3K27me3 modified histones and illustrated its capacity to reposition nucleosomes in an ATP-dependent manner [[68]9]. CHD9 associates with nuclear receptors and contributes to glucocorticoid receptor–mediated gene expression regulation [[69]23,[70]25] and might be involved in loosening the chromatin structure in mouse oocytes [[71]26]. Recent landmark study in mouse ES cells revealed that CHD9 chromatin occupancy correlates with gene expression levels and the presence of the H3K4me3 mark at a subset of loci [[72]27]. While these studies address biochemical and functional properties of CHD9, the in vivo functions of CHD9 have remained unresolved. Here, we describe the first Chd9 knockout mice and study its contribution to development and lymphomagenesis, a tumor subtype in which insertional mutagenesis experiments suggested a potential role of CHD9. Results CHD9 is dispensable for murine development and knockout does not display overt phenotypic aberrations Chd9 is ubiquitously expressed in murine tissues with the highest levels observed in brain [[73]23]. Previous studies implicated CHD9 in stem cell biology [[74]28], osteogenesis [[75]29] and steroid-hormone signaling [[76]23,[77]25], whereas insertional mutagenesis screens suggested an oncogenic driver role in murine [[78]30,[79]31] and human lymphomagenesis [[80]32]. To explore the contribution of CHD9 to development and tumorigenesis, we generated Chd9 knockout mice. The vast majority of Chd family knockouts are embryonic lethal [[81]12,[82]33,[83]34]. The reported allele targeting strategies for Chd1-8 employed gene-trap reporter constructs, the deletion of critical exons or the removal of functional domains ([[84]12] and references