Different CHD chromatin remodelers are required for expression of distinct gene sets and specific stages during development of Dictyostelium discoideum

Abstract

Control of chromatin structure is crucial for multicellular development and regulation of cell differentiation. The CHD (chromodomain-helicase-DNA binding) protein family is one of the major ATP-dependent, chromatin remodeling factors that regulate nucleosome positioning and access of transcription factors and RNA polymerase to the eukaryotic genome. There are three mammalian CHD subfamilies and their impaired functions are associated with several human diseases. Here, we identify three CHD orthologs (ChdA, ChdB and ChdC) in Dictyostelium discoideum. These CHDs are expressed throughout development, but with unique patterns. Null mutants lacking each CHD have distinct phenotypes that reflect their expression patterns and suggest functional specificity. Accordingly, using genome-wide (RNA-seq) transcriptome profiling for each null strain, we show that the different CHDs regulate distinct gene sets during both growth and development. ChdC is an apparent ortholog of the mammalian Class III CHD group that is associated with the human CHARGE syndrome, and GO analyses of aberrant gene expression in chdC nulls suggest defects in both cell-autonomous and non-autonomous signaling, which have been confirmed through analyses of chdC nulls developed in pure populations or with low levels of wild-type cells. This study provides novel insight into the broad function of CHDs in the regulation development and disease, through chromatin-mediated changes in directed gene expression.

Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression inDictyostelium

“…The RNA-seq analysis of loose-mound-stage cell differentiation extends the gene expression differences seen at the aggregation stage and largely explains the phenotypic defects of chdC nulls during multicellular differentiation (Platt et al 2013a). For example, at the loose-mound stage, >54% of genes annotated as either prespore or prestalk specific had greater than twofold reduced expression in chdC-null cells compared with the WT.…”

“…Its expression peaks at ∼8-12 h of development as cells enter the loose-mound stage, and has a major developmental role, as chdC-null cells undergo developmental arrest at this stage due to substantial misregulation (∼50%) of genes required for aggregation or cell fate organization pathways (Platt et al 2013a). The chdC-null mutants, therefore, provide a genetic probe for investigating the developmental role of nucleosome positioning and offer a paradigm for investigation of the in vivo role of CHD Type III proteins in developmental regulation.…”

“…Previously, we had shown that loss of chdC caused an extensive misexpression of genes during growth and the cAMP pulse-regulated aggregation stage of development (Platt et al 2013a). To investigate more directly the potential relationship between altered gene expression and mismodeled chromatin organization in the absence of ChdC, we made a new comparative RNA-seq analysis (Supplemental Fig.…”

“…Subtype III proteins are of particular interest as they regulate multicellular development in animals and Dictyostelium and are absent from yeasts (Marfella and Imbalzano 2007;Platt et al 2013a). Loss-of-function and haploinsufficient mutations of CHD Type III proteins are associated with abnormal multicellular development and embryonic lethality.…”

“…Upon nutrient depletion, Dictyostelium switches from a unicellular growth phase into a program of multicellular development and cell differentiation that utilizes many signaling pathway components, such as phosphotyrosine, as well as alpha-and beta-catenins, generally considered restricted to the metazoa (Kay 1997;Kim et al 1999;Grimson et al 2000;Dickinson et al 2011). We had characterized the three CHD proteins of Dictyostelium-ChdA, ChdB, and ChdC -and shown that they are required for expression of discrete subsets of genes and for distinct aspects of growth and development (Platt et al 2013a). ChdC is an ortholog of metazoan CHD Type III proteins and is absolutely required for progression through multicellular development, conceptually paralleling the congenital defects associated with human CHARGE syndrome.…”