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

Abstract

Nucleosome placement and repositioning can direct transcription of individual genes; however, the precise interactions of these events are complex and largely unresolved at the whole-genome level. The Chromodomain-Helicase-DNA binding (CHD) Type III proteins are a subfamily of SWI2/SNF2 proteins that control nucleosome positioning and are associated with several complex human disorders, including CHARGE syndrome and autism. Type III CHDs are required for multicellular development of animals and Dictyostelium but are absent in plants and yeast. These CHDs can mediate nucleosome translocation in vitro, but their in vivo mechanism is unknown. Here, we use genome-wide analysis of nucleosome positioning and transcription profiling to investigate the in vivo relationship between nucleosome positioning and gene expression during development of wild-type (WT) Dictyostelium and mutant cells lacking ChdC, a Type III CHD protein ortholog. We demonstrate major nucleosome positional changes associated with developmental gene regulation in WT. Loss of chdC caused an increase of intragenic nucleosome spacing and misregulation of gene expression, affecting ∼50% of the genes that are repositioned during WT development. These analyses demonstrate active nucleosome repositioning during Dictyostelium multicellular development, establish an in vivo function of CHD Type III chromatin remodeling proteins in this process, and reveal the detailed relationship between nucleosome positioning and gene regulation, as cells transition between developmental states.

Nucleosome dynamics of human iPSC during the early stages of neurodevelopment

“…We found that only 2.7% of nucleosomes are highly positioned in human NPC (408,152 of a theoretical total of 15 million based on an assumption of 1 nucleosome per 200 bp). This is consistent with observations from other human and mammalian cells [1,2], but contrasts with the yeasts and Dictyostelium genomes where positioned nucleosomes occupy approximately 80% of the genome [3][4][5][6]. Using the same analysis on data generated from the human lymphoblastoid cell lines, K562 and GM12878 [7] we calculated that 2.4% and 1.6% of nucleosomes respectively were highly positioned in these cell lines ( Supp Table S1).…”

“…A recent report using an alternative method based on Histone 3 ChIP-seq also showed a nucleosome array centred on CTCF of human myeloid leukaemia cells (HL60) and altered nucleosome spacing following retinoic acid induced differentiation [25]. In Dictyostelium, loss of ChdC, a type III CHD family chromatin remodeler, changes nucleosome spacing, indicating a capacity to specifically regulate spacing within nucleosomes [5]. In mammals, CTCF has been shown to complex with CHD8, an orthologue of ChdC [26], suggesting a mechanism for nucleosome translocation at these sites.…”

Nucleosome dynamics of human iPSC during neural differentiation

“…A recent report using an alternative method based on Histone 3 ChIP‐seq also showed a nucleosome array centred on CTCF of human myeloid leukaemia cells (HL60) and altered nucleosome spacing following retinoic acid‐induced differentiation . In Dictyostelium , loss of ChdC increases nucleosome spacing, indicating a capacity to specifically regulate spacing within nucleosomes . In mammals, CTCF has been shown to complex with CHD8, an orthologue of ChdC , suggesting a mechanism for nucleosome translocation at these sites.…”

“…Nucleosome interactions within chromatin are likely to be complex but can be described by the following quantitative parameters: position , the sequence coordinates where nucleosomes occur across the cell population; occupancy , the frequency that a nucleosome is present at an individual site; and accessibility , the degree to which the presence of nucleosomes restricts access to the DNA. In organisms with small genomes, such as in the yeasts and Dictyostelium , nearly 80% of nucleosomes are positioned in the same place in the genome across the cell population, forming arrays that span gene bodies . There are distinct regions of low occupancy and increased accessibility, for example in the nucleosome‐free region (NFR) found at the transcriptional start site (TSS) of genes.…”

“…Nucleosomes at active genes appear to be more positionally organised than at inactive genes and changes in nucleosome positioning, such as the specific increase in nucleosome spacing seen in a Dictyostelium mutant lacking the CHD8 homologue, ChdC, alter gene expression. Nonetheless, even in these organisms the actual correlation between positioning and gene expression can be low; for example, only 15% of genes with altered nucleosome spacing in a chdC mutant show corresponding changes in gene expression .…”