The Drosophila melanogaster CHD1 Chromatin Remodeling Factor Modulates Global Chromosome Structure and Counteracts HP1a and H3K9me2

Abstract

CHD1 is a conserved chromatin remodeling factor that localizes to active genes and functions in nucleosome assembly and positioning as well as histone turnover. Mouse CHD1 is required for the maintenance of stem cell pluripotency while human CHD1 may function as a tumor suppressor. To investigate the action of CHD1 on higher order chromatin structure in differentiated cells, we examined the consequences of loss of CHD1 and over-expression of CHD1 on polytene chromosomes from salivary glands of third instar Drosophila melanogaster larvae. We observed that chromosome structure is sensitive to the amount of this remodeler. Loss of CHD1 resulted in alterations of chromosome structure and an increase in the heterochromatin protein HP1a, while over-expression of CHD1 disrupted higher order chromatin structure and caused a decrease in levels of HP1a. Over-expression of an ATPase inactive form of CHD1 did not result in severe chromosomal defects, suggesting that the ATPase activity is required for this in vivo phenotype. Interestingly, changes in CHD1 protein levels did not correlate with changes in the levels of the euchromatin mark H3K4me3 or elongating RNA Polymerase II. Thus, while CHD1 is localized to transcriptionally active regions of the genome, it can function to alter the levels of HP1a, perhaps through changes in methylation of H3K9.

Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions

“…For example, nucleosomes are present at accessible intergenic progesterone receptor binding sites; the ensuing progesterone receptor activation accessibility is increased while total H3 occupancy remains unaltered [ 50 ]. It is also possible that CHD1 depletion leads to abnormalities in higher order chromatin structure in a similar manner to what was demonstrated in Drosophila polytene chromosomes, following CHD1 deletion [ 51 ].…”

An RNAi-Based Candidate Screen for Modifiers of the CHD1 Chromatin Remodeler and Assembly Factor in Drosophila melanogaster

“…In mouse embryonic fibroblasts, either knockdown of Chd1 or expression of Chd1 harboring the corresponding lysine to arginine substitution (K510R) resulted in reduced nucleosome occupancy in the promoter and body of active genes, suggesting that the mutation has the potential to function as a dominant negative ( Skene et al 2014 ). However, Drosophila CHD1 has not been identified in a stable protein complex ( Lusser et al 2005 ) and while overexpression of chd1 K559R in salivary glands resulted in polytene chromosomal defects, those defects did not exactly resemble chromosomal phenotypes resulting from loss of chd1 function ( Bugga et al 2013 ). Given this complexity, we chose to focus on the gain-of-function phenotype resulting from overexpression of wild-type chd1 .…”

“…In Drosophila , chd1 is not essential for life, but the gene is critical for male and female fertility as well as wing development ( McDaniel et al 2008 ), and its loss leads to general disruptions in chromosome structure ( Bugga et al 2013 ). In order to identify factors that functionally interact with CHD1 in Drosophila and gain insights into its recruitment to active genes, we investigated the colocalization of CHD1 and the H3K4me3 mark on chromosomes, developed a sensitized genetic assay, and conducted a candidate gene screen to fully characterize and validate this new genetic tool.…”

Downregulation of Aedes aegypti chromodomain helicase DNA binding protein 7/Kismet by Wolbachia and its effect on dengue virus replication

“…In mammals, there are 1–9 CHD proteins; however, in D. melanogaster , there are only three CHD proteins named CHD1, Mi2 and Kismet25. Members of the CHD family are involved in conducting a wide array of functions, including ATPase activity to maintain chromosome structure and regulation of heterochromatic elements29, nucleosome mobilization45, transcriptional regulation and elongation46474849, and development and differentiation31. Despite extensive characterization of CHD family proteins, their role in shaping host-pathogen interactions has not been much investigated.…”

“…These are further classified, on the basis of additional motif features, into three subfamilies: CHD1-2 (class I), CHD3-5 (Class II) and CHD 6-9 (class III)2528. In D. melanogaster , there are three well characterized CHD members named CHD129, Mi230 and Kismet/CHD731. CHD1 is essential for the fecundity of both males and females and is indirectly involved in transcriptional elongation32, whilst Mi2 actively participates in transcriptional repression and is vital for expression of heat shock proteins3334.…”