Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo

Abstract

Packaging of genomic DNA into nucleosomes is nearly universally conserved in eukaryotes, and many features of the nucleosome landscape are quite conserved. Nonetheless, quantitative aspects of nucleosome packaging differ between species because, for example, the average length of linker DNA between nucleosomes can differ significantly even between closely related species. We recently showed that the difference in nucleosome spacing between two Hemiascomycete species—Saccharomyces cerevisiae and Kluyveromyces lactis—is established by trans-acting factors rather than being encoded in cis in the DNA sequence. Here, we generated several S. cerevisiae strains in which endogenous copies of candidate nucleosome spacing factors are deleted and replaced with the orthologous factors from K. lactis. We find no change in nucleosome spacing in such strains in which H1 or Isw1 complexes are swapped. In contrast, the K. lactis gene encoding the ATP-dependent remodeler Chd1 was found to direct longer internucleosomal spacing in S. cerevisiae, establishing that this remodeler is partially responsible for the relatively long internucleosomal spacing observed in K. lactis. By analyzing several chimeric proteins, we find that sequence differences that contribute to the spacing activity of this remodeler are dispersed throughout the coding sequence, but that the strongest spacing effect is linked to the understudied N-terminal end of Chd1. Taken together, our data find a role for sequence evolution of a chromatin remodeler in establishing quantitative aspects of the chromatin landscape in a species-specific manner.

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

“…This is consistent with increased spacing between coding region nucleosomes from 16 to 20 base pairs with alignment to the transcriptional start site (TSS) retained. Although this is a relatively small difference, nucleosome spacing is distinct in different yeast species and determined by trans acting factors (Hughes et al, 2012;Hughes and Rando, 2015;Tsankov et al, 2010). The observation that Chd1 ∆ 57-88 directs increased inter-nucleosome spacing could result if the deletion affects the "measurement" of linker length by the enzyme.…”

Emergence of robust nucleosome patterns from an interplay of positioning mechanisms

“…Furthermore, trans-species experiments have proven useful: nucleosomes on K. lactis sequences cloned into S. cerevisiae were spaced with the shorter S. cerevisiae spacing, indicating that trans acting factors determined the spacing (Hughes et al, 2012). Similarly, replacing the endogenous gene for the remodeler Chd1 in S. cerevisiae by its K. lactis ortholog led to slightly increased nucleosome spacing (Hughes and Rando, 2016). Similar experiments with S. pombe might reveal the mechanism behind the correlation of nucleosome density and AT content.…”

“…We show here that these differences can emerge from species-specific positioning mechanisms rather than pointing to different properties of the histones, which are highly conserved across species. consensus patterns haven proven to be very reproducible, and are commonly used as quantitative signatures of the interplay between different nucleosome positioning mechanisms in different species or mutants (Gkikopoulos et al, 2011;Hughes and Rando, 2016;Tsankov et al, 2010;Zhang et al, 2011).…”

“…The qualitative shape of this consensus pattern is universal across species with the nucleosome peak to peak distance varying from 150 base pairs (bp) in the yeast S. pombe (Lantermann et al, 2010;Moyle-Heyrman et al, 2013) to more than 200 bp in humans (Schones et al, 2008;Valouev et al, 2011). Furthermore, the shape is surprisingly robust against a multitude of perturbations: introduction of foreign DNA into the genome (Hughes et al, 2012), substitution of remodeler-encoding genes by non-endogenous variants and removal of H1 linker histones (Hughes and Rando, 2016), reduction of the overall histone abundance (Celona et al, 2011;Gossett and Lieb, 2012), different growth conditions (Kaplan et al, 2009), and diamide stress all affect the oscillatory consensus pattern only mildly. The passage of RNA polymerase also appears to have only a minor influence on the gene-averaged nucleosome pattern (Bintu et al, 2011;Radman-Livaja et al, 2011;Weiner et al, 2010), given that the pattern is only weakly dependent on transcription rate in yeast (Chereji and Morozov, 2015;Weiner et al, 2010).…”

Nucleosome positioning: resources and tools online

“…SOLiD paired-end sequencing [99] SRX000426 Chlamydomonas reinhardtii: Chlamydomonas strain CC 1609. MNase-seq [100] GSE62690 Saccharomyces cerevisiae and related species, MNase-seq: S. cerevisiae hho1, ioc3isw1, and chd1 deletion mutants complemented with the corresponding copies from K. lactis [101].…”