Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans

Abstract

Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability of the underlying histone-DNA interactions affect the access of regulatory proteins to DNA. Both stability and position are regulated through DNA sequence, histone post-translational modifications, histone variants, chromatin remodelers, and transcription factors. Here, we explored the functional implications of nucleosome properties on gene expression and development in Caenorhabditis elegans embryos. We performed a time-course of micrococcal nuclease (MNase) digestion and measured the relative sensitivity or resistance of nucleosomes throughout the genome. Fragile nucleosomes were defined by nucleosomal DNA fragments that were recovered preferentially in early MNase-digestion time points. Nucleosome fragility was strongly and positively correlated with the AT content of the underlying DNA sequence. There was no correlation between promoter nucleosome fragility and the levels of histone modifications or histone variants. Genes with fragile nucleosomes in their promoters tended to be lowly expressed and expressed in a contextspecific way, operating in neuronal response, the immune system, and stress response. In addition to DNA-encoded nucleosome fragility, we also found fragile nucleosomes at locations where we expected to find destabilized nucleosomes, for example, at transcription factor binding sites where nucleosomes compete with DNA-binding factors. Our data suggest that in C. elegans promoters, nucleosome fragility is in large part DNA-encoded and that it poises genes for future context-specific activation in response to environmental stress and developmental cues.[Supplemental material is available for this article.]The fundamental unit of eukaryotic chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around an octamer of histone proteins (Luger et al. 1997). Nucleosomes have important structural and regulatory functions in organizing the genome and restricting access of regulatory factors to the DNA sequence (Henikoff 2008). As such, the interactions between nucleosomes and DNA strongly influence the regulation of gene expression by determining DNA accessibility for transcription factors (TFs) and RNA polymerase. In addition to regulated nucleosome assembly and disassembly through the action of histone chaperones and chromatin remodelers, nucleosome stability is influenced by histone modifications, histone variants, DNA features encoded in cis, and competition with DNA-binding factors in trans . A complete picture of the mechanisms governing nucleosome stability is fundamental to understanding how gene expression is dynamically regulated.Nucleosome stability has been studied in vitro using sensitivity to enzymatic digestion or salt concentration (Bloom and Anderson 1978;Burton et al. 1978;Li et al. 1993;Polach and Widom 1995;Wu and Travers 2004;Jin and Felsenfeld 2007). Genome-wide adaptations of these methods have been used to identify nuc...

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

“…However, the existence of fragile nucleosomes is controversial, since high-resolution mapping by ChIP and tiling microarray reveals scant evidence for histones at yeast promoters (Fan et al, 2010). MNase-sensitive nucleosomes have also been reported in higher eukaryotes (Chereji et al, 2016; Ishii et al, 2015; Iwafuchi-Doi et al, 2016; Jeffers and Lieb, 2016; Mieczkowski et al, 2016; Teif et al, 2014; Vera et al, 2014; West et al, 2014). …”

Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer

“…When the NDRs are wide enough (>150 bp), a common occurrence at open promoters, they might not be truly nucleosome-free, and instead, may harbor highly dynamic nucleosomes, termed ‘fragile’ nucleosomes [ 190 , 191 , 192 , 193 ] ( Figure 5 A, right). Fragile nucleosomes appear to be conserved as they have been identified in promoters of highly expressed genes in many organisms, for example, C. elegans [ 194 ], Drosophila embryos [ 195 ], and mouse Embryonic Stem Cells (ESCs) [ 196 ], and their presence and stability relate to the rate of transcription [ 197 ]. Importantly, in yeast, ‘fragile’ nucleosomes appear to be partially unwrapped nucleosomes resulting from the action of the SWI/SNF-subfamily remodeler RSC and subsequent binding of ‘general regulatory factors’ (GRFs) [ 198 ].…”

Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler

“…Unstable nucleosome-like particles, often associated with promoters of highly expressed genes, have also been found in fission yeast [68], plants [69], C. elegans [70], Drosophila [40], human [71], and mouse ES cells [21,72]. One recent study showed that binding of the PTF FoxA retains nucleosomes at active enhancers but renders them more MNase-sensitive, in part by ejecting the linker histone from chromatin [73].…”