Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

Xi, Yuanxin; Yao, Jianhui; Chen, Rui; Li, Wei; He, Xiangwei

doi:10.1101/gr.117101.110

Cited by 121 publications

(157 citation statements)

References 24 publications

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“…6A). Further, although previous reports have suggested that the histone variant H2A.Z may act to promote nucleosome instability (Jin and Felsenfeld 2007;Jin et al 2009;Xi et al 2011), we did not observe a significant overlap between previously identified H2A.Z-containing nucleosomes (Ho et al 2014) and fragile nucleosomes ( Fig. 4D; Supplemental Fig.…”

Section: Nucleosome Fragility Near Genes Is Anti-correlated With Exprcontrasting

confidence: 83%

“…Previous studies using this approach defined nucleosomes released early in the time-course as "fragile" and those released later in the time-course as "resistant" (Xi et al 2011). To identify nucleosomes of differential sensitivity genome-wide, we isolated mixed-stage embryos from C. elegans, treated them with formaldehyde to cross-link the chromatin, isolated nuclei, and digested the chromatin with MNase (Fig.…”

Section: A Digestion Time-course Identifies Nucleosomes With Differenmentioning

confidence: 99%

“…Results from yeast (Weiner et al 2010;Xi et al 2011;Kubik et al 2015), plants (Vera et al 2014), mouse (Lombraña et al 2013;Deng et al 2015;Iwafuchi-Doi et al 2016;Mieczkowski et al 2016), worm (Ooi et al 2010), and fly (Henikoff et al 2009; have identified highly labile nucleosomes in 5 ′ and 3 ′ "nucleosome-free" regions. In yeast, Xi et al (2011) observed that fragile nucleosomes were associated with H2A.Z-containing promoter nucleosomes, believed to be involved in stress response (Li et al 2005;Zhang et al 2005). In vertebrates, individual nucleosomes containing both H3.3 and H2A.Z histone variants are unstable (Jin and Felsenfeld 2007;Jin et al 2009).…”

Section: Mnase-resistant Nucleosomes Tend To Be In Gene Bodies and Comentioning

confidence: 99%

“…Genome-wide adaptations of these methods have been used to identify nucleosome position and stability in vivo. Studies in yeast, Drosophila, plants, and mammals have used varying concentrations of the enzyme micrococcal nuclease (MNase) to identify nucleosomes with differential sensitivity to MNase digestion in vivo (Weiner et al 2010;Henikoff et al 2011;Xi et al 2011;Lombraña et al 2013;Vera et al 2014;Kubik et al 2015). Nucleosomes sensitive to low concentrations of MNase have been labeled as "fragile" and have been associated with TF binding sites (TFBSs) (Vera et al 2014), active origins of replication (Lombraña et al 2013), gene promoters (Xi et al 2011), and genomic sequences with high AT content .…”

mentioning

confidence: 99%

“…However, the functional implication of nucleosome fragility remains unclear. For example, one study reported fragile nucleosomes at the promoters of repressed stress-response genes during normal growth (Xi et al 2011), while another found fragile nucleosomes at the promoters of highly transcribed genes in yeast (Kubik et al 2015). We performed a time-course of MNase digestion in Caenorhabditis elegans mixed-stage embryos to study the relationship between fragility and gene activity in a developing multicellular organism.…”

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confidence: 99%

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

Jeffers

Lieb

2016

Genome Res.

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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...

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Section: Nucleosome Fragility Near Genes Is Anti-correlated With Exprcontrasting

confidence: 83%

Section: A Digestion Time-course Identifies Nucleosomes With Differenmentioning

confidence: 99%

Section: Mnase-resistant Nucleosomes Tend To Be In Gene Bodies and Comentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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

Jeffers

Lieb

2016

Genome Res.

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

2017

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Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS). This "fragile" nucleosome (FN) promoter architecture relies on the combined action of the essential RSC (Remodels Structure of Chromatin) nucleosome remodeler and pioneer transcription factors (PTFs). FNs are associated with genes whose expression is high, coupled to cell growth, and characterized by low cell-to-cell variability (noise), suggesting that they may promote these features. Recent studies in metazoans suggest that the presence of dynamic nucleosomes upstream of the TSS at highly expressed genes may be conserved throughout evolution.

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Single‐Assay Profiling of Nucleosome Occupancy and Chromatin Accessibility

Cook

Mieczkowski

Tolstorukov

2017

CP Molecular Biology

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This unit describes a method for determining the accessibility of chromatinized DNA and nucleosome occupancy in the same assay. Enzymatic digestion of chromatin using micrococcal nuclease (MNase) is optimized for liberation, retrieval, and characterization of DNA fragments from chromatin. MNase digestion is performed in a titration series, and the DNA fragments are isolated and sequenced for each individual digest independently. These sequenced fragments are then collectively analyzed in a novel bioinformatics pipeline to produce a metric describing MNase accessibility of chromatin (MACC) and nucleosome occupancy. This approach allows profiling of the entire genome including regions of open and closed chromatin. Moreover, the MACC protocol can be supplemented with a histone immunoprecipitation step to estimate and compare both histone and non-histone DNA protection components. © 2017 by John Wiley & Sons, Inc.

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Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

Cited by 121 publications

References 24 publications

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

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

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

Single‐Assay Profiling of Nucleosome Occupancy and Chromatin Accessibility

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