Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

By T. Kelly, Yaping Liu, F. Lay, G. Liang, Benjamin Paul Berman, Peter A. Jones. 2012

429 citations recorded by the source corpus.

DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome-depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule, and thus, single cell level, that can be used to monitor disease progression and response to therapy.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, background): “Nucleosome-associated DNA has a lower rate of methylation than the more accessible linker sequences located between nucleosomes (1, 2).”
Gene Body Methylation can alter Gene Expression and is a Therapeutic Target in Cancer (2014, methodology): “We also used the highly sensitive single-molecule nucleosome occupancy and methylome sequencing (NOMe-seq) assay (Kelly et al., 2012) to analyze potential chromatin accessibility changes in selected regions of TRIB3 and STC2 gene body regions (Figure S5C).”
Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming (2015, neutral): “The MNase-seq data (GSM543311) (Kelly et al., 2012) were aligned to build version NCBI36/HG18 of the human genome, and seven replicates were pooled together generating 145,546,004 unique reads.”
The chromatin accessibility landscape of primary human cancers (2018, background): “Despite this strong correlation, many sites of differential chromatin accessibility do not show differential methylation, demonstrating the complementarity of these two data types, perhaps due to the presence of intermediate chromatin states such as poised promoters or enhancers (53, 54).”
Epigenetic Determinants of Cancer. (2016, background): “In this regard, several laboratories have highlighted how, in cancer cells, chromatin configuration found at hypermethylated CpG islands near the promoters of aberrantly silenced genes differs from when these genes are basally expressed in normal settings (Kelly et al. 2012; Yang et al. 2012).”
Gene regulatory network inference in the era of single-cell multi-omics (2023, methodology): “The most commonly used technology owing to its simple and relatively cheap protocol is the assay for transposase accessible chromatin with sequencing (ATAC-seq) 21 , but other technologies exist such as DNase-seq 43 and NOME-seq 44 (reviewed elsewhere 45 ).”