Biological Sciences Division
Published June 27, 2017 | Version v1
Journal article Open

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

Creators

  • 1. University of Chicago

Description

Gaining insights into the regulatory mechanisms that underlie the transcriptional variation observed between individual cells necessitates the development of methods that measure chromatin organization in single cells. Here I adapted Nucleosome Occupancy and Methylome-sequencing (NOMe-seq) to measure chromatin accessibility and endogenous DNA methylation in single cells (scNOMe-seq). scNOMe-seq recovered characteristic accessibility and DNA methylation patterns at DNase hypersensitive sites (DHSs). An advantage of scNOMe-seq is that sequencing reads are sampled independently of the accessibility measurement. scNOMe-seq therefore controlled for fragment loss, which enabled direct estimation of the fraction of accessible DHSs within individual cells. In addition, scNOMe-seq provided high resolution of chromatin accessibility within individual loci which was exploited to detect footprints of CTCF binding events and to estimate the average nucleosome phasing distances in single cells. scNOMe-seq is therefore well-suited to characterize the chromatin organization of single cells in heterogeneous cellular mixtures.

Data availability

The following data sets were generated:

Pott S (2016) Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells Publicly available at the NCBIGene Expression Omnibus (accession no: GSE83882). https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83882

The following previously published data sets were used:

The ENCODE Project Consortium (2012) DNaseI HS peaks; GM12878 cells Publicly available under link provided (file name: wgEncodeRegDnaseUwGm12878Peak). http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/

The ENCODE Project Consortium (2012) DNaseI HS peaks; K562 cells Publicly available under link provided (file name: wgEncodeRegDnaseUwK562Peak). http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/

The ENCODE Project Consortium (2012) CTCF ChIP-seq; GM12878 cells Publicly available under link provided (file name: wgEncodeAwgTfbsBroadGm12878CtcfUniPk.narrowPeak.gz). http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/

The ENCODE Project Consortium (2012) CTCF ChIP-seq; K562 cells Publicly available under link provided (file name: wgEncodeAwgTfbsBroadK562CtcfUniPk.narrowPeak.gz). http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/

The ENCODE Project Consortium (2012) Pu.1 ChIP-seq; GM12878 cells Publicly available under link provided (file name: wgEncodeAwgTfbsHaibGm12878Pu1Pcr1xUniPk.narrowPeak.gz). http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/

The ENCODE Project Consortium (2012) Pu.1 ChIP-seq; K562 cells Publicly available under link provided (file name: wgEncodeAwgTfbsHaibK562Pu1Pcr1xUniPk.narrowPeak.gz). http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/

The ENCODE Project Consortium (2012) EBF1 ChIP-seq; GM12878 cells Publicly available under link provided (file name: wgEncodeAwgTfbsHaibGm12878Ebf1sc137065Pcr1xUniPk.narrowPeak.gz). http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/

The ENCODE Project Consortium (2012) MNase-seq; GM12878 aligned Bam files publicly available under link provided. http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhNsome/

Lay FD (2015) NOMe-seq; K562 Publicly available at the NCBIGene Expression Omnibus (accession no: GSM1583563). https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1583563

Lay FD (2015) NOMe-seq; K562 Publicly available at the NCBIGene Expression Omnibus (accession no: GSM1583567). https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1583567

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Additional details

Identifiers

DOI
10.7554/eLife.23203
Other
oai:uchicago.tind.io:9901

UChicago Information

Division(s)
Biological Sciences Division
Department(s)
Human Genetics