Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells
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 measur...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2017-06-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/23203 |
| _version_ | 1827824768657653760 |
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| author | Sebastian Pott |
| author_facet | Sebastian Pott |
| author_sort | Sebastian Pott |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-12T02:32:26Z |
| format | Article |
| id | doaj.art-012c29ac145147fb8bdeccec67248640 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-03-12T02:32:26Z |
| publishDate | 2017-06-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-012c29ac145147fb8bdeccec672486402023-09-05T07:35:44ZengeLife Sciences Publications LtdeLife2050-084X2017-06-01610.7554/eLife.23203Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cellsSebastian Pott0https://orcid.org/0000-0002-4118-6150Department of Human Genetics, University of Chicago, Chicago, United StatesGaining 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.https://elifesciences.org/articles/23203single cell genomicschromatin organizationDNA methylationNOMe-seqsingle cell NOMe-seq |
| spellingShingle | Sebastian Pott Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells eLife single cell genomics chromatin organization DNA methylation NOMe-seq single cell NOMe-seq |
| title | Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells |
| title_full | Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells |
| title_fullStr | Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells |
| title_full_unstemmed | Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells |
| title_short | Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells |
| title_sort | simultaneous measurement of chromatin accessibility dna methylation and nucleosome phasing in single cells |
| topic | single cell genomics chromatin organization DNA methylation NOMe-seq single cell NOMe-seq |
| url | https://elifesciences.org/articles/23203 |
| work_keys_str_mv | AT sebastianpott simultaneousmeasurementofchromatinaccessibilitydnamethylationandnucleosomephasinginsinglecells |