Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called Chromatin-Associated RNA...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2018-04-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/27024 |
| _version_ | 1811199357441015808 |
|---|---|
| author | Jason C Bell David Jukam Nicole A Teran Viviana I Risca Owen K Smith Whitney L Johnson Jan M Skotheim William James Greenleaf Aaron F Straight |
| author_facet | Jason C Bell David Jukam Nicole A Teran Viviana I Risca Owen K Smith Whitney L Johnson Jan M Skotheim William James Greenleaf Aaron F Straight |
| author_sort | Jason C Bell |
| collection | DOAJ |
| description | RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells, we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing. |
| first_indexed | 2024-04-12T01:46:45Z |
| format | Article |
| id | doaj.art-0a371ee0cd154db8aeb19205e6b6b723 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T01:46:45Z |
| publishDate | 2018-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-0a371ee0cd154db8aeb19205e6b6b7232022-12-22T03:53:02ZengeLife Sciences Publications LtdeLife2050-084X2018-04-01710.7554/eLife.27024Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contactsJason C Bell0https://orcid.org/0000-0001-5480-7975David Jukam1https://orcid.org/0000-0003-4167-2754Nicole A Teran2https://orcid.org/0000-0002-9625-5010Viviana I Risca3https://orcid.org/0000-0003-2670-8704Owen K Smith4https://orcid.org/0000-0003-0880-2801Whitney L Johnson5Jan M Skotheim6William James Greenleaf7Aaron F Straight8https://orcid.org/0000-0001-5885-7881Department of Biochemistry, Stanford University, Stanford, United StatesDepartment of Biology, Stanford University, Stanford, United StatesDepartment of Biochemistry, Stanford University, Stanford, United States; Department of Genetics, Stanford University, Stanford, United StatesDepartment of Genetics, Stanford University, Stanford, United StatesDepartment of Biochemistry, Stanford University, Stanford, United States; Department of Chemical and Systems Biology, Stanford University, Stanford, United StatesDepartment of Biochemistry, Stanford University, Stanford, United StatesDepartment of Biology, Stanford University, Stanford, United StatesDepartment of Genetics, Stanford University, Stanford, United States; Department of Applied Physics, Stanford University, Stanford, United StatesDepartment of Biochemistry, Stanford University, Stanford, United States; Department of Chemical and Systems Biology, Stanford University, Stanford, United StatesRNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells, we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.https://elifesciences.org/articles/27024RNAchromatindosage compensationtranscriptiongenomicsnon-coding RNA |
| spellingShingle | Jason C Bell David Jukam Nicole A Teran Viviana I Risca Owen K Smith Whitney L Johnson Jan M Skotheim William James Greenleaf Aaron F Straight Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts eLife RNA chromatin dosage compensation transcription genomics non-coding RNA |
| title | Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts |
| title_full | Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts |
| title_fullStr | Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts |
| title_full_unstemmed | Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts |
| title_short | Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts |
| title_sort | chromatin associated rna sequencing char seq maps genome wide rna to dna contacts |
| topic | RNA chromatin dosage compensation transcription genomics non-coding RNA |
| url | https://elifesciences.org/articles/27024 |
| work_keys_str_mv | AT jasoncbell chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts AT davidjukam chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts AT nicoleateran chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts AT vivianairisca chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts AT owenksmith chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts AT whitneyljohnson chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts AT janmskotheim chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts AT williamjamesgreenleaf chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts AT aaronfstraight chromatinassociatedrnasequencingcharseqmapsgenomewidernatodnacontacts |