Distant cis-regulatory elements in human skeletal muscle differentiation
Identifying gene regulatory elements and their target genes in human cells remains a significant challenge. Despite increasing evidence of physical interactions between distant regulatory elements and gene promoters in mammalian cells, many studies consider only promoter-proximal regulatory regions....
| Main Authors: | , , , |
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| Format: | Article |
| Language: | en_US |
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Elsevier
2014
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| Online Access: | http://hdl.handle.net/1721.1/92312 |
| _version_ | 1811079750105432064 |
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| author | McCord, Rachel P. Zhou, Vicky W. Yuh, Tiffany Bulyk, Martha L. |
| author2 | Harvard University--MIT Division of Health Sciences and Technology |
| author_facet | Harvard University--MIT Division of Health Sciences and Technology McCord, Rachel P. Zhou, Vicky W. Yuh, Tiffany Bulyk, Martha L. |
| author_sort | McCord, Rachel P. |
| collection | MIT |
| description | Identifying gene regulatory elements and their target genes in human cells remains a significant challenge. Despite increasing evidence of physical interactions between distant regulatory elements and gene promoters in mammalian cells, many studies consider only promoter-proximal regulatory regions. We identify putative cis-regulatory modules (CRMs) in human skeletal muscle differentiation by combining myogenic TF binding data before and after differentiation with histone modification data in myoblasts. CRMs that are distant (> 20 kb) from muscle gene promoters are common and are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding. We find that two of these distant CRMs, known to activate transcription in differentiating myoblasts, interact physically with gene promoters (PDLIM3 and ACTA1) during differentiation. Our results highlight the importance of considering distal CRMs in investigations of mammalian gene regulation and support the hypothesis that distant CRM-promoter looping contacts are a general mechanism of gene regulation. |
| first_indexed | 2024-09-23T11:19:56Z |
| format | Article |
| id | mit-1721.1/92312 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:19:56Z |
| publishDate | 2014 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/923122022-09-27T18:44:39Z Distant cis-regulatory elements in human skeletal muscle differentiation McCord, Rachel P. Zhou, Vicky W. Yuh, Tiffany Bulyk, Martha L. Harvard University--MIT Division of Health Sciences and Technology Massachusetts Institute of Technology. Department of Biology Bulyk, Martha L. Yuh, Tiffany Identifying gene regulatory elements and their target genes in human cells remains a significant challenge. Despite increasing evidence of physical interactions between distant regulatory elements and gene promoters in mammalian cells, many studies consider only promoter-proximal regulatory regions. We identify putative cis-regulatory modules (CRMs) in human skeletal muscle differentiation by combining myogenic TF binding data before and after differentiation with histone modification data in myoblasts. CRMs that are distant (> 20 kb) from muscle gene promoters are common and are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding. We find that two of these distant CRMs, known to activate transcription in differentiating myoblasts, interact physically with gene promoters (PDLIM3 and ACTA1) during differentiation. Our results highlight the importance of considering distal CRMs in investigations of mammalian gene regulation and support the hypothesis that distant CRM-promoter looping contacts are a general mechanism of gene regulation. National Human Genome Research Institute (U.S.) (Grant R21 HG005149) 2014-12-16T13:53:18Z 2014-12-16T13:53:18Z 2011-08 2011-08 Article http://purl.org/eprint/type/JournalArticle 08887543 1089-8646 http://hdl.handle.net/1721.1/92312 McCord, Rachel Patton, Vicky W. Zhou, Tiffany Yuh, and Martha L. Bulyk. “Distant Cis-Regulatory Elements in Human Skeletal Muscle Differentiation.” Genomics 98, no. 6 (December 2011): 401–411. © 2011 Elsevier Inc. en_US http://dx.doi.org/10.1016/j.ygeno.2011.08.003 Genomics Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Elsevier Elsevier |
| spellingShingle | McCord, Rachel P. Zhou, Vicky W. Yuh, Tiffany Bulyk, Martha L. Distant cis-regulatory elements in human skeletal muscle differentiation |
| title | Distant cis-regulatory elements in human skeletal muscle differentiation |
| title_full | Distant cis-regulatory elements in human skeletal muscle differentiation |
| title_fullStr | Distant cis-regulatory elements in human skeletal muscle differentiation |
| title_full_unstemmed | Distant cis-regulatory elements in human skeletal muscle differentiation |
| title_short | Distant cis-regulatory elements in human skeletal muscle differentiation |
| title_sort | distant cis regulatory elements in human skeletal muscle differentiation |
| url | http://hdl.handle.net/1721.1/92312 |
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