High Resolution Mapping of Enhancer-Promoter Interactions
RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET Tool, discovers interaction anchors at a spat...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | en_US |
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Public Library of Science
2015
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| Online Access: | http://hdl.handle.net/1721.1/97115 https://orcid.org/0000-0003-1709-4034 |
| _version_ | 1826197612480430080 |
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| author | Reeder, Christopher Closser, Michael Poh, Huay Mei Sandhu, Kuljeet Wichterle, Hynek Gifford, David K. |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Reeder, Christopher Closser, Michael Poh, Huay Mei Sandhu, Kuljeet Wichterle, Hynek Gifford, David K. |
| author_sort | Reeder, Christopher |
| collection | MIT |
| description | RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET Tool, discovers interaction anchors at a spatial resolution that is insufficient to accurately identify individual enhancers. We introduce Germ, a computational method that estimates the likelihood that any two narrowly defined genomic locations are jointly occupied by RNA Polymerase II. Germ takes a blind deconvolution approach to simultaneously estimate the likelihood of RNA Polymerase II occupation as well as a model of the arrangement of read alignments relative to locations occupied by RNA Polymerase II. Both types of information are utilized to estimate the likelihood that RNA Polymerase II jointly occupies any two genomic locations. We apply Germ to RNA Polymerase II ChIA-PET data from embryonic stem cells to identify the genomic locations that are jointly occupied along with transcription start sites. We show that these genomic locations align more closely with features of active enhancers measured by ChIP-Seq than the locations identified using the ChIA-PET Tool. We also apply Germ to RNA Polymerase II ChIA-PET data from motor neuron progenitors. Based on the Germ results, we observe that a combination of cell type specific and cell type independent regulatory interactions are utilized by cells to regulate gene expression. |
| first_indexed | 2024-09-23T10:50:18Z |
| format | Article |
| id | mit-1721.1/97115 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:50:18Z |
| publishDate | 2015 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/971152022-09-27T15:21:20Z High Resolution Mapping of Enhancer-Promoter Interactions Reeder, Christopher Closser, Michael Poh, Huay Mei Sandhu, Kuljeet Wichterle, Hynek Gifford, David K. Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Reeder, Christopher Gifford, David K. RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET Tool, discovers interaction anchors at a spatial resolution that is insufficient to accurately identify individual enhancers. We introduce Germ, a computational method that estimates the likelihood that any two narrowly defined genomic locations are jointly occupied by RNA Polymerase II. Germ takes a blind deconvolution approach to simultaneously estimate the likelihood of RNA Polymerase II occupation as well as a model of the arrangement of read alignments relative to locations occupied by RNA Polymerase II. Both types of information are utilized to estimate the likelihood that RNA Polymerase II jointly occupies any two genomic locations. We apply Germ to RNA Polymerase II ChIA-PET data from embryonic stem cells to identify the genomic locations that are jointly occupied along with transcription start sites. We show that these genomic locations align more closely with features of active enhancers measured by ChIP-Seq than the locations identified using the ChIA-PET Tool. We also apply Germ to RNA Polymerase II ChIA-PET data from motor neuron progenitors. Based on the Germ results, we observe that a combination of cell type specific and cell type independent regulatory interactions are utilized by cells to regulate gene expression. National Institutes of Health (U.S.) (Grant 1U01HG007037) 2015-05-29T14:42:16Z 2015-05-29T14:42:16Z 2015-05 2014-11 Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/97115 Reeder, Christopher, Michael Closser, Huay Mei Poh, Kuljeet Sandhu, Hynek Wichterle, and David Gifford. “High Resolution Mapping of Enhancer-Promoter Interactions.” Edited by Charalampos Babis Spilianakis. PLOS ONE 10, no. 5 (May 13, 2015): e0122420. https://orcid.org/0000-0003-1709-4034 en_US http://dx.doi.org/10.1371/journal.pone.0122420 PLOS ONE Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science Public Library of Science |
| spellingShingle | Reeder, Christopher Closser, Michael Poh, Huay Mei Sandhu, Kuljeet Wichterle, Hynek Gifford, David K. High Resolution Mapping of Enhancer-Promoter Interactions |
| title | High Resolution Mapping of Enhancer-Promoter Interactions |
| title_full | High Resolution Mapping of Enhancer-Promoter Interactions |
| title_fullStr | High Resolution Mapping of Enhancer-Promoter Interactions |
| title_full_unstemmed | High Resolution Mapping of Enhancer-Promoter Interactions |
| title_short | High Resolution Mapping of Enhancer-Promoter Interactions |
| title_sort | high resolution mapping of enhancer promoter interactions |
| url | http://hdl.handle.net/1721.1/97115 https://orcid.org/0000-0003-1709-4034 |
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