Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET
Background: Genome-wide approaches have begun to reveal the transcriptional networks responsible for pluripotency in embryonic stem (ES) cells. Chromatin Immunoprecipitation (ChIP) followed either by hybridization to a microarray platform (ChIP-chip) or by DNA sequencing (ChIP-PET), has identified b...
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| Format: | Article |
| Language: | English |
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BioMed Central Ltd
2010
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| Online Access: | http://hdl.handle.net/1721.1/59018 https://orcid.org/0000-0001-8855-8647 https://orcid.org/0000-0003-1709-4034 https://orcid.org/0000-0003-3491-4962 |
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| author | Mathur, Divya Young, Richard A. Jaenisch, Rudolf Danford, Timothy William Boyer, Laurie Ann 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 Mathur, Divya Young, Richard A. Jaenisch, Rudolf Danford, Timothy William Boyer, Laurie Ann Gifford, David K |
| author_sort | Mathur, Divya |
| collection | MIT |
| description | Background: Genome-wide approaches have begun to reveal the transcriptional networks responsible for pluripotency in embryonic stem (ES) cells. Chromatin Immunoprecipitation (ChIP) followed either by hybridization to a microarray platform (ChIP-chip) or by DNA sequencing (ChIP-PET), has identified binding targets of the ES cell transcription factors OCT4 and NANOG in humans and mice, respectively. These studies have provided an outline of the transcriptional framework involved in maintaining pluripotency. Recent evidence with comparing multiple technologies suggests that expanding these datasets using different platforms would be a useful resource for examining the mechanisms underlying pluripotency regulation. Results: We have now identified OCT4 and NANOG genomic targets in mouse ES cells by ChIP-chip and provided the means to compare these data with previously reported ChIP-PET results in mouse ES cells. We have mapped the sequences of OCT4 and NANOG binding events from each dataset to genomic coordinates, providing a valuable resource to facilitate a better understanding of the ES cell regulatory circuitry. Interestingly, although considerable differences are observed in OCT4 and NANOG occupancy as identified by each method, a substantial number of targets in both datasets are enriched for genes that have known roles in cell-fate specification and that are differentially expressed upon Oct4 or Nanog knockdown. Conclusion: This study suggests that each dataset is a partial representation of the overall ES cell regulatory circuitry, and through integrating binding data obtained by ChIP-chip and ChIP-PET, the methods presented here provide a useful means for integrating datasets obtained by different techniques in the future. |
| first_indexed | 2024-09-23T13:31:55Z |
| format | Article |
| id | mit-1721.1/59018 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T13:31:55Z |
| publishDate | 2010 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/590182022-09-28T14:38:10Z Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET Mathur, Divya Young, Richard A. Jaenisch, Rudolf Danford, Timothy William Boyer, Laurie Ann Gifford, David K Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Whitehead Institute for Biomedical Research Mathur, Divya Danford, Timothy William Boyer, Laurie Young, Richard A. Gifford, David K. Jaenisch, Rudolf Background: Genome-wide approaches have begun to reveal the transcriptional networks responsible for pluripotency in embryonic stem (ES) cells. Chromatin Immunoprecipitation (ChIP) followed either by hybridization to a microarray platform (ChIP-chip) or by DNA sequencing (ChIP-PET), has identified binding targets of the ES cell transcription factors OCT4 and NANOG in humans and mice, respectively. These studies have provided an outline of the transcriptional framework involved in maintaining pluripotency. Recent evidence with comparing multiple technologies suggests that expanding these datasets using different platforms would be a useful resource for examining the mechanisms underlying pluripotency regulation. Results: We have now identified OCT4 and NANOG genomic targets in mouse ES cells by ChIP-chip and provided the means to compare these data with previously reported ChIP-PET results in mouse ES cells. We have mapped the sequences of OCT4 and NANOG binding events from each dataset to genomic coordinates, providing a valuable resource to facilitate a better understanding of the ES cell regulatory circuitry. Interestingly, although considerable differences are observed in OCT4 and NANOG occupancy as identified by each method, a substantial number of targets in both datasets are enriched for genes that have known roles in cell-fate specification and that are differentially expressed upon Oct4 or Nanog knockdown. Conclusion: This study suggests that each dataset is a partial representation of the overall ES cell regulatory circuitry, and through integrating binding data obtained by ChIP-chip and ChIP-PET, the methods presented here provide a useful means for integrating datasets obtained by different techniques in the future. National Institutes of Health (U.S) ( RO1-HD045022 ) National Institutes of Health (U.S) (R37-CA084198) National Institutes of Health (U.S) ( HG002688 ) 2010-10-12T14:45:31Z 2010-10-12T14:45:31Z 2008-08 2008-06 2010-09-03T16:01:20Z Article http://purl.org/eprint/type/JournalArticle 1465-6906 http://hdl.handle.net/1721.1/59018 Genome Biology. 2008 Aug 13;9(8):R126 18700969 https://orcid.org/0000-0001-8855-8647 https://orcid.org/0000-0003-1709-4034 https://orcid.org/0000-0003-3491-4962 en http://dx.doi.org/10.1186/gb-2008-9-8-r126 Genome Biology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 Mathur et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Mathur, Divya Young, Richard A. Jaenisch, Rudolf Danford, Timothy William Boyer, Laurie Ann Gifford, David K Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET |
| title | Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET |
| title_full | Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET |
| title_fullStr | Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET |
| title_full_unstemmed | Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET |
| title_short | Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET |
| title_sort | analysis of the mouse embryonic stem cell regulatory networks obtained by chip chip and chip pet |
| url | http://hdl.handle.net/1721.1/59018 https://orcid.org/0000-0001-8855-8647 https://orcid.org/0000-0003-1709-4034 https://orcid.org/0000-0003-3491-4962 |
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