DNase-capture reveals differential transcription factor binding modalities
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. We describe DNase-capture, an assay that increases the analytica...
| Main Authors: | , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Published: |
Public Library of Science
2018
|
| Online Access: | http://hdl.handle.net/1721.1/113253 https://orcid.org/0000-0003-0521-5855 https://orcid.org/0000-0003-1709-4034 |
| _version_ | 1811087242444144640 |
|---|---|
| author | Sherwood, Richard Barkal, Amira Kang, Daniel D Hashimoto, Tatsunori Benjamin Engstrom, Logan G. 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 Sherwood, Richard Barkal, Amira Kang, Daniel D Hashimoto, Tatsunori Benjamin Engstrom, Logan G. Gifford, David K |
| author_sort | Sherwood, Richard |
| collection | MIT |
| description | This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. We describe DNase-capture, an assay that increases the analytical resolution of DNase-seq by focusing its sequencing phase on selected genomic regions. We introduce a new method to compensate for capture bias called BaseNormal that allows for accurate recovery of transcription factor protection profiles from DNase-capture data. We show that these normalized data allow for nuanced detection of transcription factor binding heterogeneity with as few as dozens of sites. |
| first_indexed | 2024-09-23T13:42:20Z |
| format | Article |
| id | mit-1721.1/113253 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T13:42:20Z |
| publishDate | 2018 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/1132532022-10-01T16:40:21Z DNase-capture reveals differential transcription factor binding modalities Sherwood, Richard Barkal, Amira Kang, Daniel D Hashimoto, Tatsunori Benjamin Engstrom, Logan G. Gifford, David K Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kang, Daniel D Hashimoto, Tatsunori Benjamin Engstrom, Logan G. Gifford, David K This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. We describe DNase-capture, an assay that increases the analytical resolution of DNase-seq by focusing its sequencing phase on selected genomic regions. We introduce a new method to compensate for capture bias called BaseNormal that allows for accurate recovery of transcription factor protection profiles from DNase-capture data. We show that these normalized data allow for nuanced detection of transcription factor binding heterogeneity with as few as dozens of sites. National Institute of General Medical Sciences (U.S.) (Grant 1U01HG007037) 2018-01-22T16:10:02Z 2018-01-22T16:10:02Z 2017-12 2017-03 2018-01-19T16:34:05Z Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/113253 Kang, Daniel et al. “DNase-Capture Reveals Differential Transcription Factor Binding Modalities.” Edited by Deyou Zheng. PLOS ONE 12, 12 (December 2017): e0187046 © 2017 Kang et al https://orcid.org/0000-0003-0521-5855 https://orcid.org/0000-0003-1709-4034 http://dx.doi.org/10.1371/journal.pone.0187046 PLOS ONE Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0 application/pdf Public Library of Science PLoS |
| spellingShingle | Sherwood, Richard Barkal, Amira Kang, Daniel D Hashimoto, Tatsunori Benjamin Engstrom, Logan G. Gifford, David K DNase-capture reveals differential transcription factor binding modalities |
| title | DNase-capture reveals differential transcription factor binding modalities |
| title_full | DNase-capture reveals differential transcription factor binding modalities |
| title_fullStr | DNase-capture reveals differential transcription factor binding modalities |
| title_full_unstemmed | DNase-capture reveals differential transcription factor binding modalities |
| title_short | DNase-capture reveals differential transcription factor binding modalities |
| title_sort | dnase capture reveals differential transcription factor binding modalities |
| url | http://hdl.handle.net/1721.1/113253 https://orcid.org/0000-0003-0521-5855 https://orcid.org/0000-0003-1709-4034 |
| work_keys_str_mv | AT sherwoodrichard dnasecapturerevealsdifferentialtranscriptionfactorbindingmodalities AT barkalamira dnasecapturerevealsdifferentialtranscriptionfactorbindingmodalities AT kangdanield dnasecapturerevealsdifferentialtranscriptionfactorbindingmodalities AT hashimototatsunoribenjamin dnasecapturerevealsdifferentialtranscriptionfactorbindingmodalities AT engstromlogang dnasecapturerevealsdifferentialtranscriptionfactorbindingmodalities AT gifforddavidk dnasecapturerevealsdifferentialtranscriptionfactorbindingmodalities |