OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to...
| Main Authors: | , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2020
|
| Online Access: | https://hdl.handle.net/1721.1/126320 |
| _version_ | 1826199021021036544 |
|---|---|
| author | An, Lin Yang, Tao Yang, Jiahao Nubler, Johannes Xiang, Guanjue Hardison, Ross C Li, Qunhua Zhang, Yu |
| author2 | Massachusetts Institute of Technology. Institute for Medical Engineering & Science |
| author_facet | Massachusetts Institute of Technology. Institute for Medical Engineering & Science An, Lin Yang, Tao Yang, Jiahao Nubler, Johannes Xiang, Guanjue Hardison, Ross C Li, Qunhua Zhang, Yu |
| author_sort | An, Lin |
| collection | MIT |
| description | The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD. |
| first_indexed | 2024-09-23T11:13:29Z |
| format | Article |
| id | mit-1721.1/126320 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T11:13:29Z |
| publishDate | 2020 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | mit-1721.1/1263202022-09-27T17:59:54Z OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries An, Lin Yang, Tao Yang, Jiahao Nubler, Johannes Xiang, Guanjue Hardison, Ross C Li, Qunhua Zhang, Yu Massachusetts Institute of Technology. Institute for Medical Engineering & Science The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD. NIH (Grant R01 GM121613, R01 GM109453, R24 DK106766) NIH (Training Grant T32 GM102057) 2020-07-22T18:53:36Z 2020-07-22T18:53:36Z 2019-12-18 2019-04 2020-06-26T11:08:27Z Article http://purl.org/eprint/type/JournalArticle 1474-760X https://hdl.handle.net/1721.1/126320 An, Lin et al. "OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries." Genome Biology 20 (Dec. 2019): no. 282 doi 10.1186/s13059-019-1893-y ©2019 Author(s) en 10.1186/s13059-019-1893-y Genome Biology Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ The Author(s). application/pdf BioMed Central BioMed Central |
| spellingShingle | An, Lin Yang, Tao Yang, Jiahao Nubler, Johannes Xiang, Guanjue Hardison, Ross C Li, Qunhua Zhang, Yu OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries |
| title | OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries |
| title_full | OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries |
| title_fullStr | OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries |
| title_full_unstemmed | OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries |
| title_short | OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries |
| title_sort | ontad hierarchical domain structure reveals the divergence of activity among tads and boundaries |
| url | https://hdl.handle.net/1721.1/126320 |
| work_keys_str_mv | AT anlin ontadhierarchicaldomainstructurerevealsthedivergenceofactivityamongtadsandboundaries AT yangtao ontadhierarchicaldomainstructurerevealsthedivergenceofactivityamongtadsandboundaries AT yangjiahao ontadhierarchicaldomainstructurerevealsthedivergenceofactivityamongtadsandboundaries AT nublerjohannes ontadhierarchicaldomainstructurerevealsthedivergenceofactivityamongtadsandboundaries AT xiangguanjue ontadhierarchicaldomainstructurerevealsthedivergenceofactivityamongtadsandboundaries AT hardisonrossc ontadhierarchicaldomainstructurerevealsthedivergenceofactivityamongtadsandboundaries AT liqunhua ontadhierarchicaldomainstructurerevealsthedivergenceofactivityamongtadsandboundaries AT zhangyu ontadhierarchicaldomainstructurerevealsthedivergenceofactivityamongtadsandboundaries |