Comparison of Capture Hi-C Analytical Pipelines
<div><p>It is now evident that DNA forms an organized nuclear architecture, which is essential to maintain the structural and functional integrity of the genome. Chromatin organization can be systematically studied due to the recent boom in chromosome conformation capture technologies (e...
Saved in:
| Main Author: | |
|---|---|
| Other Authors: | , , |
| Published: |
2022
|
| Subjects: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1864513519279407104 |
|---|---|
| author | Dina Aljogol (12011672) |
| author2 | I. Richard Thompson (4278694) Cameron S. Osborne (7244990) Borbala Mifsud (3907267) |
| author2_role | author author author |
| author_facet | Dina Aljogol (12011672) I. Richard Thompson (4278694) Cameron S. Osborne (7244990) Borbala Mifsud (3907267) |
| author_role | author |
| dc.creator.none.fl_str_mv | Dina Aljogol (12011672) I. Richard Thompson (4278694) Cameron S. Osborne (7244990) Borbala Mifsud (3907267) |
| dc.date.none.fl_str_mv | 2022-01-28T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.3389/fgene.2022.786501 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Comparison_of_Capture_Hi-C_Analytical_Pipelines/25532968 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics epigenetics gene regulation computational pipeline capture Hi-C chromatin organization |
| dc.title.none.fl_str_mv | Comparison of Capture Hi-C Analytical Pipelines |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <div><p>It is now evident that DNA forms an organized nuclear architecture, which is essential to maintain the structural and functional integrity of the genome. Chromatin organization can be systematically studied due to the recent boom in chromosome conformation capture technologies (e.g., 3C and its successors 4C, 5C and Hi-C), which is accompanied by the development of computational pipelines to identify biologically meaningful chromatin contacts in such data. However, not all tools are applicable to all experimental designs and all structural features. Capture Hi-C (CHi-C) is a method that uses an intermediate hybridization step to target and select predefined regions of interest in a Hi-C library, thereby increasing effective sequencing depth for those regions. It allows researchers to investigate fine chromatin structures at high resolution, for instance promoter-enhancer loops, but it introduces additional biases with the capture step, and therefore requires specialized pipelines. Here, we compare multiple analytical pipelines for CHi-C data analysis. We consider the effect of retaining multi-mapping reads and compare the efficiency of different statistical approaches in both identifying reproducible interactions and determining biologically significant interactions. At restriction fragment level resolution, the number of multi-mapping reads that could be rescued was negligible. The number of identified interactions varied widely, depending on the analytical method, indicating large differences in type I and type II error rates. The optimal pipeline depends on the project-specific tolerance level of false positive and false negative chromatin contacts.</p><p> </p></div><h2>Other Information</h2> <p> Published in: Frontiers in Genetics<br> License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.3389/fgene.2022.786501" target="_blank">https://dx.doi.org/10.3389/fgene.2022.786501</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_31d3ea3d8cee49f48bbc265f53763002 |
| identifier_str_mv | 10.3389/fgene.2022.786501 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/25532968 |
| publishDate | 2022 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Comparison of Capture Hi-C Analytical PipelinesDina Aljogol (12011672)I. Richard Thompson (4278694)Cameron S. Osborne (7244990)Borbala Mifsud (3907267)Biological sciencesGeneticsepigeneticsgene regulationcomputational pipelinecapture Hi-Cchromatin organization<div><p>It is now evident that DNA forms an organized nuclear architecture, which is essential to maintain the structural and functional integrity of the genome. Chromatin organization can be systematically studied due to the recent boom in chromosome conformation capture technologies (e.g., 3C and its successors 4C, 5C and Hi-C), which is accompanied by the development of computational pipelines to identify biologically meaningful chromatin contacts in such data. However, not all tools are applicable to all experimental designs and all structural features. Capture Hi-C (CHi-C) is a method that uses an intermediate hybridization step to target and select predefined regions of interest in a Hi-C library, thereby increasing effective sequencing depth for those regions. It allows researchers to investigate fine chromatin structures at high resolution, for instance promoter-enhancer loops, but it introduces additional biases with the capture step, and therefore requires specialized pipelines. Here, we compare multiple analytical pipelines for CHi-C data analysis. We consider the effect of retaining multi-mapping reads and compare the efficiency of different statistical approaches in both identifying reproducible interactions and determining biologically significant interactions. At restriction fragment level resolution, the number of multi-mapping reads that could be rescued was negligible. The number of identified interactions varied widely, depending on the analytical method, indicating large differences in type I and type II error rates. The optimal pipeline depends on the project-specific tolerance level of false positive and false negative chromatin contacts.</p><p> </p></div><h2>Other Information</h2> <p> Published in: Frontiers in Genetics<br> License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.3389/fgene.2022.786501" target="_blank">https://dx.doi.org/10.3389/fgene.2022.786501</a></p>2022-01-28T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.3389/fgene.2022.786501https://figshare.com/articles/journal_contribution/Comparison_of_Capture_Hi-C_Analytical_Pipelines/25532968CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/255329682022-01-28T03:00:00Z |
| spellingShingle | Comparison of Capture Hi-C Analytical Pipelines Dina Aljogol (12011672) Biological sciences Genetics epigenetics gene regulation computational pipeline capture Hi-C chromatin organization |
| status_str | publishedVersion |
| title | Comparison of Capture Hi-C Analytical Pipelines |
| title_full | Comparison of Capture Hi-C Analytical Pipelines |
| title_fullStr | Comparison of Capture Hi-C Analytical Pipelines |
| title_full_unstemmed | Comparison of Capture Hi-C Analytical Pipelines |
| title_short | Comparison of Capture Hi-C Analytical Pipelines |
| title_sort | Comparison of Capture Hi-C Analytical Pipelines |
| topic | Biological sciences Genetics epigenetics gene regulation computational pipeline capture Hi-C chromatin organization |