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High-resolution TADs reveal DNA sequences underlying genome organization in flies
Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Droso...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768762/ https://www.ncbi.nlm.nih.gov/pubmed/29335486 http://dx.doi.org/10.1038/s41467-017-02525-w |
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author | Ramírez, Fidel Bhardwaj, Vivek Arrigoni, Laura Lam, Kin Chung Grüning, Björn A. Villaveces, José Habermann, Bianca Akhtar, Asifa Manke, Thomas |
author_facet | Ramírez, Fidel Bhardwaj, Vivek Arrigoni, Laura Lam, Kin Chung Grüning, Björn A. Villaveces, José Habermann, Bianca Akhtar, Asifa Manke, Thomas |
author_sort | Ramírez, Fidel |
collection | PubMed |
description | Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by the M1BP protein, and two new boundary motifs. In contrast to mammals, the CTCF motif is only enriched on a small fraction of boundaries flanking inactive chromatin while most active boundaries contain the motifs bound by the M1BP or Beaf-32 proteins. We demonstrate that boundaries can be accurately predicted using only the motif sequences at open chromatin sites. We propose that DNA sequence guides the genome architecture by allocation of boundary proteins in the genome. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogenome.ie-freiburg.mpg.de. |
format | Online Article Text |
id | pubmed-5768762 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-57687622018-01-19 High-resolution TADs reveal DNA sequences underlying genome organization in flies Ramírez, Fidel Bhardwaj, Vivek Arrigoni, Laura Lam, Kin Chung Grüning, Björn A. Villaveces, José Habermann, Bianca Akhtar, Asifa Manke, Thomas Nat Commun Article Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by the M1BP protein, and two new boundary motifs. In contrast to mammals, the CTCF motif is only enriched on a small fraction of boundaries flanking inactive chromatin while most active boundaries contain the motifs bound by the M1BP or Beaf-32 proteins. We demonstrate that boundaries can be accurately predicted using only the motif sequences at open chromatin sites. We propose that DNA sequence guides the genome architecture by allocation of boundary proteins in the genome. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogenome.ie-freiburg.mpg.de. Nature Publishing Group UK 2018-01-15 /pmc/articles/PMC5768762/ /pubmed/29335486 http://dx.doi.org/10.1038/s41467-017-02525-w Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Ramírez, Fidel Bhardwaj, Vivek Arrigoni, Laura Lam, Kin Chung Grüning, Björn A. Villaveces, José Habermann, Bianca Akhtar, Asifa Manke, Thomas High-resolution TADs reveal DNA sequences underlying genome organization in flies |
title | High-resolution TADs reveal DNA sequences underlying genome organization in flies |
title_full | High-resolution TADs reveal DNA sequences underlying genome organization in flies |
title_fullStr | High-resolution TADs reveal DNA sequences underlying genome organization in flies |
title_full_unstemmed | High-resolution TADs reveal DNA sequences underlying genome organization in flies |
title_short | High-resolution TADs reveal DNA sequences underlying genome organization in flies |
title_sort | high-resolution tads reveal dna sequences underlying genome organization in flies |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768762/ https://www.ncbi.nlm.nih.gov/pubmed/29335486 http://dx.doi.org/10.1038/s41467-017-02525-w |
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