High-resolution, genome-wide mapping of positive supercoiling in chromosomes
<jats:p>Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we des...
| Main Authors: | , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications, Ltd
2021
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| Online Access: | https://hdl.handle.net/1721.1/135346 |
| _version_ | 1826193611190960128 |
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| author | Guo, Monica S Kawamura, Ryo Littlehale, Megan L Marko, John F Laub, Michael T |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Guo, Monica S Kawamura, Ryo Littlehale, Megan L Marko, John F Laub, Michael T |
| author_sort | Guo, Monica S |
| collection | MIT |
| description | <jats:p>Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to <jats:italic>Escherichia coli</jats:italic> and <jats:italic>Saccharomyces cerevisiae</jats:italic>, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently oriented genes, consistent with the ‘twin-domain’ model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin-binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.</jats:p> |
| first_indexed | 2024-09-23T09:41:51Z |
| format | Article |
| id | mit-1721.1/135346 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T09:41:51Z |
| publishDate | 2021 |
| publisher | eLife Sciences Publications, Ltd |
| record_format | dspace |
| spelling | mit-1721.1/1353462024-01-02T19:17:08Z High-resolution, genome-wide mapping of positive supercoiling in chromosomes Guo, Monica S Kawamura, Ryo Littlehale, Megan L Marko, John F Laub, Michael T Massachusetts Institute of Technology. Department of Biology Howard Hughes Medical Institute <jats:p>Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to <jats:italic>Escherichia coli</jats:italic> and <jats:italic>Saccharomyces cerevisiae</jats:italic>, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently oriented genes, consistent with the ‘twin-domain’ model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin-binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.</jats:p> 2021-10-27T20:23:03Z 2021-10-27T20:23:03Z 2021-07-19 2021-07-21T14:32:47Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/135346 en 10.7554/elife.67236 eLife Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf eLife Sciences Publications, Ltd eLife |
| spellingShingle | Guo, Monica S Kawamura, Ryo Littlehale, Megan L Marko, John F Laub, Michael T High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
| title | High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
| title_full | High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
| title_fullStr | High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
| title_full_unstemmed | High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
| title_short | High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
| title_sort | high resolution genome wide mapping of positive supercoiling in chromosomes |
| url | https://hdl.handle.net/1721.1/135346 |
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