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| Status |
Public on Jun 25, 2021 |
| Title |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-Seq 2] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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 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 E. coli and S. cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and 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, replication-transcription encounters, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach that can be applied in any organism to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.
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| Overall design |
Sequencing data from E. coli MG1655 and S. cerevisiae. (i) E. coli GapR and GapR1-76 ChIP-seq, (ii) E. coli RNA-seq +/- GapR-3xFLAG expression, (iii) S. cerevisiae GapR ChIP-seq in raffinose +/- alpha-factor and in glycerol, (iv) S. cerevisiae RNA-seq +/- GapR, and (v) S. cerevisiae RNA-seq in raffinose +/- alpha-factor and in glycerol after GapR induction
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| Contributor(s) |
Guo MS, Kawamura R, Littlehale M, Marko JF, Laub MT |
| Citation(s) |
34279217 |
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| Submission date |
Jan 04, 2021 |
| Last update date |
Sep 24, 2021 |
| Contact name |
Monica S Guo |
| E-mail(s) |
msguo@uw.edu
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| Organization name |
University of Washington
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| Department |
Microbiology
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| Lab |
Guo
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| Street address |
750 Republican St
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (1) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
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| Samples (7)
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| GSM5001907 |
ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in raffinose and induced with galactose, replicate 1 |
| GSM5001908 |
ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in raffinose and induced with galactose, replicate 2 |
| GSM5001909 |
ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in raffinose, alpha-factor arrested, and induced with galactose, replicate 1 |
| GSM5001910 |
ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in raffinose, alpha-factor arrested, and induced with galactose, replicate 2 |
| GSM5001911 |
ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in glycerol and induced with galactose |
| GSM5001912 |
ML3287 (OAY470), in raffinose and induced with galactose, replicate 1 |
| GSM5001913 |
ML3287 (OAY470), in raffinose and induced with galactose, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE152882 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
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| Relations |
| BioProject |
PRJNA689471 |
| SRA |
SRP300171 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE164186_RAW.tar |
1010.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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