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| Status |
Public on Jan 01, 2023 |
| Title |
MNase-seq facilitates quantitative analysis of nucleosome positioning of wild type and mutant SWI/SNF complexes |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goal of this study is to evaluate potentially direct targets of altered chromatin remodeller SWI/SNF on nucleosome positioning at gene promoters by means of MNase-sequencing from synchronised L1-staged swsn‑1 single mutant, swsn‑1; snfc‑5 double mutants, swsn‑1; snfc‑5; ubr‑5 triple mutants compared to wild-type animals to achieve genome-wide nucleosome coverage profiles.
Methods: In vivo MNAse-seq profiles of WT (N2), swsn-1-/- (MH2354, SX3714), swsn-1-/-; snfc-5-/- (SX3622, SX3715), swsn-1-/-; snfc-5-/-; ubr-5-/- (SX3627) C. elegans L1s were generated by deep sequencing, in duplicate, using Illumina NextSeq 2000. The sequence reads that passed quality filters were mapped to C. elegans (ce11) genome using bowtie2 aligner v.2.2.9. The resulting bam files were converted to bigwig tracks using deeptools bamCoverage.
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the C elegans genome (build ce11). MNase-Seq data was further analysed locus-by-locus for nucleosome positioning around transcription start site of ubiquitous genes in the mutants relative to wild-type coverage. Swsn-1 single mutants showed strongly reduced +1 nucleosome coverage in compare to the wild-type animals. The +1-nucleosome coverage in both the swsn-1; snfc-5 double and swsn-1; snfc-5; ubr-5 triple suppressor mutants was higher than in swsn-1 single mutants. We also established that the subsets of ubiquitously up and downregulated SWI/SNF-dependent genes have a higher nucleosome coverage in wild-type animals when compared to all ubiquitous genes in wild-type animals.
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| Overall design |
In vivo MNAse-Seq profiles of WT, swsn-1-/-, swsn-1-/-; snfc-5-/- , swsn-1-/-; snfc-5-/-; ubr-5-/- C. elegans L1
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| Contributor(s) |
Ghosh S, Sarkies P, Lampersberger L, Burton NO |
| Citation(s) |
36689659 |
| |
| Submission date |
Nov 26, 2022 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Jonathan Lewis Price |
| Organization name |
University of Cambridge
|
| Department |
Biochemistry
|
| Lab |
Miska Lab
|
| Street address |
The Sanger Building Tennis Court Road
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| City |
cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
| GPL26672 |
Illumina NovaSeq 6000 (Caenorhabditis elegans) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA905658 |
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