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| Status |
Public on Dec 24, 2023 |
| Title |
Genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has been the dominant hypothesis in the field for decades. However, a systematic testing of this hypothesis has not been conducted, primarily due to the absence of suitable experimental techniques. In this study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale. By applying MChIP-C to study H3K4me3 promoter-centered interactions in K562 cells, we found that it had greatly improved resolution and sensitivity compared to restriction endonuclease-based C-methods. This allowed us to identify EP300 histone acetyltransferase and the SWI/SNF remodelling complex as potential candidates for establishing and/or maintaining enhancer-promoter interactions. Finally, leveraging data from published CRISPRi screens, we found that most functionally-verified enhancers do physically interact with their cognate promoters, supporting the enhancer-promoter looping model.
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| Overall design |
Crosslinked K562 cells were subjected to MNase digestion, proximity ligation, chromatin immunoprecipitation with H3K4me3 antibodies (Active motif, 39016) and deep sequencing, the whole procedure was dubbed MChIP-C. MChIP-C was performed in 4 biological replicates. Conventional H3K4me3 (Active motif, 39016) ChIP-seq was performed in one replicate.
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| Contributor(s) |
Golov AK, Gavrilov AA, Kaplan N, Razin SV |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Feb 10, 2023 |
| Last update date |
Dec 25, 2023 |
| Contact name |
Arkadiy Golov |
| E-mail(s) |
golovstein@gmail.com
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| Organization name |
Institute of Gene Biology, RAS
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| Street address |
Vavilova, 34/5
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| City |
Moscow |
| ZIP/Postal code |
119334 |
| Country |
Russia |
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| Platforms (2) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA933713 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE225087_MChIPC_ind_profiles.tar.gz |
467.1 Mb |
(ftp)(http) |
TAR |
| GSE225087_MChIPC_interactions.bedpe.gz |
1.3 Mb |
(ftp)(http) |
BEDPE |
| GSE225087_MChIPC_merged.100bp.bw |
80.5 Mb |
(ftp)(http) |
BW |
| GSE225087_MChIPC_merged.250bp.bw |
41.9 Mb |
(ftp)(http) |
BW |
| GSE225087_MChIPC_viewpoints.bed.gz |
133.6 Kb |
(ftp)(http) |
BED |
| GSE225087_RAW.tar |
134.7 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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