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| Status |
Public on Jul 06, 2020 |
| Title |
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains [ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Insulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that potent insulation is provided by multiple CTCF binding sites. Furthermore, CTCF-mediated insulation is dependent on DNA sequences adjacent to its core binding motifs, and CTCF binding sites from topologically associating domains (TAD) boundaries are more likely to function as insulators than those outside TAD boundaries independent of binding strength. Using chromosomal conformation capture assays and high resolution chromatin imaging techniques, we demonstrate that insulators reduce enhancer-promoter contacts by forming local chromatin domains. Taken together, our results provide strong genetic, molecular and imaging evidence connecting chromatin topology to action of insulators in the mammalian genome.
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| Overall design |
Examination of insulator activity of CTCF binding seqences and their effects on chromatin topology in mouse embryonic cells
Chromosome coordinates of variants:
'4CBS' was inserted between chr3:34,726,762-34,727,258; mm10
'4CBS downstream' was inserted between chr3:34,794,087-34,794,154; mm10.
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| |
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| Contributor(s) |
Hui H, Bing R |
| Citation(s) |
34002095 |
| |
| Submission date |
Jun 27, 2020 |
| Last update date |
Feb 23, 2022 |
| Contact name |
Bing Ren |
| Organization name |
University of California, San Diego School of Medicine
|
| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL21626 |
NextSeq 550 (Mus musculus) |
|
| Samples (67)
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| This SubSeries is part of SuperSeries: |
| GSE153403 |
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains |
|
| Relations |
| BioProject |
PRJNA642298 |
| SRA |
SRP269016 |
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