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| Status |
Public on Mar 05, 2023 |
| Title |
SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
SATB1, a nuclear matrix-associated protein, has long been proposed to function as a global chromatin loop organizer in T cells. However, the precise roles of SATB1 in chromatin organization remain elusive. Here we show that the depletion of SATB1 in immortalized T cells led to pronounced changes in gene expression, particularly for genes involved in cell proliferation and T cell activation, as well as 3D genome architecture at multiple scales, including the A/B compartment, topologically associating domains (TADs), and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 led to increased association among the SATB1/CTCF co-occupied sites, as well as increased chromatin contacts across these sites, thereby altering the genome-wide chromatin loop landscape. SATB1 does not regulate genome architecture by modulating CTCF occupancy. Rather, the topological effects imposed by SATB1 may be attributed to SATB1-dependent anchoring of CTCF to the salt extraction-resistant nuclear matrix. Together, our findings suggest that the functional interplay between nuclear matrix and CTCF plays a critical role in orchestrating 3D genome organization.
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| Overall design |
Refer to individual Series
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| Web link |
https://www.cell.com/cell-reports/fulltext/S2211-1247(23)00334-0
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| Citation(s) |
37000624 |
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| Submission date |
Mar 19, 2022 |
| Last update date |
May 04, 2023 |
| Contact name |
bao wang |
| Organization name |
shanghai jiao tong university school of medicine
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| Street address |
jin zun road
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| City |
shanghai |
| ZIP/Postal code |
200000 |
| Country |
China |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (36)
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| GSM5942380 |
shSATB1, Jurkat, Hi-C, Rep 2 |
| GSM5942381 |
shCtrl, Jurkat, Hi-C, All Replicates, Merged |
| GSM5942382 |
shSATB1, Jurkat, Hi-C, All Replicates, Merged |
| GSM5942500 |
shCtrl, Jurkat, SATB1, CUT_Tag, Rep 1 |
| GSM5942501 |
shCtrl, Jurkat, SATB1, CUT_Tag, Rep 2 |
| GSM5942502 |
shCtrl, Jurkat, H3K27Ac, CUT_Tag, Rep 1 |
| GSM5942503 |
shCtrl, Jurkat, H3K27Ac, CUT_Tag, Rep 2 |
| GSM5942504 |
shSATB1, Jurkat, H3K27Ac, CUT_Tag, Rep 1 |
| GSM5942505 |
shSATB1, Jurkat, H3K27Ac, CUT_Tag, Rep 2 |
| GSM5942506 |
shCtrl, Jurkat, CTCF, CUT_Tag, Rep 1 |
| GSM5942507 |
shCtrl, Jurkat, CTCF, CUT_Tag, Rep 2 |
| GSM5942508 |
shCtrl, Jurkat, CTCF, CUT_Tag, Rep 3 |
| GSM5942509 |
shSATB1, Jurkat, CTCF, CUT_Tag, Rep 1 |
| GSM5942510 |
shSATB1, Jurkat, CTCF, CUT_Tag, Rep 2 |
| GSM5942511 |
shSATB1, Jurkat, CTCF, CUT_Tag, Rep 3 |
| GSM5962253 |
shCtrl, RNA-seq, rep 1 |
| GSM5962254 |
shCtrl, RNA-seq, rep 2 |
| GSM5962255 |
shCtrl, RNA-seq, rep 3 |
| GSM5962256 |
shSATB1, RNA-seq, rep 1 |
| GSM5962257 |
shSATB1, RNA-seq, rep 2 |
| GSM5962258 |
shSATB1, RNA-seq, rep 3 |
| GSM6035221 |
Matrin_3_CUT&Tag_Rep_1 |
| GSM6035222 |
Matrin_3_CUT&Tag_Rep_2 |
| GSM7030513 |
CD4+ T cells, CTCF-Rep1 |
| GSM7030514 |
CD4+ T cells, CTCF-Rep2 |
| GSM7030515 |
CD4+ T cells, SATB1-Rep1 |
| GSM7030516 |
CD4+ T cells, SATB1-Rep2 |
| GSM7030517 |
Naive CD4+ T cells, Control_Rep1 |
| GSM7030518 |
Naive CD4+ T cells, Control_Rep2 |
| GSM7030519 |
Naive CD4+ T cells, Control_Rep3 |
| GSM7030520 |
Naive CD4+ T cells, Satb1_cko_Rep1 |
| GSM7030521 |
Naive CD4+ T cells, Satb1_cko_Rep2 |
| GSM7030522 |
Naive CD4+ T cells, Satb1_cko_Rep3 |
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| This SuperSeries is composed of the following SubSeries:
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| GSE198259 |
SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [Hi-C] |
| GSE198267 |
SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [CUT&Tag] |
| GSE199006 |
SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites |
| GSE224728 |
SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [CUT&Tag] |
| GSE224729 |
SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [RNA-seq] |
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| Relations |
| BioProject |
PRJNA817814 |
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