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| Status |
Public on Nov 27, 2024 |
| Title |
Ldb1 establishes multi-enhancer networks to regulate gene expression |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. Furthermore, an engineered/forced, LDB1-driven chromatin loop can form in the absence of cohesin. Yet, in a fraction of cases cohesin driven extrusion may promote LDB1 anchored loops. Leveraging the dynamic reorganization of nuclear architecture during the transition from mitosis to G1 phase, we establish a relationship between LDB1-dependent interactions in the context of TAD organization and gene activation. Tri-C and Region Capture Micro-C reveal that LDB1 organizes multi-enhancer networks to activate transcription. This establishes LDB1 as direct driver of connectivity between regulatory elements.
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| Overall design |
Region Capture Micro-C was performed in LDB1-AID cells (untreated and 4 hour auxin-treated conditions).
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| Contributor(s) |
Aboreden NG, Blobel GA, Goel VY, Hansen AS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
May 02, 2024 |
| Last update date |
Nov 27, 2024 |
| Contact name |
Viraat Yogi Goel |
| E-mail(s) |
[email protected]
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| Organization name |
Massachusetts Institute of Technology (MIT)
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| Department |
Biological Engineering
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| Lab |
Anders Hansen Lab
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| Street address |
32 Vassar St, 56-722
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL34328 |
Illumina NovaSeq X (Mus musculus) |
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| Samples (4)
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| GSM8247156 |
G1E-ER4 LDB1-AID RCMC, Untreated, Biological Replicate 1 |
| GSM8247157 |
G1E-ER4 LDB1-AID RCMC, Untreated, Biological Replicate 2 |
| GSM8247158 |
G1E-ER4 LDB1-AID RCMC, Auxin 4 hr, Biological Replicate 1 |
| GSM8247159 |
G1E-ER4 LDB1-AID RCMC, Auxin 4 hr, Biological Replicate 2 |
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| Relations |
| BioProject |
PRJNA1107208 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE266450_RCMC_Ldb1_0hr_mm9.merged.50.mcool |
325.3 Mb |
(ftp)(http) |
MCOOL |
| GSE266450_RCMC_Ldb1_4hr_mm9.merged.50.mcool |
324.1 Mb |
(ftp)(http) |
MCOOL |
SRA Run Selector |
| Raw data are available in SRA |
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