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Series GSE264584 Query DataSets for GSE264584
Status Public on Jan 22, 2025
Title Ldb1 establishes multi-enhancer networks to regulate gene expression (TT-seq)
Organism Mus musculus
Experiment type Other
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.
 
Overall design Transient transcriptome sequencing (TT-seq) in LDB1-AID cells (untreated and 4 hour auxin-treated conditions).
 
Contributor(s) Wang S, Aboreden NG, Blobel GA
Citation(s) 39721581
Submission date Apr 22, 2024
Last update date Jan 22, 2025
Contact name Siqing Wang
E-mail(s) wangs16@chop.edu
Organization name Children’s Hospital of Philadelphia
Department Department of Pediatrics, Division of Hematology
Lab Gerd Blobel's Lab
Street address 3401 Civic Center Blvd
City Philadelphia
State/province PENNSYLVANIA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (6)
GSM8223054 LDB1_AID_untreated_TT-seq_rep1
GSM8223055 LDB1_AID_untreated_TT-seq_rep2
GSM8223056 LDB1_AID_untreated_TT-seq_rep3
Relations
BioProject PRJNA1103188

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE264584_3_LDB1_A-G1E_TT-seq_0322.0405.0524.0531_merged.mm9_CPM_dr_fwd.bw 376.2 Mb (ftp)(http) BW
GSE264584_3_LDB1_A-G1E_TT-seq_0322.0405.0524.0531_merged.mm9_CPM_dr_rev.bw 375.1 Mb (ftp)(http) BW
GSE264584_4_LDB1_A+G1E_TT-seq_0322.0405.0524.0531_merged.mm9_CPM_dr_fwd.bw 387.8 Mb (ftp)(http) BW
GSE264584_4_LDB1_A+G1E_TT-seq_0322.0405.0524.0531_merged.mm9_CPM_dr_rev.bw 382.4 Mb (ftp)(http) BW
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