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| Status |
Public on Mar 29, 2018 |
| Title |
Ldb1 mediates trans enhancement in mammals |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The monoallelic expression of olfactory receptor (OR) genes is governed by a large number of intergenic enhancer elements that are located in intergenic regions of OR gene clusters. In mature olfactory sensory neurons (OSNs), multiple OR enhancers colocalize in an interchromosomal enhancer hub together with the active OR allele. Here we show that in OSNs OR enhancers are bound by Ldb1, but not general purpose mediators of nuclear architecture (CTCF or the cohesin complex subunit Rad21). Conditional deletion of Ldb1 in OSNs results in the dissolution of long range and interchromosomal contacts between OR Enhancers and in pervasive reductions in OR gene expression.
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| Overall design |
Two types of data are included: Crosslinked ChIP-Seq data identifies sites bound by CTCF, Rad21, or Ldb1 and RNA-Seq data profiles changes in gene expression in Ldb1 deleted mOSNs, Lhx2 deleted cells, or Enhancer Knockout mOSNs. The number of replicates varies between experiments.
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| Contributor(s) |
Monahan K, Lomvardas S |
| Citation(s) |
30626972 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| F32 GM108474 |
Developmental Control of Gene Expression and Nuclear Architecture by Cohesin |
University of California San Francisco |
Kevin Monahan |
| R01 DC013560 |
Understanding the Role of Nuclear Architecture in Olfactory Receptor Choice |
Trustees of Columbia University in the City of New York |
Stavros Lomvardas |
| R01 DC015451 |
Deciphering the molecular principles of olfactory receptor gene choice |
Trustees of Columbia University in the City of New York |
Stavros Lomvardas |
| U01 DA040582 |
Deciphering nuclear bodies and compartments that govern singular olfactory receptor expression. |
Trustees of Columbia University in the City of New York |
Stavros Lomvardas |
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| |
| Submission date |
Mar 21, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Kevin Monahan |
| E-mail(s) |
km1339@dls.rutgers.edu
|
| Organization name |
Rutgers University
|
| Department |
Molecular Biology and Biochemistry
|
| Street address |
604 Allison Rd
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
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| Platforms (3) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA439446 |
| SRA |
SRP136181 |
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