|
| Status |
Public on Nov 24, 2010 |
| Title |
Bcl6 and NFkB cistromes mediate opposing reulation of the innate immune response |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Here, using ChIP-seq, we define the NF-κB cistrome which is comprised of 31,070 cis-acting binding sites responsive to LPS-induced signaling. In addition, we demonstrate that the transcriptional repressor B-cell lymphoma 6 (Bcl-6) regulates nearly a third of the Tlr4-regulated transcriptome and that 90% of the Bcl-6 cistrome is collapsed following Tlr4 activation. Bcl-6 deficient macrophages are acutely hypersensitive to lipopolysaccharide (LPS) and, using comparative ChIP-seq analyses, we find that the Bcl-6 and NF-κB cistromes intersect, within nucleosomal distance, at nearly half of Bcl-6 binding sites in stimulated macrophages to promote opposing epigenetic modifications of the local chromatin. These results reveal a genomic strategy for controlling the innate immune response in which repressive and inductive cistromes establish a dynamic balance between macrophage quiescence and activation via epigenetically marked cis-regulatory elements.
keywords: Genome-wide location analysis
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| |
|
| Overall design |
Identification of BCL6 and NFkB binding sites in unstimulated and LPS-stimulated primary bone-marrow derived macrophages.
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| |
|
| Contributor(s) |
Yu RT, Barish GD, Evans RM |
| Citation(s) |
21106671 |
| Submission date |
Jun 19, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruth T Yu |
| Organization name |
Salk Institute
|
| Department |
Gene Expression Lab
|
| Lab |
Ronald Evans
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
|
| Samples (10)
|
|
| Relations |
| SRA |
SRP001843 |
| BioProject |
PRJNA117485 |
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