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Series GSE16723 Query DataSets for GSE16723
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
Overall design Identification of BCL6 and NFkB binding sites in unstimulated and LPS-stimulated primary bone-marrow derived macrophages.
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)
GSM419049 macrophage_BCL6_ChIPSeq
GSM419050 macrophage_IgG_ChIPSeq
GSM419051 macrophage_input_DNA
SRA SRP001843
BioProject PRJNA117485

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Supplementary file Size Download File type/resource
GSE16723_BCL6_combined.ucsc.bed.gz 51.2 Mb (ftp)(http) BED
GSE16723_BCL6_combined_0.01_peaks.txt.gz 438.8 Kb (ftp)(http) TXT
GSE16723_RAW.tar 9.1 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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