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| Status |
Public on Aug 29, 2014 |
| Title |
The NF-kB genomic landscape in lymphoblastoid B-cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The nuclear factor kB (NF-kB) subunits RelA, RelB, c-Rel, p50 and p52 are each critical for B-cell development and function. To systematically characterize their responses to canonical and non-canonical NF-kB pathways activity, we performed ChIP-seq analysis in lymphoblastoid B-cells. We found a surprisingly complex NF-kB binding landscape, which did not readily reflect the two NF-kB pathway paradigm. Instead, ten subunit binding patterns were observed at promoters and eleven at enhancers. Surprisingly, nearly one-third of NF-kB binding sites lacked kB motifs. De novo motif finding uncovered distinct modes of NF-kB recruitment at these sites. The oncogenic forkhead box protein FOXM1 and NF-kB co-occupied many kB sites despite the absence of a FOXM1 DNA motif. FoxM1 knockdown decreased expression of key NF-kB targets and caused apoptosis. Our study highlights opportunities for selective therapeutic NF-kB blockade.
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| Overall design |
ChIP-seq was used to define the genomic landscape of NF-kB DNA binding in lymphoblastoid cells.
The raw data for GSM2628089 are not available.
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| Contributor(s) |
Zhao B, Barrera LA, Ersing I, Willox B, Schmidt S, Zhou H, Shi T, Mollo S, Greenfeld H, Takasaki K, Jiang S, Cahir-McFarland E, Kellis M, Bulyk ML, Kieff E, Gewurz B |
| Citation(s) |
25159142, 25255445 |
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| Submission date |
Feb 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin Gewurz |
| E-mail(s) |
bgewurz@bwh.harvard.edu
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| Organization name |
Brigham and Women's Hospital
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| Department |
Medicine
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| Street address |
181 Longwood Ave
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA238539 |
| SRA |
SRP107497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE55105_RelA.TagDens.bd150.st50.wig.tdf |
418.3 Mb |
(ftp)(http) |
TDF |
| GSE55105_RelB.TagDens.bd150.st50.wig.tdf |
418.0 Mb |
(ftp)(http) |
TDF |
| GSE55105_cRel.TagDens.bd150.st50.wig.tdf |
418.5 Mb |
(ftp)(http) |
TDF |
| GSE55105_p50.TagDens.bd150.st50.wig.tdf |
414.0 Mb |
(ftp)(http) |
TDF |
| GSE55105_p52.TagDens.bd150.st50.wig.tdf |
417.3 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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