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| Status |
Public on Jul 16, 2012 |
| Title |
Genome-wide Detection of Genes Targeted by Aberrant Somatic Hypermutation in Lymphoma |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We report a novel approach to identify genome-wide somatic hypermutation hotspots from short Illumina H3K4me3 ChIPseq reads in diffuse large B-cell lymphoma cells (DLBCL). Abberant somatic hypermation are known to occur at the promoters of several proto-oncogenes in DLBCL. To identify such events genome-wide, we performed H3K4me3 ChIPseq experiments (as to enrich promoter sequences of actively transcribed genes) in 2 DLBCL cells lines (OCI-Ly1 and OCI-Ly8) and their normal B-cell counterparts, Naive B cells (NBC) and Germinal Center B cells (GCBs). We discover new genes that harbor mutations in their promoter regions that are potentially introduced by the aberrant activation-induced cytosine deaminase activity in lymphoma cell lines, and many of these genes are important for the B cell biology. Moreover, we show that these mutations can affect the activities of these promoters. Our study provides a feasible approach for the detection of promoter mutations and broadens our knowledge on promoter mutations in lymphomas.
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| |
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| Overall design |
Examination of 1 histone mark (H3K4me3) in 4 different cell types.
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| |
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| Contributor(s) |
Jiang Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Yanwen Jiang |
| E-mail(s) |
yaj2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Street address |
413 E. 69th St. BB1462
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| SRA |
SRP009676 |
| BioProject |
PRJNA151499 |
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