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| Status |
Public on Jul 06, 2016 |
| Title |
RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2 |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The RAG1/RAG2 endonuclease initiates V(D)J recombination at antigen receptor loci but also binds to thousands of places outside of these loci. RAG2 localizes directly to lysine 4 trimethylated histone 3 (H3K4me3) through a PHD finger. The relative contribution of RAG2-dependent and RAG1-intrinsic mechanisms in determining RAG1 binding patterns is not known. Through analysis of deep RAG1 ChIP-seq data, we provide a quantitative description of the forces underlying genome-wide targeting of RAG1. Surprisingly, sequence-specific DNA binding contributes minimally to RAG1 targeting outside of antigen receptor loci. Instead, RAG1 binding is driven by two distinct modes of interaction with chromatin: the first is driven by H3K4me3, promoter-focused, and dependent on the RAG2 PHD, and the second is defined by H3K27Ac, enhancer-focused, and dependent on "non-core" portions of RAG1. Based on this and additional chromatin and genomic features, we formulated a predictive model of RAG1 targeting to the genome. RAG1 binding sites predicted by our model correlate well with observed patterns of RAG1-mediated breaks in human pro-B acute lymphoblastic leukemia. Overall, this study provides an integrative model for RAG1 genome-wide binding and off-target activity, and reveals a novel role for the RAG1 non-core region in RAG1 targeting.
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| |
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| Overall design |
ChIP-seq profiles of RAG1 from mouse thymocytes, and H3K27Ac from human REH cell line
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| |
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| Contributor(s) |
Maman Y, Teng G, Seth R, Kleinstein S, Schatz D |
| Citation(s) |
27436288 |
| Submission date |
Jul 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yaakov Maman |
| Organization name |
Bar-Ilan University
|
| Department |
Azrieli Faculty of Medicine
|
| Lab |
Genome Instability & Cancer
|
| Street address |
Henrietta Szold 8
|
| City |
Safed |
| ZIP/Postal code |
1311502 |
| Country |
Israel |
| |
|
| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (4)
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| Relations |
| BioProject |
PRJNA327870 |
| SRA |
SRP077929 |
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