RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2

Yaakov Maman; Grace Teng; Rashu Seth; Steven H. Kleinstein; David G. Schatz

doi:10.1093/nar/gkw633

RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2

Yaakov Maman, Grace Teng, Rashu Seth, Steven H. Kleinstein, David G. Schatz

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

Abstract

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 plant homeodomain (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.

Original language	English
Pages (from-to)	9624-9637
Number of pages	14
Journal	Nucleic Acids Research
Volume	44
Issue number	20
DOIs	https://doi.org/10.1093/nar/gkw633
State	Published - 16 Nov 2016
Externally published	Yes

Bibliographical note

Publisher Copyright:
© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Funding

The authors wish to thank Yoram Louzoun and Gilad Liberman for valuable insight and advice regarding computational approaches used in this study, and to Lindsay Cowell and Min Kim for genome-wide RSS scanning. National Institutes of Health [R37 AI32524 to D.G.S.]; NRSA Institutional Postdoctoral Training Grant [T32 AI007019]; Cancer Research Institute Irvington Postdoctoral Fellowship [to G.T]. Funding for open access charge: National Institutes of Health [R37 AI32524 to D.G.S.]. D.G.S. is an investigator of the Howard Hughes Medical Institute. Conflict of interest statement. None declared.

Funders	Funder number
National Institutes of Health
Howard Hughes Medical Institute
National Institute of Allergy and Infectious Diseases	R37AI032524
Cancer research institute
Israel National Road Safety Authority	T32 AI007019

Access to Document

10.1093/nar/gkw633

Cite this

@article{86aa304c21f74023a7ab3659ffed5226,

title = "RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2",

abstract = "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 plant homeodomain (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.",

author = "Yaakov Maman and Grace Teng and Rashu Seth and Kleinstein, {Steven H.} and Schatz, {David G.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2016",

month = nov,

day = "16",

doi = "10.1093/nar/gkw633",

language = "אנגלית",

volume = "44",

pages = "9624--9637",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "20",

}

TY - JOUR

T1 - RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2

AU - Maman, Yaakov

AU - Teng, Grace

AU - Seth, Rashu

AU - Kleinstein, Steven H.

AU - Schatz, David G.

PY - 2016/11/16

Y1 - 2016/11/16

N2 - 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 plant homeodomain (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.

AB - 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 plant homeodomain (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.

UR - http://www.scopus.com/inward/record.url?scp=85016127472&partnerID=8YFLogxK

U2 - 10.1093/nar/gkw633

DO - 10.1093/nar/gkw633

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 27436288

AN - SCOPUS:85016127472

SN - 0305-1048

VL - 44

SP - 9624

EP - 9637

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 20

ER -

RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2

Abstract

Bibliographical note

Funding

Access to Document

Other files and links

Fingerprint

Cite this