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RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination

Abstract

Nuclear processes such as transcription, DNA replication and recombination are dynamically regulated by chromatin structure. Eukaryotic transcription is known to be regulated by chromatin-associated proteins containing conserved protein domains that specifically recognize distinct covalent post-translational modifications on histones. However, it has been unclear whether similar mechanisms are involved in mammalian DNA recombination. Here we show that RAG2—an essential component of the RAG1/2 V(D)J recombinase, which mediates antigen-receptor gene assembly1—contains a plant homeodomain (PHD) finger that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3). The high-resolution crystal structure of the mouse RAG2 PHD finger bound to H3K4me3 reveals the molecular basis of H3K4me3-recognition by RAG2. Mutations that abrogate RAG2’s recognition of H3K4me3 severely impair V(D)J recombination in vivo. Reducing the level of H3K4me3 similarly leads to a decrease in V(D)J recombination in vivo. Notably, a conserved tryptophan residue (W453) that constitutes a key structural component of the K4me3-binding surface and is essential for RAG2’s recognition of H3K4me3 is mutated in patients with immunodeficiency syndromes. Together, our results identify a new function for histone methylation in mammalian DNA recombination. Furthermore, our results provide the first evidence indicating that disrupting the read-out of histone modifications can cause an inherited human disease.

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Figure 1: The RAG2 PHD finger is a novel H3K4me3-binding module.
Figure 2: The molecular basis of H3K4me3-recognition by RAG2PHD.
Figure 3: Recognition of H3K4me3 by RAG2 PHD is dispensable for RAG2 in vitro enzymatic activity, but essential for RAG2 binding to native histones.
Figure 4: Recognition of H3K4me3 is crucial for RAG1/2 recombinase activity in vivo.

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Acknowledgements

We thank K.-J. Armache and J.-J. Song for the generous gift of recombinant mononucleosomes; R. Kingston and members of the Kingston laboratory for helpful discussions; and N. Lau, J.-J. Song, and M. Gellert for critical reading of this manuscript. This work was supported by NIH grants (M.A.O., O.G., D.I. and T.G.K.), as well as a Korea Research Foundation grant (S.H.). O.G. is a recipient of a Burroughs Wellcome Career Award in Biomedical Sciences and a Kimmel Scholar Award. S.R.-M. has been the recipient of a fellowship from the Human Frontier Science Program. A.J.K. is funded by Stanford University through a Genentech Foundation Predoctoral Fellowship. A.G.W.M. is a Howard Hughes Medical Institute Predoctoral Fellow.

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Correspondence to Or Gozani or Marjorie A. Oettinger.

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The file contains Supplementary Figures S1-S13 with Legends, Supplementary Table 1 and additional references. The Supplementary Figures support the general conclusion that the RAG2PHD-H3K4me3 interaction plays an important role in regulating V(D)J recombination, Supplementary Figure 1 providing a model for how H3K4me3-binding by RAG2 influences V(D)J recombination. (PDF 2669 kb)

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Matthews, A., Kuo, A., Ramón-Maiques, S. et al. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450, 1106–1110 (2007). https://doi.org/10.1038/nature06431

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