title: 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 assembly--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.
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Adam G W
authors.initials: AG
authors.lastname: Matthews
authors.forename: Alex J
authors.initials: AJ
authors.lastname: Kuo
authors.forename: Santiago
authors.initials: S
authors.lastname: Ramón-Maiques
authors.forename: Sunmi
authors.initials: S
authors.lastname: Han
authors.forename: Karen S
authors.initials: KS
authors.lastname: Champagne
authors.forename: Dmitri
authors.initials: D
authors.lastname: Ivanov
authors.forename: Mercedes
authors.initials: M
authors.lastname: Gallardo
authors.forename: Dylan
authors.initials: D
authors.lastname: Carney
authors.forename: Peggie
authors.initials: P
authors.lastname: Cheung
authors.forename: David N
authors.initials: DN
authors.lastname: Ciccone
authors.forename: Kay L
authors.initials: KL
authors.lastname: Walter
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Utz
authors.forename: Yang
authors.initials: Y
authors.lastname: Shi
authors.forename: Tatiana G
authors.initials: TG
authors.lastname: Kutateladze
authors.forename: Wei
authors.initials: W
authors.lastname: Yang
authors.forename: Or
authors.initials: O
authors.lastname: Gozani
authors.forename: Marjorie A
authors.initials: MA
authors.lastname: Oettinger
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D015322:Gene Rearrangement, B-Lymphocyte; D006657:Histones / Q000737:chemistry / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000235:genetics; D008239:Lysine / Q000737:chemistry / Q000378:metabolism*; D008745:Methylation; D051379:Mice; D008958:Models, Molecular; D011485:Protein Binding; D011995:Recombination, Genetic; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014364:Tryptophan / Q000235:genetics / Q000378:metabolism; D045567:VDJ Recombinases / Q000737:chemistry / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D006657:Histones; D018398:Homeodomain Proteins; C499308:Rag2 protein, mouse; D014364:Tryptophan; D045567:VDJ Recombinases; D008239:Lysine