RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination.
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.
Matthews
Adam G W
AG
Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
Kuo
Alex J
AJ
Ramón-Maiques
Santiago
S
Han
Sunmi
S
Champagne
Karen S
KS
Ivanov
Dmitri
D
Gallardo
Mercedes
M
Carney
Dylan
D
Cheung
Peggie
P
Ciccone
David N
DN
Walter
Kay L
KL
Utz
Paul J
PJ
Shi
Yang
Y
Kutateladze
Tatiana G
TG
Yang
Wei
W
Gozani
Or
O
Oettinger
Marjorie A
MA
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*
D004268:DNA-Binding Proteins; D006657:Histones; D018398:Homeodomain Proteins; C499308:Rag2 protein, mouse; D014364:Tryptophan; D045567:VDJ Recombinases; D008239:Lysine