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

• Gellert, M. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu. Rev. Biochem. 71, 101–132 (2002)
  Article CAS Google Scholar
• Oettinger, M. A. How to keep V(D)J recombination under control. Immunol. Rev. 200, 165–181 (2004)
  Article CAS Google Scholar
• Chowdhury, D. & Sen, R. Stepwise activation of the immunoglobulin μ heavy chain gene locus. EMBO J. 20, 6394–6403 (2001)
  Article CAS Google Scholar
• Johnson, K., Angelin-Duclos, C., Park, S. & Calame, K. L. Changes in histone acetylation are associated with differences in accessibility of VH gene segments to V-DJ recombination during B-cell ontogeny and development. Mol. Cell. Biol. 23, 2438–2450 (2003)
  Article CAS Google Scholar
• Morshead, K. B., Ciccone, D. N., Taverna, S. D., Allis, C. D. & Oettinger, M. A. Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4. Proc. Natl Acad. Sci. USA 100, 11577–11582 (2003)
  Article CAS ADS Google Scholar
• Callebaut, I. & Mornon, J. P. The V(D)J recombination activating protein RAG2 consists of a six-bladed propeller and a PHD fingerlike domain, as revealed by sequence analysis. Cell. Mol. Life Sci. 54, 880–891 (1998)
  Article CAS Google Scholar
• Elkin, S. K. et al. A PHD finger motif in the C terminus of RAG2 modulates recombination activity. J. Biol. Chem. 280, 28701–28710 (2005)
  Article CAS Google Scholar
• Ragvin, A. et al. Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300. J. Mol. Biol. 337, 773–788 (2004)
  Article CAS Google Scholar
• Shi, X. et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442, 96–99 (2006)
  Article CAS ADS Google Scholar
• Wysocka, J. et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442, 86–90 (2006)
  Article CAS ADS Google Scholar
• West, K. L. et al. A direct interaction between the RAG2 C terminus and the core histones is required for efficient V(D)J recombination. Immunity 23, 203–212 (2005)
  Article CAS Google Scholar
• Li, H. et al. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442, 91–95 (2006)
  Article CAS ADS Google Scholar
• Pena, P. V. et al. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442, 100–103 (2006)
  Article CAS ADS Google Scholar
• Taverna, S. D. et al. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol. Cell 24, 785–796 (2006)
  Article CAS Google Scholar
• Ruthenburg, A. J., Allis, C. D. & Wysocka, J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell 25, 15–30 (2007)
  Article CAS Google Scholar
• Ramon-Maiques, S. et al. The PHD finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.0709170104 (in the press)
• Shi, X. et al. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J. Biol. Chem. 282, 2450–2455 (2007)
  Article CAS Google Scholar
• Gomez, C. A. et al. Mutations in conserved regions of the predicted RAG2 kelch repeats block initiation of V(D)J recombination and result in primary immunodeficiencies. Mol. Cell. Biol. 20, 5653–5664 (2000)
  Article CAS Google Scholar
• Villa, A. et al. Partial V(D)J recombination activity leads to Omenn syndrome. Cell 93, 885–896 (1998)
  Article CAS Google Scholar
• Baumann, M., Mamais, A., McBlane, F., Xiao, H. & Boyes, J. Regulation of V(D)J recombination by nucleosome positioning at recombination signal sequences. EMBO J. 22, 5197–5207 (2003)
  Article CAS Google Scholar
• Sims, R. J. & Reinberg, D. Histone H3 Lys 4 methylation: caught in a bind? Genes Dev. 20, 2779–2786 (2006)
  Article CAS Google Scholar
• Iwase, S. et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128, 1077–1088 (2007)
  Article CAS Google Scholar
• Perkins, E. J., Kee, B. L. & Ramsden, D. A. Histone 3 lysine 4 methylation during the pre-B to immature B-cell transition. Nucleic Acids Res. 32, 1942–1947 (2004)
  Article CAS Google Scholar
• Akamatsu, Y. et al. Deletion of the RAG2 C terminus leads to impaired lymphoid development in mice. Proc. Natl Acad. Sci. USA 100, 1209–1214 (2003)
  Article CAS ADS Google Scholar
• Corneo, B. et al. Rag mutations reveal robust alternative end joining. Nature 449, 483–486 (2007)
  Article CAS ADS Google Scholar
• Kirch, S. A., Rathbun, G. A. & Oettinger, M. A. Dual role of RAG2 in V(D)J recombination: catalysis and regulation of ordered Ig gene assembly. EMBO J. 17, 4881–4886 (1998)
  Article CAS Google Scholar
• Liang, H. E. et al. The “dispensable” portion of RAG2 is necessary for efficient V-to-DJ rearrangement during B and T cell development. Immunity 17, 639–651 (2002)
  Article CAS Google Scholar
• Shi, Y. & Whetstine, J. R. Dynamic regulation of histone lysine methylation by demethylases. Mol. Cell 25, 1–14 (2007)
  Article CAS Google Scholar
• Tenney, K. & Shilatifard, A. A. COMPASS in the voyage of defining the role of trithorax/MLL-containing complexes: linking leukemogensis to covalent modifications of chromatin. J. Cell. Biochem. 95, 429–436 (2005)
  Article CAS Google Scholar
• Liu, Y., Subrahmanyam, R., Chakraborty, T., Sen, R. & Desiderio, S. A plant homeodomain in Rag-2 that binds hypermethylated lysine 4 of histone H3 is necessary for efficient antigen-receptor-gene rearrangement. Immunity 4, 561–571 (2007)
  Article Google Scholar
• Matthews, A. G., Elkin, S. K. & Oettinger, M. A. Ordered DNA release and target capture in RAG transposition. EMBO J. 23, 1198–1206 (2004)
  Article CAS Google Scholar
• Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251–260 (1997)
  Article CAS ADS Google Scholar
• Ottinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)
  Article Google Scholar
• McCoy, A. J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D Biol. Crystallogr. 63, 32–41 (2007)
  Article CAS Google Scholar
• Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
  Article Google Scholar
• Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)
  Article CAS Google Scholar
• Sheldrick, G. M. & Schneider, T. R. SHELXL: High-resolution refinement. Methods Enzymol. 277, 319–343 (1997)
  Article CAS Google Scholar
• Elkin, S. K., Matthews, A. G. & Oettinger, M. A. The C-terminal portion of RAG2 protects against transposition in vitro . EMBO J. 22, 1931–1938 (2003)
  Article CAS Google Scholar
• Dai, Y. et al. Nonhomologous end joining and V(D)J recombination require an additional factor. Proc. Natl Acad. Sci. USA 100, 2462–2467 (2003)
  Article CAS ADS Google Scholar
• Gauss, G. H. & Lieber, M. R. Unequal signal and coding joint formation in human V(D)J recombination. Mol. Cell. Biol. 13, 3900–3906 (1993)
  Article CAS Google Scholar
• Schlissel, M. S., Corcoran, L. M. & Baltimore, D. Virus-transformed pre-B cells show ordered activation but not inactivation of immunoglobulin gene rearrangement and transcription. J. Exp. Med. 173, 711–720 (1991)
  Article CAS Google Scholar