Step-Wise Methylation of Histone H3K9 Positions Heterochromatin at the Nuclear Periphery

Akhtar, 2007, The nuclear envelope and transcriptional control, Nat. Rev. Genet., 8, 507, 10.1038/nrg2122 Andersen, 2007, Two C. elegans histone methyltransferases repress lin-3 EGF transcription to inhibit vulval development, Development, 134, 2991, 10.1242/dev.009373 Azzaria, 1996, A fork head/HNF-3 homolog expressed in the pharynx and intestine of the Caenorhabditis elegans embryo, Dev. Biol., 178, 289, 10.1006/dbio.1996.0219 Bannister, 2001, Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain, Nature, 410, 120, 10.1038/35065138 Bender, 2004, The MES-2/MES-3/MES-6 complex and regulation of histone H3 methylation in C. elegans, Curr. Biol., 14, 1639, 10.1016/j.cub.2004.08.062 Bender, 2006, MES-4: an autosome-associated histone methyltransferase that participates in silencing the X chromosomes in the C. elegans germ line, Development, 133, 3907, 10.1242/dev.02584 Bessler, 2010, Differential localization and independent acquisition of the H3K9me2 and H3K9me3 chromatin modifications in the Caenorhabditis elegans adult germ line, PLoS Genet., 6, e1000830, 10.1371/journal.pgen.1000830 Black, 2011, Chromatin landscape: methylation beyond transcription, Epigenetics, 6, 9, 10.4161/epi.6.1.13331 Capowski, 1991, Identification of grandchildless loci whose products are required for normal germ-line development in the nematode Caenorhabditis elegans, Genetics, 129, 1061, 10.1093/genetics/129.4.1061 Dennis, 2003, DAVID: Database for Annotation, Visualization, and Integrated Discovery, Genome Biol., 4, 3, 10.1186/gb-2003-4-5-p3 Frøkjaer-Jensen, 2008, Single-copy insertion of transgenes in Caenorhabditis elegans, Nat. Genet., 40, 1375, 10.1038/ng.248 Furuhashi, 2010, Trans-generational epigenetic regulation of C. elegans primordial germ cells, Epigenetics Chromatin, 3, 15, 10.1186/1756-8935-3-15 Goldman, 2002, Nuclear lamins: building blocks of nuclear architecture, Genes Dev., 16, 533, 10.1101/gad.960502 Guelen, 2008, Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions, Nature, 453, 948, 10.1038/nature06947 Hansen, 2008, A model for transmission of the H3K27me3 epigenetic mark, Nat. Cell Biol., 10, 1291, 10.1038/ncb1787 Hsieh, 2000, Recognition and silencing of repeated DNA, Annu. Rev. Genet., 34, 187, 10.1146/annurev.genet.34.1.187 Ikegami, 2010, Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2, Genome Biol., 11, R120, 10.1186/gb-2010-11-12-r120 Kamath, 2003, Systematic functional analysis of the Caenorhabditis elegans genome using RNAi, Nature, 421, 231, 10.1038/nature01278 Kind, 2010, Genome-nuclear lamina interactions and gene regulation, Curr. Opin. Cell Biol., 22, 320, 10.1016/j.ceb.2010.04.002 Koester-Eiserfunke, 2011, H3K9me2/3 binding of the MBT domain protein LIN-61 is essential for Caenorhabditis elegans vulva development, PLoS Genet., 7, e1002017, 10.1371/journal.pgen.1002017 Lachner, 2001, Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins, Nature, 410, 116, 10.1038/35065132 Lehner, 2006, RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions, Nat. Protoc., 1, 1617, 10.1038/nprot.2006.245 Liu, 2011, Broad chromosomal domains of histone modification patterns in C. elegans, Genome Res., 21, 227, 10.1101/gr.115519.110 Loyola, 2006, PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state, Mol. Cell, 24, 309, 10.1016/j.molcel.2006.08.019 Loyola, 2009, The HP1α-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin, EMBO Rep., 10, 769, 10.1038/embor.2009.90 Luo, 2009, The nuclear periphery of embryonic stem cells is a transcriptionally permissive and repressive compartment, J. Cell Sci., 122, 3729, 10.1242/jcs.052555 Maison, 2004, HP1 and the dynamics of heterochromatin maintenance, Nat. Rev. Mol. Cell Biol., 5, 296, 10.1038/nrm1355 Margalit, 2007, Barrier-to-autointegration factor—a BAFfling little protein, Trends Cell Biol., 17, 202, 10.1016/j.tcb.2007.02.004 Martin, 1996, The vagaries of variegating transgenes, Bioessays, 18, 919, 10.1002/bies.950181111 Mattout, 2011, An EDMD mutation in C. elegans lamin blocks muscle-specific gene relocation and compromises muscle integrity, Curr. Biol., 21, 1603, 10.1016/j.cub.2011.08.030 Meister, 2010, The spatial dynamics of tissue-specific promoters during C. elegans development, Genes Dev., 24, 766, 10.1101/gad.559610 Peric-Hupkes, 2010, Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation, Mol. Cell, 38, 603, 10.1016/j.molcel.2010.03.016 Peters, 2001, Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability, Cell, 107, 323, 10.1016/S0092-8674(01)00542-6 Peters, 2003, Partitioning and plasticity of repressive histone methylation states in mammalian chromatin, Mol. Cell, 12, 1577, 10.1016/S1097-2765(03)00477-5 Pickersgill, 2006, Characterization of the Drosophila melanogaster genome at the nuclear lamina, Nat. Genet., 38, 1005, 10.1038/ng1852 Pinheiro, 2012, Prdm3 and Prdm16 are H3K9me1 Methyltransferases Required for Mammalian Heterochromatin Integrity, Cell, 150, 948, 10.1016/j.cell.2012.06.048 Rea, 2000, Regulation of chromatin structure by site-specific histone H3 methyltransferases, Nature, 406, 593, 10.1038/35020506 Sassi, 2005, Gene CATCHR—gene cloning and tagging for Caenorhabditis elegans using yeast homologous recombination: a novel approach for the analysis of gene expression, Nucleic Acids Res., 33, e163, 10.1093/nar/gni164 Schott, 2006, Unique and redundant functions of C. elegans HP1 proteins in post-embryonic development, Dev. Biol., 298, 176, 10.1016/j.ydbio.2006.06.039 Shevelyov, 2009, The B-type lamin is required for somatic repression of testis-specific gene clusters, Proc. Natl. Acad. Sci. USA, 106, 3282, 10.1073/pnas.0811933106 Tachibana, 2002, G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis, Genes Dev., 16, 1779, 10.1101/gad.989402 Timmons, 2001, Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans, Gene, 263, 103, 10.1016/S0378-1119(00)00579-5 Wen, 2009, Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells, Nat. Genet., 41, 246, 10.1038/ng.297 Ye, 1996, Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1, J. Biol. Chem., 271, 14653, 10.1074/jbc.271.25.14653 Yuzyuk, 2009, The polycomb complex protein mes-2/E(z) promotes the transition from developmental plasticity to differentiation in C. elegans embryos, Dev. Cell, 16, 699, 10.1016/j.devcel.2009.03.008 Zhang, 2008, Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin, Nat. Struct. Mol. Biol., 15, 381, 10.1038/nsmb.1406 Andersen, E.C., and Horvitz, H.R. (2007). Two C. elegans histone methyltransferases repress lin-3 EGF transcription to inhibit vulval development. Development 134, 2991–2999. Azzaria, M., Goszczynski, B., Chung, M.A., Kalb, J.M., and McGhee, J.D. (1996). A fork head/HNF-3 homolog expressed in the pharynx and intestine of the Caenorhabditis elegans embryo. Dev. Biol. 178, 289–303. Bessler, J.B., Andersen, E.C., and Villeneuve, A.M. (2010). Differential localization and independent acquisition of the H3K9me2 and H3K9me3 chromatin modifications in the Caenorhabditis elegans adult germ line. PLoS Genet. 6, e1000830. Development Core Team (2004). R: A language and enviroment for statistical computing. R foundation for statistical computing (Vienna, Austria). http://www.r-project.org. Frøkjaer-Jensen, C., Davis, M.W., Hopkins, C.E., Newman, B.J., Thummel, J.M., Olesen, S.-P., Grunnet, M., and Jorgensen, E.M. (2008). Single-copy insertion of transgenes in Caenorhabditis elegans. Nat. Genet. 40, 1375–1383. Garcia, B.A., Mollah, S., Ueberheide, B.M., Busby, S.A., Muratore, T.L., Shabanowitz, J., and Hunt, D.F. (2007). Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc. 2, 933–938. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80. Greil, F., Moorman, C., van Steensel, B. (2006). DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol. 410, 342–359. Ihaka, R., and Gentleman, R. (1996). R: A Language for Data Analysis and Graphics. J. Comput. Graph. Statist. 5, 299–314. Kamath, R.S., Fraser, A.G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., et al. (2003). Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–237. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. Lehner, B., Tischler, J., and Fraser, A.G. (2006). RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions. Nat. Protoc. 1, 1617–1620. Meister, P., Towbin, B.D., Pike, B.L., Ponti, A., and Gasser, S.M. (2010). The spatial dynamics of tissue-specific promoters during C. elegans development. Genes Dev. 24, 766–782. Peters, A.H.F.M., Kubicek, S., Mechtler, K., O’Sullivan, R.J., Derijck, A.A.H.A., Perez-Burgos, L., Kohlmaier, A., Opravil, S., Tachibana, M., Shinkai, Y., et al. (2003). Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12, 1577–1589. Tijsterman, M., May, R.C., Simmer, F., Okihara, K.L., and Plasterk, R.H.A. (2004). Genes required for systemic RNA interference in Caenorhabditis elegans. Curr. Biol. 14, 111–116. Toedling, J., Skylar, O., Krueger, T., Fischer, J.J., Sperling, S., and Huber, W. (2007). Ringo—an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics 8, 221.