HP1 Proteins Form Distinct Complexes and Mediate Heterochromatic Gene Silencing by Nonoverlapping Mechanisms

Aagaard, 1999, Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3–9 encode centromere-associated proteins which complex with the heterochromatin component M31, EMBO J., 18, 1923, 10.1093/emboj/18.7.1923 Agalioti, 2002, Deciphering the transcriptional histone acetylation code for a human gene, Cell, 111, 381, 10.1016/S0092-8674(02)01077-2 Allshire, 1995, Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation, Genes Dev., 9, 218, 10.1101/gad.9.2.218 Arcangioli, 1991, A novel switch-activating site (SAS1) and its cognate binding factor (SAP1) required for efficient mat1 switching in Schizosaccharomyces pombe, EMBO J., 10, 3025, 10.1002/j.1460-2075.1991.tb07853.x Bahler, 1998, Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe, Yeast, 14, 943, 10.1002/(SICI)1097-0061(199807)14:10<943::AID-YEA292>3.0.CO;2-Y Bannister, 2001, Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain, Nature, 410, 120, 10.1038/35065138 Bernstein, 2005, RNA meets chromatin, Genes Dev., 19, 1635, 10.1101/gad.1324305 Bjerling, 2002, Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity, Mol. Cell. Biol., 22, 2170, 10.1128/MCB.22.7.2170-2181.2002 Bjerling, 2004, A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe, Nucleic Acids Res., 32, 4421, 10.1093/nar/gkh780 Brasher, 2000, The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer, EMBO J., 19, 1587, 10.1093/emboj/19.7.1587 Braunstein, 1996, Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern, Mol. Cell. Biol., 16, 4349, 10.1128/MCB.16.8.4349 Brower-Toland, 2007, Drosophila PIWI associates with chromatin and interacts directly with HP1a, Genes Dev., 21, 2300, 10.1101/gad.1564307 Buhler, 2006, Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing, Cell, 125, 873, 10.1016/j.cell.2006.04.025 Buhler, 2007, RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing, Cell, 129, 707, 10.1016/j.cell.2007.03.038 Cryderman, 2005, Role of Drosophila HP1 in euchromatic gene expression, Dev. Dyn., 232, 767, 10.1002/dvdy.20310 Ekwall, 1994, Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast, Genetics, 136, 53, 10.1093/genetics/136.1.53 Ekwall, 1995, The chromodomain protein Swi6: a key component at fission yeast centromeres, Science, 269, 1429, 10.1126/science.7660126 Fuks, 2003, The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase, Nucleic Acids Res., 31, 2305, 10.1093/nar/gkg332 Gilbert, 2004, Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation, Mol. Cell, 14, 457, 10.1016/S1097-2765(04)00239-4 Grewal, 2003, Heterochromatin and epigenetic control of gene expression, Science, 301, 798, 10.1126/science.1086887 Halverson, 2000, A novel member of the Swi6p family of fission yeast chromo domain-containing proteins associates with the centromere in vivo and affects chromosome segregation, Mol. Gen. Genet., 264, 492, 10.1007/s004380000338 Huang, 2003, Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing, Genes Dev., 17, 2162, 10.1101/gad.1108403 Hurt, 2004, Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex, Proc. Natl. Acad. Sci. USA, 101, 1858, 10.1073/pnas.0308663100 Irvine, 2006, Argonaute slicing is required for heterochromatic silencing and spreading, Science, 313, 1134, 10.1126/science.1128813 Jacobs, 2002, Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail, Science, 295, 2080, 10.1126/science.1069473 Jacobs, 2001, Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3, EMBO J., 20, 5232, 10.1093/emboj/20.18.5232 Jae Yoo, 2002, Hrp3, a chromodomain helicase/ATPase DNA binding protein, is required for heterochromatin silencing in fission yeast, Biochem. Biophys. Res. Commun., 295, 970, 10.1016/S0006-291X(02)00797-0 Jambunathan, 2005, Multiple bromodomain genes are involved in restricting the spread of heterochromatic silencing at the Saccharomyces cerevisiae HMR-tRNA boundary, Genetics, 171, 913, 10.1534/genetics.105.046938 Jia, 2004, RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins, Science, 304, 1971, 10.1126/science.1099035 Klar, 1991, swi6, a gene required for mating-type switching, prohibits meiotic recombination in the mat2-mat3 “cold spot” of fission yeast, Genetics, 129, 1033, 10.1093/genetics/129.4.1033 Krings, 2005, Sap1p binds to Ter1 at the ribosomal DNA of Schizosaccharomyces pombe and causes polar replication fork arrest, J. Biol. Chem., 280, 39135, 10.1074/jbc.M508996200 Lachner, 2001, Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins, Nature, 410, 116, 10.1038/35065132 Leeds, 1991, The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon, Genes Dev., 5, 2303, 10.1101/gad.5.12a.2303 Lejeune, 2007, The chromatin-remodeling factor FACT contributes to centromeric heterochromatin independently of RNAi, Curr. Biol., 17, 1219, 10.1016/j.cub.2007.06.028 Lomberk, 2006, The Heterochromatin Protein 1 family, Genome Biol., 7, 228, 10.1186/gb-2006-7-7-228 Maison, 2004, HP1 and the dynamics of heterochromatin maintenance, Nat. Rev. Mol. Cell Biol., 5, 296, 10.1038/nrm1355 Mellone, 2003, Centromere silencing and function in fission yeast is governed by the amino terminus of histone H3, Curr. Biol., 13, 1748, 10.1016/j.cub.2003.09.031 Motamedi, 2004, Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs, Cell, 119, 789, 10.1016/j.cell.2004.11.034 Muchardt, 2002, Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1alpha, EMBO Rep., 3, 975, 10.1093/embo-reports/kvf194 Nakagawa, 2002, Fission yeast CENP-B homologs nucleate centromeric heterochromatin by promoting heterochromatin-specific histone tail modifications, Genes Dev., 16, 1766, 10.1101/gad.997702 Nakayama, 2001, Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly, Science, 292, 110, 10.1126/science.1060118 Nielsen, 2001, Rb targets histone H3 methylation and HP1 to promoters, Nature, 412, 561, 10.1038/35087620 Nielsen, 2002, Selective interaction between the chromatin-remodeling factor BRG1 and the heterochromatin-associated protein HP1alpha, EMBO J., 21, 5797, 10.1093/emboj/cdf560 Noguchi, 2007, Sap1 promotes the association of the replication fork protection complex with chromatin and is involved in the replication checkpoint in Schizosaccharomyces pombe, Genetics, 175, 553, 10.1534/genetics.106.065334 Pak, 1997, Association of the origin recognition complex with heterochromatin and HP1 in higher eukaryotes, Cell, 91, 311, 10.1016/S0092-8674(00)80415-8 Partridge, 2002, cis-acting DNA from fission yeast centromeres mediates histone H3 methylation and recruitment of silencing factors and cohesin to an ectopic site, Curr. Biol., 12, 1652, 10.1016/S0960-9822(02)01177-6 Perrini, 2004, HP1 controls telomere capping, telomere elongation, and telomere silencing by two different mechanisms in Drosophila, Mol. Cell, 15, 467, 10.1016/j.molcel.2004.06.036 Pokholok, 2005, Genome-wide map of nucleosome acetylation and methylation in yeast, Cell, 122, 517, 10.1016/j.cell.2005.06.026 Rea, 2000, Regulation of chromatin structure by site-specific histone H3 methyltransferases, Nature, 406, 593, 10.1038/35020506 Richards, 2002, Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects, Cell, 108, 489, 10.1016/S0092-8674(02)00644-X Rigaut, 1999, A generic protein purification method for protein complex characterization and proteome exploration, Nat. Biotechnol., 17, 1030, 10.1038/13732 Sadaie, 2004, A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast, EMBO J., 23, 3825, 10.1038/sj.emboj.7600401 Schotta, 2002, Central role of Drosophila SU(VAR)3–9 in histone H3–K9 methylation and heterochromatic gene silencing, EMBO J., 21, 1121, 10.1093/emboj/21.5.1121 Shareef, 2001, Drosophila heterochromatin protein 1 (hp1)/origin recognition complex (orc) protein is associated with hp1 and orc and functions in heterochromatin-induced silencing, Mol. Biol. Cell, 12, 1671, 10.1091/mbc.12.6.1671 Song, 2001, Human Ku70 interacts with heterochromatin protein 1alpha, J. Biol. Chem., 276, 8321, 10.1074/jbc.M008779200 Stewart, 2005, Relationship between histone H3 lysine 9 methylation, transcription repression, and heterochromatin protein 1 recruitment, Mol. Cell. Biol., 25, 2525, 10.1128/MCB.25.7.2525-2538.2005 Sugiyama, 2005, RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production, Proc. Natl. Acad. Sci. USA, 102, 152, 10.1073/pnas.0407641102 Sugiyama, 2007, SHREC, an effector complex for heterochromatic transcriptional silencing, Cell, 128, 491, 10.1016/j.cell.2006.12.035 Suka, 2001, Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin, Mol. Cell, 8, 473, 10.1016/S1097-2765(01)00301-X Thompson, 1994, Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast, Nature, 369, 245, 10.1038/369245a0 Thon, 2000, Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations, Genetics, 155, 551, 10.1093/genetics/155.2.551 Vakoc, 2005, Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin, Mol. Cell, 19, 381, 10.1016/j.molcel.2005.06.011 Verdel, 2005, Labeling and characterization of small RNAs associated with the RNA interference effector complex RITS, Methods Enzymol., 392, 297, 10.1016/S0076-6879(04)92017-4 Verdel, 2004, RNAi-mediated targeting of heterochromatin by the RITS complex, Science, 303, 672, 10.1126/science.1093686 Volpe, 2002, Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi, Science, 297, 1833, 10.1126/science.1074973 Walfridsson, 2005, The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres, Nucleic Acids Res., 33, 2868, 10.1093/nar/gki579 Yamada, 2005, The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast, Mol. Cell, 20, 173, 10.1016/j.molcel.2005.10.002 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 Zhang, 2002, Association of class II histone deacetylases with heterochromatin protein 1: potential role for histone methylation in control of muscle differentiation, Mol. Cell. Biol., 22, 7302, 10.1128/MCB.22.20.7302-7312.2002