- Kouzarides, T. Histone methylation in transcriptional control. Curr. Opin. Genet. Dev. 12, 198–209 (2002)
Article CAS PubMed Google Scholar
- Bhaumik, S. R., Smith, E. & Shilatifard, A. Covalent modifications of histones during development and disease pathogenesis. Nature Struct. Mol. Biol. 14, 1008–1016 (2007)
Article CAS Google Scholar
- Lachner, M., O’Sullivan, R. J. & Jenuwein, T. An epigenetic road map for histone lysine methylation. J. Cell Sci. 116, 2117–2124 (2003)
Article CAS PubMed Google Scholar
- Ruthenburg, A. J., Li, H., Patel, D. J. & Allis, C. D. Multivalent engagement of chromatin modifications by linked binding modules. Nature Rev. Mol. Cell Biol. 8, 983–994 (2007)
Article CAS Google Scholar
- Klose, R. J., Kallin, E. M. & Zhang, Y. JmjC-domain-containing proteins and histone demethylation. Nature Rev. Genet. 7, 715–727 (2006)
Article CAS PubMed Google Scholar
- Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009)
Article ADS CAS PubMed PubMed Central Google Scholar
- Mellor, J. It takes a PHD to read the histone code. Cell 126, 22–24 (2006)
Article CAS PubMed Google Scholar
- Loenarz, C. et al. PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an _N_ε-dimethyl lysine demethylase. Hum. Mol. Genet. 19, 217–222 (2010)
Article CAS PubMed Google Scholar
- Fortschegger, K. et al. PHF8 targets histone methylation and RNA polymerase II to activate transcription. Mol. Cell Biol. advance online publication, 10.1128/MCB.01520-09 (26 April 2010)
- Horton, J. R. et al. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nature Struct. Mol. Biol. 17, 38–43 (2010)
Article CAS Google Scholar
- Kleine-Kohlbrecher, D. et al. A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Mol. Cell 38, 165–178 (2010)
Article CAS PubMed PubMed Central Google Scholar
- Feng, W., Yonezawa, M., Ye, J., Jenuwein, T. & Grummt, I. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nature Struct. Mol. Biol. 17, 445–450 (2010)
Article CAS Google Scholar
- Jørgensen, S. et al. The histone methyltransferase SET8 is required for S-phase progression. J. Cell Biol. 179, 1337–1345 (2007)
Article PubMed PubMed Central Google Scholar
- Tardat, M., Murr, R., Herceg, Z., Sardet, C. & Julien, E. PR-Set7-dependent lysine methylation ensures genome replication and stability through S phase. J. Cell Biol. 179, 1413–1426 (2007)
Article CAS PubMed PubMed Central Google Scholar
- Houston, S. I. et al. Catalytic function of the PR-Set7 histone H4 lysine 20 monomethyltransferase is essential for mitotic entry and genomic stability. J. Biol. Chem. 283, 19478–19488 (2008)
Article CAS PubMed PubMed Central Google Scholar
- Yin, Y., Yu, V. C., Zhu, G. & Chang, D. C. SET8 plays a role in controlling G1/S transition by blocking lysine acetylation in histone through binding to H4 N-terminal tail. Cell Cycle 7, 1423–1432 (2008)
Article CAS PubMed Google Scholar
- Oda, H. et al. Monomethylation of histone H4-lysine 20 is involved in chromosome structure and stability and is essential for mouse development. Mol. Cell. Biol. 29, 2278–2295 (2009)
Article CAS PubMed PubMed Central Google Scholar
- Tyagi, S., Chabes, A. L., Wysocka, J. & Herr, W. E2F activation of S phase promoters via association with HCF-1 and the MLL family of histone H3K4 methyltransferases. Mol. Cell 27, 107–119 (2007)
Article CAS PubMed Google Scholar
- Wysocka, J., Myers, M. P., Laherty, C. D., Eisenman, R. N. & Herr, W. Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3–K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes Dev. 17, 896–911 (2003)
Article CAS PubMed PubMed Central Google Scholar
- Trojer, P. et al. L3MBTL1, a histone-methylation-dependent chromatin lock. Cell 129, 915–928 (2007)
Article CAS PubMed Google Scholar
- Julien, E. & Herr, W. Proteolytic processing is necessary to separate and ensure proper cell growth and cytokinesis functions of HCF-1. EMBO J. 22, 2360–2369 (2003)
Article CAS PubMed PubMed Central Google Scholar
- Losada, A. & Hirano, T. Dynamic molecular linkers of the genome: the first decade of SMC proteins. Genes Dev. 19, 1269–1287 (2005)
Article CAS PubMed Google Scholar
- Hudson, D. F., Marshall, K. M. & Earnshaw, W. C. Condensin: architect of mitotic chromosomes. Chromosome Res. 17, 131–144 (2009)
Article CAS PubMed Google Scholar
- Belmont, A. S. Mitotic chromosome structure and condensation. Curr. Opin. Cell Biol. 18, 632–638 (2006)
Article CAS PubMed Google Scholar
- Haering, C. H. Foreword: the many fascinating functions of SMC protein complexes. Chromosome Res. 17, 127–129 (2009)
Article CAS PubMed Google Scholar
- Wolf, F., Sigl, R. & Geley, S. '… The end of the beginning': cdk1 thresholds and exit from mitosis. Cell Cycle 6, 1408–1411 (2007)
Article CAS PubMed Google Scholar
- Ono, T. et al. Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. Cell 115, 109–121 (2003)
Article CAS PubMed Google Scholar
- Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41–45 (2000)
Article ADS CAS PubMed Google Scholar
- Neuwald, A. F. & Hirano, T. HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions. Genome Res. 10, 1445–1452 (2000)
Article CAS PubMed PubMed Central Google Scholar
- Andrade, M. A. & Bork, P. HEAT repeats in the Huntington’s disease protein. Nature Genet. 11, 115–116 (1995)
Article CAS PubMed Google Scholar
- Garcia-Bassets, I. et al. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell 128, 505–518 (2007)
Article CAS PubMed PubMed Central Google Scholar
- Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009)
Article PubMed PubMed Central Google Scholar
- Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008)
Article PubMed PubMed Central Google Scholar
- Zang, C. et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952–1958 (2009)
Article CAS PubMed PubMed Central Google Scholar
- Huang D. W, Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57 (2009)
Article Google Scholar
- Maere, S., Heymans, K. & Kuiper, M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448–3449 (2005)
Article CAS PubMed Google Scholar
- Šášik, R., Woelk, C. H. & Corbeil, J. Microarray truths and consequences. J. Mol. Endocrinol. 33, 1–9 (2004)
Article PubMed Google Scholar
- Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001)
Article ADS CAS PubMed PubMed Central Google Scholar
- Saeed, A. I. et al. TM4 microarray software suite. Methods Enzymol. 411, 134–193 (2006)
Article CAS PubMed Google Scholar
- Schwender, H. & Ickstadt, K. Empirical Bayes analysis of single nucleotide polymorphisms. BMC Bioinformatics 9, 144 (2008)
Article PubMed PubMed Central Google Scholar
- Tanner, S. et al. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626–4639 (2005)
Article CAS PubMed Google Scholar
- Yeong, F. M. et al. Identification of a subunit of a novel Kleisin-β/SMC complex as a potential substrate of protein phosphatase 2A. Curr. Biol. 13, 2058–2064 (2003)
Article CAS PubMed Google Scholar