Heterochromatin Is Required for Normal Distribution of Neurospora crassa CenH3

REFERENCES

• Alonso, A., et al. 2007. Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres. Genome Biol. 8: R148.
   PubMedGoogle Scholar
• Barratt, R. W., D. Newmeyer, D. D. Perkins, and L. Garnjobst. 1954. Map construction in Neurospora crassa. Adv. Genet. 6: 1–93.
   PubMed Web of Science ®Google Scholar
• Baum, M., K. Sanyal, P. K. Mishra, N. Thaler, and J. Carbon. 2006. Formation of functional centromeric chromatin is specified epigenetically in Candida albicans. Proc. Natl. Acad. Sci. U. S. A. 103: 14877–14882.
   PubMed Web of Science ®Google Scholar
• Bergmann, J. H., et al. 2011. Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore. EMBO J. 30: 328–340.
   PubMed Web of Science ®Google Scholar
• Bernard, P., et al. 2001. Requirement of heterochromatin for cohesion at centromeres. Science 294: 2539–2542.
   PubMed Web of Science ®Google Scholar
• Black, B. E., et al. 2007. Centromere identity maintained by nucleosomes assembled with histone H3 containing the CENP-A targeting domain. Mol. Cell 25: 309–322.
   PubMed Web of Science ®Google Scholar
• Blower, M. D., and G. H. Karpen. 2001. The role of Drosophila CID in kinetochore formation, cell-cycle progression and heterochromatin interactions. Nat. Cell Biol. 3: 730–739.
   PubMedGoogle Scholar
• Blower, M. D., B. A. Sullivan, and G. H. Karpen. 2002. Conserved organization of centromeric chromatin in flies and humans. Dev. Cell 2: 319–330.
   PubMedGoogle Scholar
• Borkovich, K. A., et al. 2004. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol. Mol. Biol. Rev. 68: 1–108.
   PubMed Web of Science ®Google Scholar
• Cam, H. P., et al. 2005. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat. Genet. 37: 809–819.
   PubMed Web of Science ®Google Scholar
• Cambareri, E. B., R. Aisner, and J. Carbon. 1998. Structure of the chromosome VII centromere region in Neurospora crassa: degenerate transposons and simple repeats. Mol. Cell. Biol. 18: 5465–5477.
   PubMedGoogle Scholar
• Cambareri, E. B., J. Helber, and J. A. Kinsey. 1994. Tad1-1, an active LINE-like element of Neurospora crassa. Mol. Gen. Genet. 242: 658–665.
   PubMedGoogle Scholar
• Cambareri, E. B., M. J. Singer, and E. U. Selker. 1991. Recurrence of repeat-induced point mutation (RIP) in Neurospora crassa. Genetics 127: 699–710.
   PubMed Web of Science ®Google Scholar
• Carroll, C. W., K. J. Milks, and A. F. Straight. 2010. Dual recognition of CENP-A nucleosomes is required for centromere assembly. J. Cell Biol. 189: 1143–1155.
   PubMed Web of Science ®Google Scholar
• Centola, M., and J. Carbon. 1994. Cloning and characterization of centromeric DNA from Neurospora crassa. Mol. Cell. Biol. 14: 1510–1519.
   PubMedGoogle Scholar
• Chicas, A., C. Cogoni, and G. Macino. 2004. RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa. Nucleic Acids Res. 32: 4237–4243.
   PubMedGoogle Scholar
• Cleveland, D. W., Y. Mao, and K. F. Sullivan. 2003. Centromeres and kinetochores: from epigenetics to mitotic checkpoint signaling. Cell 112: 407–421.
   PubMed Web of Science ®Google Scholar
• Coleman, J. J., et al. 2009. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet. 5: e1000618.
   PubMed Web of Science ®Google Scholar
• Colot, H. V., et al. 2006. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc. Natl. Acad. Sci. U. S. A. 103: 10352–10357.
   PubMed Web of Science ®Google Scholar
• Cuomo, C. A., et al. 2007. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317: 1400–1402.
   PubMed Web of Science ®Google Scholar
• Davis, R. H. 2000. Neurospora: contributions of a model organism. Oxford University Press, Oxford, United Kingdom.
   Google Scholar
• Dawe, R. K., and S. Henikoff. 2006. Centromeres put epigenetics in the driver's seat. Trends Biochem. Sci. 31: 662–669.
   PubMedGoogle Scholar
• Du, Y., C. N. Topp, and R. K. Dawe. 2010. DNA binding of centromere protein C (CENPC) is stabilized by single-stranded RNA. PLoS Genet. 6: e1000835.
   PubMedGoogle Scholar
• Dunleavy, E. M., et al. 2009. HJURP is a cell-cycle-dependent maintenance and deposition factor of CENP-A at centromeres. Cell 137: 485–497.
   PubMed Web of Science ®Google Scholar
• Fahlgren, N., et al. 2009. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15: 992–1002.
   PubMedGoogle Scholar
• Fedorova, N. D., et al. 2008. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 4: e1000046.
   PubMed Web of Science ®Google Scholar
• Fischer, T., et al. 2009. Diverse roles of HP1 proteins in heterochromatin assembly and functions in fission yeast. Proc. Natl. Acad. Sci. U. S. A. 106: 8998–9003.
   PubMed Web of Science ®Google Scholar
• Folco, H. D., A. L. Pidoux, T. Urano, and R. C. Allshire. 2008. Heterochromatin and RNAi are required to establish CENP-A chromatin at centromeres. Science 319: 94–97.
   PubMed Web of Science ®Google Scholar
• Foltz, D. R., et al. 2009. Centromere-specific assembly of CENP-A nucleosomes is mediated by HJURP. Cell 137: 472–484.
   PubMed Web of Science ®Google Scholar
• Foltz, D. R., et al. 2006. The human CENP-A centromeric nucleosome-associated complex. Nat. Cell Biol. 8: 458–469.
   PubMed Web of Science ®Google Scholar
• Freitag, M., P. C. Hickey, T. K. Khlafallah, N. D. Read, and E. U. Selker. 2004. HP1 is essential for DNA methylation in Neurospora. Mol. Cell 13: 427–434.
   PubMed Web of Science ®Google Scholar
• Freitag, M., et al. 2004. DNA methylation is independent of RNA interference in Neurospora. Science 304: 1939.
   PubMedGoogle Scholar
• Galagan, J. E., et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859–868.
   PubMed Web of Science ®Google Scholar
• Gopalakrishnan, S., B. A. Sullivan, S. Trazzi, G. Della Valle, and K. D. Robertson. 2009. DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions. Hum. Mol. Genet. 18: 3178–3193.
   PubMedGoogle Scholar
• Guenatri, M., D. Bailly, C. Maison, and G. Almouzni. 2004. Mouse centric and pericentric satellite repeats form distinct functional heterochromatin. J. Cell Biol. 166: 493–505.
   PubMed Web of Science ®Google Scholar
• Hayashi, T., et al. 2004. Mis16 and Mis18 are required for CENP-A loading and histone deacetylation at centromeres. Cell 118: 715–729.
   PubMed Web of Science ®Google Scholar
• Hays, S. M., J. Swanson, and E. U. Selker. 2002. Identification and characterization of the genes encoding the core histones and histone variants of Neurospora crassa. Genetics 160: 961–973.
   PubMed Web of Science ®Google Scholar
• Hegemann, J. H., and U. N. Fleig. 1993. The centromere of budding yeast. Bioessays 15: 451–460.
   PubMedGoogle Scholar
• Hellwig, D., et al. 2008. Live-cell imaging reveals sustained centromere binding of CENP-T via CENP-A and CENP-B. J. Biophotonics 1: 245–254.
   PubMedGoogle Scholar
• Hemmerich, P., et al. 2008. Dynamics of inner kinetochore assembly and maintenance in living cells. J. Cell Biol. 180: 1101–1114.
   PubMed Web of Science ®Google Scholar
• Henikoff, S., K. Ahmad, and H. S. Malik. 2001. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293: 1098–1102.
   PubMed Web of Science ®Google Scholar
• Honda, S., and E. U. Selker. 2008. Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Mol. Cell. Biol. 28: 6044–6055.
   PubMedGoogle Scholar
• Honda, S., and E. U. Selker. 2009. Tools for fungal proteomics: multifunctional Neurospora vectors for gene replacement, protein expression and protein purification. Genetics 182: 11–23.
   PubMed Web of Science ®Google Scholar
• Hori, T., et al. 2008. CCAN makes multiple contacts with centromeric DNA to provide distinct pathways to the outer kinetochore. Cell 135: 1039–1052.
   PubMed Web of Science ®Google Scholar
• Johnson, D. S., A. Mortazavi, R. M. Myers, and B. Wold. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497–1502.
   PubMed Web of Science ®Google Scholar
• Kagansky, A., et al. 2009. Synthetic heterochromatin bypasses RNAi and centromeric repeats to establish functional centromeres. Science 324: 1716–1719.
   PubMed Web of Science ®Google Scholar
• Kouzminova, E. A., and E. U. Selker. 2001. Dim-2 encodes a DNA-methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J. 20: 4309–4323.
   PubMed Web of Science ®Google Scholar
• Lagana, A., et al. 2010. A small GTPase molecular switch regulates epigenetic centromere maintenance by stabilizing newly incorporated CENP-A. Nat. Cell Biol. 12: 1186–1193.
   PubMed Web of Science ®Google Scholar
• Lam, A. L., C. D. Boivin, C. F. Bonney, M. K. Rudd, and B. A. Sullivan. 2006. Human centromeric chromatin is a dynamic chromosomal domain that can spread over noncentromeric DNA. Proc. Natl. Acad. Sci. U. S. A. 103: 4186–4191.
   PubMedGoogle Scholar
• Lamb, J. C., W. Yu, F. Han, and J. A. Birchler. 2007. Plant chromosomes from end to end: telomeres, heterochromatin and centromeres. Curr. Opin. Plant Biol. 10: 116–122.
   PubMedGoogle Scholar
• Lee, H. C., et al. 2010. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol. Cell 38: 803–814.
   PubMed Web of Science ®Google Scholar
• Lewis, Z. A., et al. 2010. DNA methylation and normal chromosome behavior in Neurospora depend on five components of a histone methyltransferase complex, DCDC. PLoS Genet. 6: e1001196.
   PubMedGoogle Scholar
• Lewis, Z. A., et al. 2009. Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res. 19: 427–437.
   PubMed Web of Science ®Google Scholar
• Li, H., et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078–2079.
   PubMed Web of Science ®Google Scholar
• Li, H., J. Ruan, and R. Durbin. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18: 1851–1858.
   PubMed Web of Science ®Google Scholar
• Lowary, P. T., and J. Widom. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276: 19–42.
   PubMed Web of Science ®Google Scholar
• Malik, H. S., and J. J. Bayes. 2006. Genetic conflicts during meiosis and the evolutionary origins of centromere complexity. Biochem. Soc Trans. 34: 569–573.
   PubMedGoogle Scholar
• Malik, H. S., and S. Henikoff. 2002. Conflict begets complexity: the evolution of centromeres. Curr. Opin. Genet. Dev. 12: 711–718.
   PubMedGoogle Scholar
• Mavrich, T. N., et al. 2008. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 18: 1073–1083.
   PubMed Web of Science ®Google Scholar
• Mavrich, T. N., et al. 2008. Nucleosome organization in the Drosophila genome. Nature 453: 358–362.
   PubMed Web of Science ®Google Scholar
• Mikkelsen, T. S., et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553–560.
   PubMed Web of Science ®Google Scholar
• Mizuno, H., et al. 2006. Identification and mapping of expressed genes, simple sequence repeats and transposable elements in centromeric regions of rice chromosomes. DNA Res. 13: 267–274.
   PubMedGoogle Scholar
• Nakashima, H., et al. 2005. Assembly of additional heterochromatin distinct from centromere-kinetochore chromatin is required for de novo formation of human artificial chromosome. J. Cell Sci. 118: 5885–5898.
   PubMedGoogle Scholar
• Nonaka, N., et al. 2002. Recruitment of cohesin to heterochromatic regions by Swi6/HP1 in fission yeast. Nat. Cell Biol. 4: 89–93.
   PubMed Web of Science ®Google Scholar
• Padmanabhan, S., J. Thakur, R. Siddharthan, and K. Sanyal. 2008. Rapid evolution of Cse4p-rich centromeric DNA sequences in closely related pathogenic yeasts, Candida albicans and Candida dubliniensis. Proc. Natl. Acad. Sci. U. S. A. 105: 19797–19802.
   PubMedGoogle Scholar
• Perkins, D. D. 1953. The detection of linkage in tetrad analysis. Genetics 38: 187–197.
   PubMed Web of Science ®Google Scholar
• Perkins, D. D., A. Radford, D. Newmeyer, and M. Björkman. 1982. Chromosomal loci of Neurospora crassa. Microbiol. Rev. 46: 426–570.
   PubMedGoogle Scholar
• Perkins, D. D., A. Radford, and M. S. Sachs. 2001. The Neurospora Compendium. Academic Press, San Diego, CA.
   Google Scholar
• Peters, A. H., et al. 2001. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107: 323–337.
   PubMed Web of Science ®Google Scholar
• Polizzi, C., and L. Clarke. 1991. The chromatin structure of centromeres from fission yeast: differentiation of the central core that correlates with function. J. Cell Biol. 112: 191–201.
   PubMedGoogle Scholar
• Pomraning, K. R., K. M. Smith, and M. Freitag. 2009. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47: 142–150.
   PubMed Web of Science ®Google Scholar
• Rountree, M. R., and E. U. Selker. 1997. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev. 11: 2383–2395.
   PubMed Web of Science ®Google Scholar
• Rudd, M. K., M. G. Schueler, and H. F. Willard. 2003. Sequence organization and functional annotation of human centromeres. Cold Spring Harb. Symp. Quant Biol. 68: 141–149.
   PubMedGoogle Scholar
• Sakuno, T., K. Tada, and Y. Watanabe. 2009. Kinetochore geometry defined by cohesion within the centromere. Nature 458: 852–858.
   PubMedGoogle Scholar
• Sakuno, T., and Y. Watanabe. 2009. Studies of meiosis disclose distinct roles of cohesion in the core centromere and pericentromeric regions. Chromosome Res. 17: 239–249.
   PubMed Web of Science ®Google Scholar
• Sanyal, K., M. Baum, and J. Carbon. 2004. Centromeric DNA sequences in the pathogenic yeast Candida albicans are all different and unique. Proc. Natl. Acad. Sci. U. S. A. 101: 11374–11379.
   PubMed Web of Science ®Google Scholar
• Schueler, M. G., A. W. Higgins, M. K. Rudd, K. Gustashaw, and H. F. Willard. 2001. Genomic and genetic definition of a functional human centromere. Science 294: 109–115.
   PubMedGoogle Scholar
• Segal, E., et al. 2006. A genomic code for nucleosome positioning. Nature 442: 772–778.
   PubMed Web of Science ®Google Scholar
• Selker, E. U. 1990. Premeiotic instability of repeated sequences in Neurospora crassa. Annu. Rev. Genet. 24: 579–613.
   PubMed Web of Science ®Google Scholar
• Selker, E. U., et al. 2003. The methylated component of the Neurospora crassa genome. Nature 422: 893–897.
   PubMed Web of Science ®Google Scholar
• Shibata, F., and M. Murata. 2004. Differential localization of the centromere-specific proteins in the major centromeric satellite of Arabidopsis thaliana. J. Cell Sci. 117: 2963–2970.
   PubMed Web of Science ®Google Scholar
• Shiu, P. K., D. Zickler, N. B. Raju, G. Ruprich-Robert, and R. L. Metzenberg. 2006. SAD-2 is required for meiotic silencing by unpaired DNA and perinuclear localization of SAD-1 RNA-directed RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 103: 2243–2248.
   PubMedGoogle Scholar
• Smith, K. M., et al. 2008. The fungus Neurospora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9. Epigenetics Chromatin 1: 5.
   PubMedGoogle Scholar
• Song, J. S., X. Liu, X. S. Liu, and X. He. 2008. A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Res. 18: 1064–1072.
   PubMed Web of Science ®Google Scholar
• Sullivan, B. A., and G. H. Karpen. 2004. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nat. Struct. Mol. Biol. 11: 1076–1083.
   PubMed Web of Science ®Google Scholar
• Sun, X., H. D. Le, J. M. Wahlstrom, and G. H. Karpen. 2003. Sequence analysis of a functional Drosophila centromere. Genome Res. 13: 182–194.
   PubMedGoogle Scholar
• Takahashi, K., et al. 1992. A low copy number central sequence with strict symmetry and unusual chromatin structure in fission yeast centromere. Mol. Biol. Cell 3: 819–835.
   PubMedGoogle Scholar
• Tamaru, H., and E. U. Selker. 2001. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414: 277–283.
   PubMed Web of Science ®Google Scholar
• Tamaru, H., and E. U. Selker. 2003. Synthesis of signals for de novo DNA methylation in Neurospora crassa. Mol. Cell. Biol. 23: 2379–2394.
   PubMed Web of Science ®Google Scholar
• Tamaru, H., et al. 2003. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat. Genet. 34: 75–79.
   PubMed Web of Science ®Google Scholar
• Tanaka, K., H. L. Chang, A. Kagami, and Y. Watanabe. 2009. CENP-C functions as a scaffold for effectors with essential kinetochore functions in mitosis and meiosis. Dev. Cell 17: 334–343.
   PubMed Web of Science ®Google Scholar
• Valdeolmillos, A., et al. 2004. Drosophila cohesins DSA1 and Drad21 persist and colocalize along the centromeric heterochromatin during mitosis. Biol. Cell 96: 457–462.
   PubMedGoogle Scholar
• Wolfgruber, T. K., et al. 2009. Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons. PLoS Genet. 5: e1000743.
   PubMedGoogle Scholar
• Wu, C., et al. 2009. Characterization of chromosome ends in the filamentous fungus Neurospora crassa. Genetics 181: 1129–1145.
   PubMedGoogle Scholar
• Yan, H., et al. 6 May 2010. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J. [Epub ahead of print.] doi:10.1111/j.1365-313X.2010.04246.x.
   Google Scholar
• Zhang, W., H. R. Lee, D. H. Koo, and J. Jiang. 2008. Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize. Plant Cell 20: 25–34.
   PubMed Web of Science ®Google Scholar