A three-dimensional model of the yeast genome (original) (raw)
References
Misteli, T. Beyond the sequence: cellular organization of genome function. Cell128, 787–800 (2007) ArticleCAS Google Scholar
Lanctôt, C., Cheutin, T., Cremer, M., Cavalli, G. & Cremer, T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nature Rev. Genet.8, 104–115 (2007) Article Google Scholar
Zhao, R., Bodnar, M. S. & Spector, D. L. Nuclear neighborhoods and gene expression. Curr. Opin. Genet. Dev.19, 172–179 (2009) ArticleCAS Google Scholar
Heun, P., Laroche, T., Shimada, K., Furrer, P. & Gasser, S. M. Chromosome dynamics in the yeast interphase nucleus. Science294, 2181–2186 (2001) ArticleADSCAS Google Scholar
Gasser, S. M. Visualizing chromatin dynamics in interphase nuclei. Science296, 1412–1416 (2002) ArticleADSCAS Google Scholar
Stone, E. M., Heun, P., Laroche, T., Pillus, L. & Gasser, S. M. MAP kinase signaling induces nuclear reorganization in budding yeast. Curr. Biol.10, 373–382 (2000) ArticleCAS Google Scholar
Casolari, J. M., Brown, C. R., Drubin, D. A., Rando, O. J. & Silver, P. A. Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev.19, 1188–1198 (2005) ArticleCAS Google Scholar
Osborne, C. S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nature Genet.36, 1065–1071 (2004) ArticleCAS Google Scholar
Kitamura, E., Blow, J. J. & Tanaka, T. U. Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell125, 1297–1308 (2006) ArticleCAS Google Scholar
Bystricky, K., Laroche, T., van Houwe, G., Blaszczyk, M. & Gasser, S. M. Chromosome looping in yeast: telomere pairing and coordinated movement reflect anchoring efficiency and territorial organization. J. Cell Biol.168, 375–387 (2005) ArticleCAS Google Scholar
Schober, H. et al. Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast. Genome Res.18, 261–271 (2008) ArticleCAS Google Scholar
Berger, A. B. et al. High-resolution statistical mapping reveals gene territories in live yeast. Nature Methods5, 1031–1037 (2008) ArticleCAS Google Scholar
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science295, 1306–1311 (2002) ArticleADSCAS Google Scholar
Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genet.38, 1348–1354 (2006) ArticleCAS Google Scholar
Murrell, A., Heeson, S. & Reik, W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nature Genet.36, 889–893 (2004) ArticleCAS Google Scholar
Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R. & Flavell, R. A. Interchromosomal associations between alternatively expressed loci. Nature435, 637–645 (2005) ArticleADSCAS Google Scholar
Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genet.38, 1341–1347 (2006) ArticleCAS Google Scholar
Fullwood, M. J. & Ruan, Y. ChIP-based methods for the identification of long-range chromatin interactions. J. Cell. Biochem.107, 30–39 (2009) ArticleCAS Google Scholar
Fullwood, M. J. et al. An oestrogen-receptor-α-bound human chromatin interactome. Nature462, 58–64 (2009) ArticleADSCAS Google Scholar
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science326, 289–293 (2009) ADSCASPubMedPubMed Central Google Scholar
Simonis, M., Kooren, J. & de Laat, W. An evaluation of 3C-based methods to capture DNA interactions. Nature Methods4, 895–901 (2007) ArticleCAS Google Scholar
Venema, J. & Tollervey, D. Ribosome synthesis in Saccharomyces cerevisiae . Annu. Rev. Genet.33, 261–311 (1999) ArticleCAS Google Scholar
Jin, Q., Trelles-Sticken, E., Scherthan, H. & Loidl, J. Yeast nuclei display prominent centromere clustering that is reduced in nondividing cells and in meiotic prophase. J. Cell Biol.141, 21–29 (1998) ArticleCAS Google Scholar
Gotta, M. et al. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae . J. Cell Biol.134, 1349–1363 (1996) ArticleCAS Google Scholar
Haeusler, R. A., Pratt-Hyatt, M., Good, P. D., Gipson, T. A. & Engelke, D. R. Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes. Genes Dev.22, 2204–2214 (2008) ArticleCAS Google Scholar
Thompson, M., Haeusler, R. A., Good, P. D. & Engelke, D. R. Nucleolar clustering of dispersed tRNA genes. Science302, 1399–1401 (2003) ArticleADSCAS Google Scholar
Di Rienzi, S. C., Collingwood, D., Raghuraman, M. K. & Brewer, B. J. Fragile genomic sites are associated with origins of replication. Genome. Biol. Evol.2009, 350–363 (2009) Article Google Scholar
Haber, J. E. & Leung, W. Y. Lack of chromosome territoriality in yeast: promiscuous rejoining of broken chromosome ends. Proc. Natl Acad. Sci. USA93, 13949–13954 (1996) ArticleADSCAS Google Scholar
Lorenz, A., Fuchs, J., Trelles-Sticken, E., Scherthan, H. & Loidl, J. Spatial organisation and behaviour of the parental chromosome sets in the nuclei of Saccharomyces cerevisiae × S. paradoxus hybrids. J. Cell Sci.115, 3829–3835 (2002) ArticleCAS Google Scholar
Bystricky, K., Heun, P., Gehlen, L., Langowski, J. & Gasser, S. M. Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. Proc. Natl Acad. Sci. USA101, 16495–16500 (2004) ArticleADSCAS Google Scholar