Taddei A, Gasser SM. Structure and function in the budding yeast nucleus. Genetics. 2012;192:107–29.
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–93.
Mirny LA. The fractal globule as a model of chromatin architecture in the cell. Chromosom Res. 2011;19:37–51.
Botta M, Haider S, Leung IX, Lio P, Mozziconacci J. Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide. Mol Syst Biol. 2010;6:426.
Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM. Form and function of topologically associating genomic domains in budding yeast. Proc Natl Acad Sci U S A. 2017;114:E3061–70.
Hsieh TH, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping nucleosome resolution chromosome folding in yeast by micro-C. Cell. 2015;162:108–19.
Heun P, Laroche T, Shimada K, Furrer P, Gasser SM. Chromosome dynamics in the yeast interphase nucleus. Science. 2001;294:2181–6.
Stone EM, Heun P, Laroche T, Pillus L, Gasser SM. MAP kinase signaling induces nuclear reorganization in budding yeast. Curr Biol. 2000;10:373–82.
Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. A three-dimensional model of the yeast genome. Nature. 2010;465:363–7.
Iborra FJ, Pombo A, Jackson DA, Cook PR. Active RNA polymerases are localized within discrete transcription factories in human nuclei. J Cell Sci. 1996;109(6):1427–36.
Rieder D, Trajanoski Z, McNally JG. Transcription factories. Front Genet. 2012;3:221.
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 2004;431:99–104.
Kim KD, Tanizawa H, Iwasaki O, Noma K. Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast. Nat Genet. 2016;48:1242–52.
Cai M, Davis RW. Yeast centromere binding protein CBF1, of the helix-loop-helix protein family, is required for chromosome stability and methionine prototrophy. Cell. 1990;61:437–46.
Heermann DW, Jerabek H, Liu L, Li Y. A model for the 3D chromatin architecture of pro and eukaryotes. Methods. 2012;58:307–14.
Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010;33:1–22.
Zou H, Hastie T. Regularization and Variable Selection via the Elastic Net. J Royal Stat Soc Series B (Statistical Methodol). 2003;67:301–20.
Hu Y, Yan C, Hsu CH, Chen QR, Niu K, Komatsoulis GA, Meerzaman D. OmicCircos: a simple-to-use R package for the circular visualization of multidimensional omics data. Cancer Inform. 2014;13:13–20.
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, et al. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45:D362–8.
Ohkuni K, Kitagawa K. Endogenous transcription at the centromere facilitates centromere activity in budding yeast. Curr Biol. 2011;21:1695–703.
Cook JG, Bardwell L, Kron SJ, Thorner J. Two novel targets of the MAP kinase Kss1 are negative regulators of invasive growth in the yeast Saccharomyces cerevisiae. Genes Dev. 1996;10:2831–48.
Bardwell L, Cook JG, Zhu-Shimoni JX, Voora D, Thorner J. Differential regulation of transcription: repression by unactivated mitogen-activated protein kinase Kss1 requires the Dig1 and Dig2 proteins. Proc Natl Acad Sci U S A. 1998;95:15400–5.
Olson KA, Nelson C, Tai G, Hung W, Yong C, Astell C, Sadowski I. Two regulators of Ste12p inhibit pheromone-responsive transcription by separate mechanisms. Mol Cell Biol. 2000;20:4199–209.
Gelli A. Rst1 and Rst2 are required for the a/alpha diploid cell type in yeast. Mol Microbiol. 2002;46:845–54.
McCullagh E, Seshan A, El-Samad H, Madhani HD. Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nat Cell Biol. 2010;12:954–62.
Randise-Hinchliff C, Brickner JH. Transcription factors dynamically control the spatial organization of the yeast genome. Nucleus. 2016;7:369–74.
O’Connell KF, Baker RE. Possible cross-regulation of phosphate and sulfate metabolism in Saccharomyces cerevisiae. Genetics. 1992;132:63–73.
Hemmerich P, Stoyan T, Wieland G, Koch M, Lechner J, Diekmann S. Interaction of yeast kinetochore proteins with centromere-protein/transcription factor Cbf1. Proc Natl Acad Sci U S A. 2000;97:12583–8.
Chan FL, Wong LH. Transcription in the maintenance of centromere chromatin identity. Nucleic Acids Res. 2012;40:11178–88.
Ha CW, Sung MK, Huh WK. Nsi1 plays a significant role in the silencing of ribosomal DNA in Saccharomyces cerevisiae. Nucleic Acids Res. 2012;40:4892–903.
Fleischer TC, Weaver CM, McAfee KJ, Jennings JL, Link AJ. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev. 2006;20:1294–307.
Mohanty BK, Bastia D. Binding of the replication terminator protein Fob1p to the Ter sites of yeast causes polar fork arrest. J Biol Chem. 2004;279:1932–41.
Reiter A, Hamperl S, Seitz H, Merkl P, Perez-Fernandez J, Williams L, Gerber J, Nemeth A, Leger I, Gadal O, et al. The Reb1-homologue Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J. 2012;31:3480–93.
Winston F, Chaleff DT, Valent B, Fink GR. Mutations affecting ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae. Genetics. 1984;107:179–97.
Perez-Martin J, Johnson AD. The C-terminal domain of Sin1 interacts with the SWI-SNF complex in yeast. Mol Cell Biol. 1998;18:4157–64.
Hershkovits G, Bangio H, Cohen R, Katcoff DJ. Recruitment of mRNA cleavage/polyadenylation machinery by the yeast chromatin protein Sin1p/Spt2p. Proc Natl Acad Sci U S A. 2006;103:9808–13.