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Research: Sir3 mediates long-range chromosome interactions in budding yeast
- Myriam Ruault,
- Vittore F. Scolari,
- Luciana Lazar-Stefanita,
- Antoine Hocher,
- Isabelle Loïodice,
- Romain Koszul,
- and Angela Taddei
Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
...genes located, respectively, in telomere-proximal regions of Chromosome I's right arm, left arm, and IX's right arm (Supplemental Fig. S5C). Further analysis at the read level revealed that the apparent interaction between FLO1 and FLO9 could stem from an alignment artifact. However...
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Research: High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
- Houssam Hajjoul,
- Julien Mathon,
- Hubert Ranchon,
- Isabelle Goiffon,
- Julien Mozziconacci,
- Benjamin Albert,
- Pascal Carrivain,
- Jean-Marc Victor,
- Olivier Gadal,
- Kerstin Bystricky,
- and Aurélien Bancaud
Genome Res. November 2013 23: 1829-1838; Published in Advance September 27, 2013, doi:10.1101/gr.157008.113
...Houwe G, Sage D, Unser M, Gartenberg M, Gasser S. 2008. Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast. Genome Res 18: 261. Schober H, FerreiraH, Kalck V, Gehlen LR, Gasser SM. 2009. Yeast telomerase and the SUN domain protein Mps3 anchor telomeres...
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Research: Physical tethering and volume exclusion determine higher-order genome organization in budding yeast
- Harianto Tjong,
- Ke Gong,
- Lin Chen,
- and Frank Alber
Genome Res. July 2012 22: 1295-1305; Published in Advance May 22, 2012, doi:10.1101/gr.129437.111
...simulation. To further improve these interactions it is necessary to include these regions in future simulations (see Supplemental Material). Principles of 3D organization in yeast Genome Research 1299 www..org length, the subtelomere is able to reach all points on the NE. Further increases in arm length do...
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Letter: The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion
- Angela Taddei,
- Griet Van Houwe,
- Shigeki Nagai,
- Ionas Erb,
- Erik van Nimwegen,
- and Susan M. Gasser
Genome Res. April 2009 19: 611-625; Published in Advance January 29, 2009, doi:10.1101/gr.083881.108
...-regulation. To understand whether gene position along the chromosome arm affected a locus' response to yku70 esc1 deletion, we first calculated for each yeast gene the significance ( Z -value) for its change in expression (log expression change) as compared to the wild-type control, and then calculated the average...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
...Francisco, California 94143, USA; 4Chan-Zuckerberg Biohub, San Francisco, California 94158, USA Corresponding author: katherine.pollard@gladstone.ucsf.eduAbstractRecombination enables reciprocal exchange of genomic information between parental chromosomes and successful segregation of homologous chromosomes...
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Resource: Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline
- Nicholas Stong,
- Zhong Deng,
- Ravi Gupta,
- Sufen Hu,
- Shiela Paul,
- Amber K. Weiner,
- Evan E. Eichler,
- Tina Graves,
- Catrina C. Fronick,
- Laura Courtney,
- Richard K. Wilson,
- Paul M. Lieberman,
- Ramana V. Davuluri,
- and Harold Riethman
Genome Res. June 2014 24: 1039-1050; Published in Advance March 27, 2014, doi:10.1101/gr.166983.113
...aspects of chromosome biology, including chromatin insulator, enhancer blocker, transcriptional activator and repressor, DNA methylation–sensitive parental imprinting, and DNA-loop formation between transcriptional control elements (Bushey et al. 2008; Phillips and Corces 2009; Ohlsson et al. 2010...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...). These analyses also revealed the precise fusion point of the autosome-to-X-chromosome translocation that added what now comprises the larger portion of the short arm of the human X chromosome to the ancestral eutherian X subsequent to the metatherian–eutherian divergence ( Lahn and Page 1999 ; Kohn et al. 2004...

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