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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
..., the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here, we investigate the well-conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3–5 foci in exponentially growing cells. This clustering is functionally...
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Research: Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery
- Xiuli Bi,
- Ying-Juan Cheng,
- Bo Hu,
- Xiaoli Ma,
- Rui Wu,
- Jia-Wei Wang,
- and Chang Liu
Genome Res. July 2017 27: 1162-1173; Published in Advance April 6, 2017, doi:10.1101/gr.215186.116
...the chromocenters decondensed, the regions corresponding to the 5S RNA repeats remained anchored at the nuclear periphery (Wang et al. 2013). This suggests the need to investigate higher-order crwn mutants to clarify their potential roles in tethering chromatin. In this study, many highly expressed genes were also...
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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
...been proposed to describe the folding of chromosomes (Lieberman-Aiden et al. 2009; Bohn and Heermann 2010; Bancaud et al. 2012), the physical principles governing this organization are still largely debated. Despite its small size, budding yeast has become a unique model that recapitulates some...
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Research: Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome
- Kyle R. Fowler,
- Mariko Sasaki,
- Neta Milman,
- Scott Keeney,
- and Gerald R. Smith
Genome Res. October 2014 24: 1650-1664; Published in Advance July 14, 2014, doi:10.1101/gr.172122.114
..., the mechanisms and machinery of meiotic recombination are highly diverse among species. Developmentally programmed DNA double-strand breaks (DSBs) initiate meiotic recombination in the organisms studied most thoroughly at the molecular level, the budding yeast Saccharomyces cerevisiae and the fission yeast...
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Research: Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
- Ferhat Ay,
- Evelien M. Bunnik,
- Nelle Varoquaux,
- Sebastiaan M. Bol,
- Jacques Prudhomme,
- Jean-Philippe Vert,
- William Stafford Noble,
- and Karine G. Le Roch
Genome Res. June 2014 24: 974-988; Published in Advance March 26, 2014, doi:10.1101/gr.169417.113
...structure (Supplemental Tables 11, 12). Discussion This study presents the first analysis of architecture during the cell cycle of a eukaryotic pathogen. Overall, our data demonstrate that the of P. falciparum exhibits a higher degree of organization than the similarly sized budding yeast . Although...
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Research: Orc4 spatiotemporally stabilizes centromeric chromatin
- Lakshmi Sreekumar,
- Kiran Kumari,
- Krishnendu Guin,
- Asif Bakshi,
- Neha Varshney,
- Bhagya C. Thimmappa,
- Leelavati Narlikar,
- Ranjith Padinhateeri,
- Rahul Siddharthan,
- and Kaustuv Sanyal
Genome Res. April 2021 31: 607-621; Published in Advance January 29, 2021, doi:10.1101/gr.265900.120
...can be converted to linear distance approximations and averaged across populations to generate computational models that yield an ensemble of genomic conformations (Berger et al. 2008; Gürsoy et al. 2017). To study the higher-order chromosomal organization of the C. albicans , we resorted to polymer...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...; Rhind et al. 2011; Melters et al. 2013; Logsdon et al. 2023; Wlodzimierz et al. 2023b). For instance, the smallest centromeres, found in budding yeast, are ∼120 bp (Fitzgerald-Hayes et al. 1982; Furuyama and Biggins 2007). These centromere sequences support the loading of a single Cse4 (the CENH3...
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Research: Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions
- Antoine Hocher,
- Myriam Ruault,
- Petra Kaferle,
- Marc Descrimes,
- Mickaël Garnier,
- Antonin Morillon,
- and Angela Taddei
Genome Res. December 2018 28: 1867-1881; Published in Advance October 24, 2018, doi:10.1101/gr.236554.118
...of silencing effectors and drives the formation of heterochromatin domains (Richards and Elgin 2002; Wang et al. 2016). However, the spread of heterochromatin must be limited to prevent encroaching on euchromatin (Donze and Kamakaka 2002).In budding yeast, the silent information regulator (SIR) proteins—Sir2...
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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
...; Yamada et al. 2017). However, H3K4me3 may promote crossovers downstream from DSB formation, via tethering repair sites to the chromosome axis, as in budding yeast and mammals (Borde et al. 2009; Acquaviva et al. 2013; Sommermeyer et al. 2013; Imai et al. 2017). It is also important to note...

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