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Research: Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis
- Mihaela Ola,
- Caoimhe E. O'Brien,
- Aisling Y. Coughlan,
- Qinxi Ma,
- Paul D. Donovan,
- Kenneth H. Wolfe,
- and Geraldine Butler
Genome Res. May 2020 30: 684-696; Published in Advance May 18, 2020, doi:10.1101/gr.257816.119
...- or trimethylation at lysine 9 of histone H3 (H3K9me2/3). The position of the centromere in most species is determined by the presence of a variant of histone H3, called CENPA in mammals or Cse4 in yeast.Centromere repositioning occurs on an evolutionary timescale, leading to the formation of evolutionarily new...
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Research: A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin
- J. Peter Svensson,
- Manu Shukla,
- Victoria Menendez-Benito,
- Ulrika Norman-Axelsson,
- Pauline Audergon,
- Indranil Sinha,
- Jason C. Tanny,
- Robin C. Allshire,
- and Karl Ekwall
Genome Res. June 2015 25: 872-883; Published in Advance March 16, 2015, doi:10.1101/gr.188870.114
...time a comprehensive high-resolution nucleosome turnover map for the fission yeast S. pombe. We utilized an epitope-tag exchange system to precisely locate endogenously expressed old and new histones at subnucleosomal resolution using ChIP-exo methodology. We also mapped the three methylation states...
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Research: Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
- Alex Tsankov,
- Yoshimi Yanagisawa,
- Nicholas Rhind,
- Aviv Regev,
- and Oliver J. Rando
Genome Res. November 2011 21: 1851-1862; Published in Advance September 13, 2011, doi:10.1101/gr.122267.111
...processes that involve DNA (Kornberg and Lorch 1999; Radman-Livaja and Rando 2010). Genome-wide mapping of nucleosome positions in budding yeast shows thatmost genes contain a long nucleosome-depleted region in their proximal promoter, commonly called the ‘‘nucleosome-free region’’ (NFR) (Rando and Ahmad...
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Research: Stable and dynamic nucleosome states during a meiotic developmental process
- Liye Zhang,
- Hong Ma,
- and B. Franklin Pugh
Genome Res. June 2011 21: 875-884; Published in Advance April 22, 2011, doi:10.1101/gr.117465.110
...in fission yeast. PLoS Genet 3: e141. doi: 10.1371/journal.pgen.0030141. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM. 2006. A high-resolution map of transcription in the yeast . Proc Natl Acad Sci 103: 5320–5325. de Massy B, Rocco V, Nicolas A. 1995...
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Research: Nucleosome occupancy as a novel chromatin parameter for replication origin functions
- Jairo Rodriguez,
- Laura Lee,
- Bryony Lynch,
- and Toshio Tsukiyama
Genome Res. February 2017 27: 269-277; Published in Advance November 28, 2016, doi:10.1101/gr.209940.116
...by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/17; www..org Genome Research 269 www..org In order to identify chromatin parameters that correlate with origin properties, we performed high-resolution histone chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and found nucleosome...
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LETTER: Sequence Analysis of a Functional Drosophila Centromere
- Xiaoping Sun,
- Hiep D. Le,
- Janice M. Wahlstrom,
- and Gary H. Karpen
Genome Res. February 1, 2003 13: 182-194; doi:10.1101/gr.681703
...do not provide high-resolution information about the size and complexity of simple sequence arrays. Although pulsed field gel electrophoresis (PFGE) provides one method for spanning the gap between short-satellite sequences and cytological mapping ( Sun et al. 1997 ), the dispersion of repetitive...
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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
...chromatin regions and chromosomes; (3) the emergence, shape, and position of gene territories; (4) the mean distances between pairs of telomeres; and (5) even the co-location of functionally related gene loci, including early replication start sites and tRNA genes. Therefore, most aspects of the yeast...
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Research: Identification and characterization of centromeric sequences in Xenopus laevis
- Owen K. Smith,
- Charles Limouse,
- Kelsey A. Fryer,
- Nicole A. Teran,
- Kousik Sundararajan,
- Rebecca Heald,
- and Aaron F. Straight
Genome Res. June 2021 31: 958-967; Published in Advance April 19, 2021, doi:10.1101/gr.267781.120
...the Xenopus laevis centromere repeat sequences. By in situ hybridization, we show that Xenopus laevis centromeres contain diverse repeat sequences, and we map the centromere position on each Xenopus laevis chromosome using the distribution of centromere-enriched k-mers. Our identification of Xenopus laevis...
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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
...to the replicated centromere DNA by a CENPA-specific chaperone, the Holliday junction recognition protein (HJURP) in mammals or Scm3 in yeast (Kato et al. 2007). HJURP stabilizes soluble CENPA-H4 dimers before they are incorporated into centromeric nucleosomes (Dunleavy et al. 2009; Foltz et al. 2009) with the help...
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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
..., with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant , we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes...

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