Searching journal content for articles similar to Ramachandran et al. 25 (3): 381.

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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...to UV mutagenesis. However, the impact of genomic context and chromatin architecture on CPD deamination rates in cells remains poorly understood. Here, we develop a method known as dCPD-seq to map deaminated CPDs (dCPDs) across the of repair-deficient yeast cells at single-nucleotide resolution. Our d...
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Research: Asymmetric repair of UV damage in nucleosomes imposes a DNA strand polarity on somatic mutations in skin cancer
- Peng Mao,
- Michael J. Smerdon,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2020 30: 12-21; Published in Advance December 23, 2019, doi:10.1101/gr.253146.119
...of these “out” positions to DNase I and the NER machinery.DiscussionHere, we have shown that the repair of UV damage in nucleosomes is asymmetric. High-resolution genomic repair maps in both yeast and human cells indicate that CPD lesions on the 5′ side of the central dyad axis are more efficiently repaired...
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Research: CENPT bridges adjacent CENPA nucleosomes on young human α-satellite dimers
- Jitendra Thakur and
- Steven Henikoff
Genome Res. September 2016 26: 1178-1187; Published in Advance July 6, 2016, doi:10.1101/gr.204784.116
.... Thakur and Henikoff 1184 Genome Research www..org a right-handed wrap, opposite the wrap of octameric nucleosomes (Takeuchi et al. 2014). Insofar as budding yeast CENPA nucleosomes also wrap DNA with right-handed chirality in vivo (Furuyama and Henikoff 2009; Huang et al. 2011; Díaz-Ingelmo et al. 2015...
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Research: Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1
- Neeman Mohibullah and
- Scott Keeney
Genome Res. February 2017 27: 278-288; Published in Advance December 6, 2016, doi:10.1101/gr.213587.116
...-“cold” domains, DSBs are particularly enriched in small (typically <250 bp) regions known as “hotspots.” In Saccharomyces cerevisiae, most hotspots correspond to evolutionarily conserved nucleosome-depleted promoters (Lam and Keeney 2015b). However, the factors shaping the DSB landscape at larger size scales...
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Research: Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
- Patrick van Eijk,
- Shuvro Prokash Nandi,
- Shirong Yu,
- Mark Bennett,
- Matthew Leadbitter,
- Yumin Teng,
- and Simon H. Reed
Genome Res. January 2019 29: 74-84; Published in Advance December 14, 2018, doi:10.1101/gr.237198.118
...-NER into higher-order chromatin domains reduces the genomic search space for DNA damage detection, thus promoting the efficient recognition and repair of DNA lesions throughout the .ResultsIdentification of changes to the -wide linear arrangement of nucleosomes in response to UV damageIn order to determine how...
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Research: Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots
- Loris Mularoni,
- Yulian Zhou,
- Tyson Bowen,
- Sunil Gangadharan,
- Sarah J. Wheelan,
- and Jef D. Boeke
Genome Res. April 2012 22: 693-703; Published in Advance January 4, 2012, doi:10.1101/gr.129460.111
...of a tagged Ty1 element and its flanking yeast genomic sequences. We find that Ty1 targets all types of Pol III genes and that the nuclear tRNA gene upstream regions are hit at a very high frequency; 93.6% of all of the recovered insertions occurred within 2 kb of the 275 nuclear tRNA genes, and 272...
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Method: A unified model for yeast transcript definition
- Carl G. de Boer,
- Harm van Bakel,
- Kyle Tsui,
- Joyce Li,
- Quaid D. Morris,
- Corey Nislow,
- Jack F. Greenblatt,
- and Timothy R. Hughes
Genome Res. January 2014 24: 154-166; Published in Advance October 29, 2013, doi:10.1101/gr.164327.113
...sequence features detectable by the yeast cell, which we integrate into a Unified Model (UM) that models transcription as a whole. The cis -elements that denote where transcription initiates function primarily through nucleosome depletion, and, using a synthetic promoter system, we show that most...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
...protein. The most novel structural insight revealed by single-nucleotide-resolution epigenomic assays has been the recent discovery of asymmetric nucleosomes associated with the budding yeast . Nucleosome asymmetry was revealed by ChIP-exo analysis of several core histones and histone modifications (Rhee...
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Research: Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin
- Shirong Yu,
- Katie Evans,
- Patrick van Eijk,
- Mark Bennett,
- Richard M. Webster,
- Matthew Leadbitter,
- Yumin Teng,
- Raymond Waters,
- Stephen P. Jackson,
- and Simon H. Reed
Genome Res. October 2016 26: 1376-1387; Published in Advance July 28, 2016, doi:10.1101/gr.209106.116
.... To study this, we measured the distribution of nucleotide excision repair (NER) rates for UV-induced lesions throughout the budding yeast genome. By plotting these repair rates in relation to genes and their associated flanking sequences, we reveal that, in normal cells, genomic repair rates display...
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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
...to cell. These previously undetected, low-level DSBs thus play an outsized and crucial role in meiosis. We further find that the influence of underlying nucleotide sequence and chromosomal architecture differs in multiple ways from that in budding yeast. DSBs are not strongly restricted to nucleosome...

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