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Methods: High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
- Assaf Weiner,
- Amanda Hughes,
- Moran Yassour,
- Oliver J. Rando,
- and Nir Friedman
Genome Res. January 2010 20: 90-100; Published in Advance October 21, 2009, doi:10.1101/gr.098509.109
...High-resolution nucleosome mapping reveals transcription-dependent promoter packaging Assaf Weiner 1 , Amanda Hughes 2 , Moran Yassour 1 , 3 , Oliver J. Rando 2 , 5 and Nir Friedman 1 , 4 , 5 1 School of Computer...
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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
...Evolutionary divergence of intrinsic and trans -regulated nucleosome positioning sequences reveals plastic rules for chromatin organization Alex Tsankov 1 , 2 , Yoshimi Yanagisawa 3 , Nicholas Rhind 3 , 6 , Aviv Regev 1 , 2 , 4 , 5 , 6...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
...; Gerstein et al. 2010; Liu et al. 2011b; Hsu et al. 2015; Evans et al. 2016), high-resolution, -wide chromatin accessibility maps throughout development have not yet been reported. In this study, we show that studying high-resolution chromatin accessibility dynamics in synchronized C. elegans populations...
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Research: High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
- Sevinç Ercan,
- Yaniv Lubling,
- Eran Segal,
- and Jason D. Lieb
Genome Res. February 2011 21: 237-244; Published in Advance December 22, 2010, doi:10.1101/gr.115931.110
...position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18: 1051–1063. Visnapuu ML, Greene EC. 2009. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition.Nat Struct Mol Biol 16: 1056–1062. Widlak P, GarrardWT. 2006...
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Research: Canonical nucleosome organization at promoters forms during genome activation
- Yong Zhang,
- Nadine L. Vastenhouw,
- Jianxing Feng,
- Kai Fu,
- Chenfei Wang,
- Ying Ge,
- Andrea Pauli,
- Paul van Hummelen,
- Alexander F. Schier,
- and X. Shirley Liu
Genome Res. February 2014 24: 260-266; Published in Advance November 27, 2013, doi:10.1101/gr.157750.113
...Struct Mol Biol 19: 1185–1192. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, et al. 2008. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18: 1051–1063. Valouev A...
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Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- Phillippa C. Taberlay,
- Aaron L. Statham,
- Theresa K. Kelly,
- Susan J. Clark,
- and Peter A. Jones
Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
...in DNA methylation of enhancers and insulator elements. Results Nucleosome-depleted regions (NDRs) are largely unique to individual cell types We recently developed a method for high-resolution simultaneous wide mapping of DNA methylation and nucleosomeoccupancywithin individual DNA strands...
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Letter: A novel strategy of transcription regulation by intragenic nucleosome ordering
- Cédric Vaillant,
- Leonor Palmeira,
- Guillaume Chevereau,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Claude Thermes,
- and Alain Arneodo
Genome Res. January 2010 20: 59-67; Published in Advance October 26, 2009, doi:10.1101/gr.096644.109
...2009). In yeast, recent high-resolution experiments revealed a specific gene promoter nucleosome pattern characterized by a nucleosome depleted region (NFR) of typical size 100–200 base pairs (bp) upstream of the transcription start site (TSS) and, to a lesser extent, at the gene 39 end (Yuan et al...
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Resource: The transcription start site landscape of C. elegans
- Taro Leo Saito,
- Shin-ichi Hashimoto,
- Sam Guoping Gu,
- J. Jason Morton,
- Michael Stadler,
- Thomas Blumenthal,
- Andrew Fire,
- and Shinichi Morishita
Genome Res. August 2013 23: 1348-1361; Published in Advance May 1, 2013, doi:10.1101/gr.151571.112
...-specific expression and/or conservation among six worm species. Comparing TSS features between trans -spliced and non- trans -spliced genes, we found stronger signals among outron TSSs for preferentially positioning of flanking nucleosomes and for downstream Pol II enrichment. Our data provide an enabling resource...
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Research: Core promoter T-blocks correlate with gene expression levels in C. elegans
- Vladislav Grishkevich,
- Tamar Hashimshony,
- and Itai Yanai
Genome Res. May 2011 21: 707-717; Published in Advance March 2, 2011, doi:10.1101/gr.113381.110
...). To examine nucleosome positioning within C. elegans core promoters, we invoked a published data set (Valouev et al. 2008) to determine -wide nucleosome occupancies. For each set of genes with a particular number of T-blocks, we calculated the mean nucleosome occupancy (Fig. 3A). We found a negative...
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Letter: Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes
- Michael Y. Tolstorukov,
- Peter V. Kharchenko,
- Joseph A. Goldman,
- Robert E. Kingston,
- and Peter J. Park
Genome Res. June 2009 19: 967-977; Published in Advance February 26, 2009, doi:10.1101/gr.084830.108
...(TSS) and involved in transcriptional activation, was extensively studied in several organisms ( Zlatanova and Thakar 2008 ). The H2A.Z-containing nucleosomes were recently mapped in the entire yeast with high resolution using pyrosequencing ( Albert et al. 2007 ). Genome-wide distribution of 20...

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