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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...-specific nucleosome signatures in cells of origin, as derived here for CLL or for breast cancer in our recent study (Jacob et al. 2023), could provide a novel approach to dissect the disease course from liquid biopsies. Thus, mapping changes in nucleosome positioning in tumor versus nonmalignant cells provides...
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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
...with high splicing efficiency. Our data reveal a complex link between GC content, nucleosome positioning, and intron evolution in Paramecium.In eukaryotes, genomic DNA is compacted by histones into chromatin. The basic unit of chromatin is the nucleosome, which comprises a histone octamer made of the four...
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Research: Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome
- Sara González,
- Alicia García,
- Enrique Vázquez,
- Rebeca Serrano,
- Mar Sánchez,
- Luis Quintales,
- and Francisco Antequera
Genome Res. November 2016 26: 1532-1543; Published in Advance September 23, 2016, doi:10.1101/gr.207241.116
...in the human made up of intrinsic nucleosome-depleted regions flanked by two or three nucleosomes whose positioning is encoded in the GC content (Drillon et al. 2016). These results suggest that nucleosomal signatures could have a positive selective value for their contribution to nucleosome positioning...
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Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
- Marina Veil,
- Lev Y. Yampolsky,
- Björn Grüning,
- and Daria Onichtchouk
Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
...: post-ZGA nucleosome depletion by synergistic action of Pou5f3 and Nanog in the presence of SoxB1We detected widespread alignment of nucleosomes on their DNA-encoded nucleosome positioning signals from pre- to post-ZGA (Fig. 4C, black arrows). Increase of nucleosome positioning strength was previously...
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Method: Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
- Theresa K. Kelly,
- Yaping Liu,
- Fides D. Lay,
- Gangning Liang,
- Benjamin P. Berman,
- and Peter A. Jones
Genome Res. December 2012 22: 2497-2506; Published in Advance September 7, 2012, doi:10.1101/gr.143008.112
.... Combinatorial epigenomic signatures reveal functional chromatin Unlike any other method used to assess nucleosome occupancy or DNA methylation, NOMe-seq includes both nucleosome positioning and DNA methylation data for individual DNA strands, enabling a correlation between the two features at the single...
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Research: Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains
- Ying-Tao Zhao,
- Deborah Y. Kwon,
- Brian S. Johnson,
- Maria Fasolino,
- Janine M. Lamonica,
- Yoon Jung Kim,
- Boxuan Simen Zhao,
- Chuan He,
- Golnaz Vahedi,
- Tae Hoon Kim,
- and Zhaolan Zhou
Genome Res. July 2018 28: 933-942; Published in Advance May 30, 2018, doi:10.1101/gr.233775.117
...elongation and enhancer activity at tumor-suppressor genes. Nat Genet 47: 1149–1157. ↵Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845–1848. ↵De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE...
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Research: Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast
- Danny A. Bitton,
- Sophie R. Atkinson,
- Charalampos Rallis,
- Graeme C. Smith,
- David A. Ellis,
- Yuan Y.C. Chen,
- Michal Malecki,
- Sandra Codlin,
- Jean-François Lemay,
- Cristina Cotobal,
- François Bachand,
- Samuel Marguerat,
- Juan Mata,
- and Jürg Bähler
Genome Res. June 2015 25: 884-896; Published in Advance April 16, 2015, doi:10.1101/gr.185371.114
...Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast Danny A. Bitton 1 , Sophie R. Atkinson 1 , Charalampos Rallis 1 , Graeme C. Smith 1 , David A. Ellis 1 , Yuan Y.C. Chen 1 , 4 , Michal...
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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
...phasing has also been detected at other transcriptional regulator binding sites (Wang et al. 2012b), raising the possibility that nucleosome phasing surrounding regulatory factors may be widespread. To determine the extent of nucleosome organization, wemapped nucleosome occupancy and DNAmethylation...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome...
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Research: Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
- Gangqing Hu,
- Dustin E. Schones,
- Kairong Cui,
- River Ybarra,
- Daniel Northrup,
- Qingsong Tang,
- Luca Gattinoni,
- Nicholas P. Restifo,
- Suming Huang,
- and Keji Zhao
Genome Res. October 2011 21: 1650-1658; Published in Advance July 27, 2011, doi:10.1101/gr.121145.111
..., Sigal N, Barkai N. 2010. Widespread remodeling of mid-coding sequence nucleosomes by Isw1. Genome Biol 11: R49. doi: 10.1186/gb2010-11-5-r49. Tripic T, Deng W, Cheng Y, Zhang Y, Vakoc CR, Gregory GD, Hardison RC, Blobel GA. 2009. SCL and associated proteins distinguish active from repressive GATA...

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