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Method: A synergistic DNA logic predicts genome-wide chromatin accessibility
- Tatsunori Hashimoto,
- Richard I. Sherwood,
- Daniel D. Kang,
- Nisha Rajagopal,
- Amira A. Barkal,
- Haoyang Zeng,
- Bart J.M. Emons,
- Sharanya Srinivasan,
- Tommi Jaakkola,
- and David K. Gifford
Genome Res. October 2016 26: 1430-1440; Published in Advance July 25, 2016, doi:10.1101/gr.199778.115
...A synergistic DNA logic predicts genome-wide chromatin accessibility Tatsunori Hashimoto 1 , 3 , Richard I. Sherwood 2 , 3 , Daniel D. Kang 1 , 3 , Nisha Rajagopal 1 , Amira A. Barkal 1 , 2 , Haoyang Zeng 1 , Bart J...
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Research: Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells
- Luciano Pirola,
- Aneta Balcerczyk,
- Richard W. Tothill,
- Izhak Haviv,
- Antony Kaspi,
- Sebastian Lunke,
- Mark Ziemann,
- Tom Karagiannis,
- Stephen Tonna,
- Adam Kowalczyk,
- Bryan Beresford-Smith,
- Geoff Macintyre,
- Ma Kelong,
- Zhang Hongyu,
- Jingde Zhu,
- and Assam El-Osta
Genome Res. October 2011 21: 1601-1615; Published in Advance September 2, 2011, doi:10.1101/gr.116095.110
...to understand the dynamic role of some of the diverse epigenetic changes mediated by hyperglycemia at single loci, yet elevated glucose levels are thought to regulate genome-wide changes, and this still remains poorly understood. In this article we describe genome-wide histone H3K9/K14 hyperacetylation and DNA...
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LETTER: Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
- Ali Mortazavi,
- Evonne Chen Leeper Thompson,
- Sarah T. Garcia,
- Richard M. Myers,
- and Barbara Wold
Genome Res. October 2006 16: 1208-1221; Published in Advance September 8, 2006, doi:10.1101/gr.4997306
...Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire Ali Mortazavi 1 , Evonne Chen Leeper Thompson 2 , Sarah T. Garcia 2 , Richard M. Myers 2 , and Barbara Wold 1 , 3...
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Research: Natural variation of histone modification and its impact on gene expression in the rat genome
- Carola Rintisch,
- Matthias Heinig,
- Anja Bauerfeind,
- Sebastian Schafer,
- Christin Mieth,
- Giannino Patone,
- Oliver Hummel,
- Wei Chen,
- Stuart Cook,
- Edwin Cuppen,
- Maria Colomé-Tatché,
- Frank Johannes,
- Ritsert C. Jansen,
- Helen Neil,
- Michel Werner,
- Michal Pravenec,
- Martin Vingron,
- and Norbert Hubner
Genome Res. June 2014 24: 942-953; Published in Advance May 2, 2014, doi:10.1101/gr.169029.113
...in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among...
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Research: Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver
- Brad G. Hoffman,
- Gordon Robertson,
- Bogard Zavaglia,
- Mike Beach,
- Rebecca Cullum,
- Sam Lee,
- Galina Soukhatcheva,
- Leping Li,
- Elizabeth D. Wederell,
- Nina Thiessen,
- Mikhail Bilenky,
- Timothee Cezard,
- Angela Tam,
- Baljit Kamoh,
- Inanc Birol,
- Derek Dai,
- YongJun Zhao,
- Martin Hirst,
- C. Bruce Verchere,
- Cheryl D. Helgason,
- Marco A. Marra,
- Steven J.M. Jones,
- and Pamela A. Hoodless
Genome Res. August 2010 20: 1037-1051; Published in Advance June 15, 2010, doi:10.1101/gr.104356.109
...Genome-wide identification of FOXA2-, PDX1-, and HNF4A-occupied loci in adult islets and liver We used ChIP-seq to globally identify loci occupied by FOXA2 in adultmouse islets and liver, PDX1 in islets, andHNF4A in liver. The antibodies used produced only the expected bands in Western blots...
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Research: Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program
- Joris van Arensbergen,
- Javier García-Hurtado,
- Ignasi Moran,
- Miguel Angel Maestro,
- Xiaobo Xu,
- Mark Van de Casteele,
- Anouchka L. Skoudy,
- Matteo Palassini,
- Harry Heimberg,
- and Jorge Ferrer
Genome Res. June 2010 20: 722-732; Published in Advance April 15, 2010, doi:10.1101/gr.101709.109
...organisms are poorly understood. To gain insights into how pancreatic beta-cells are programmed, we profiled key histone methylations and transcripts in embryonic stem cells, multipotent progenitors of the nascent embryonic pancreas, purified beta-cells, and 10 differentiated tissues. We report that despite...
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Method: methyl-ATAC-seq measures DNA methylation at accessible chromatin
- Roman Spektor,
- Nathaniel D. Tippens,
- Claudia A. Mimoso,
- and Paul D. Soloway
Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
..., Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA Corresponding author: soloway@cornell.eduAbstractChromatin features are characterized by -wide assays for nucleosome location, protein binding sites, three-dimensional interactions, and modifications to histones and DNA...
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Method: Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
- Roger Pique-Regi,
- Jacob F. Degner,
- Athma A. Pai,
- Daniel J. Gaffney,
- Yoav Gilad,
- and Jonathan K. Pritchard
Genome Res. March 2011 21: 447-455; Published in Advance November 24, 2010, doi:10.1101/gr.112623.110
..., University of Chicago, Chicago, Illinois 60637, USA ↵ 4 These authors contributed equally to this work. Abstract Accurate functional annotation of regulatory elements is essential for understanding global gene regulation. Here, we report a genome-wide map of 827,000 transcription...
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Research: Maps of open chromatin highlight cell type–restricted patterns of regulatory sequence variation at hematological trait loci
- Dirk S. Paul,
- Cornelis A. Albers,
- Augusto Rendon,
- Katrin Voss,
- Jonathan Stephens,
- HaemGen Consortium,
- Pim van der Harst,
- John C. Chambers,
- Nicole Soranzo,
- Willem H. Ouwehand,
- and Panos Deloukas
Genome Res. July 2013 23: 1130-1141; Published in Advance April 9, 2013, doi:10.1101/gr.155127.113
...Kingdom ↵ 13 These authors contributed equally to this work. Abstract Nearly three-quarters of the 143 genetic signals associated with platelet and erythrocyte phenotypes identified by meta-analyses of genome-wide association (GWA) studies are located at non...
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Research: DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
- Deborah R. Winter,
- Lingyun Song,
- Sayan Mukherjee,
- Terrence S. Furey,
- and Gregory E. Crawford
Genome Res. July 2013 23: 1118-1129; Published in Advance May 8, 2013, doi:10.1101/gr.150482.112
...of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina 27708, USA Abstract DNase-seq is primarily used to identify nucleosome-depleted DNase I hypersensitive (DHS) sites genome-wide that correspond to active regulatory elements. However, ∼40 yr ago it was demonstrated...

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