Searching journal content for articles similar to Cotney et al. 22 (6): 1069.

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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...gene regulation in mole-rats, we generated histone mark chromatin immunoprecipitation (ChIP)-sequencing data to identify promoters and enhancers active in two somatic tissues with distinct metabolic and functional roles (liver and heart) from the naked mole-rat, Damaraland mole-rat, and two outgroup...
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Research: A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells
- Gurdeep Singh,
- Shanelle Mullany,
- Sakthi D. Moorthy,
- Richard Zhang,
- Tahmid Mehdi,
- Ruxiao Tian,
- Andrew G. Duncan,
- Alan M. Moses,
- and Jennifer A. Mitchell
Genome Res. April 2021 31: 564-575; Published in Advance March 12, 2021, doi:10.1101/gr.272468.120
...are required to regulate tissue-specific gene expression during normal development, and -wide association studies (GWASs) reveal that disease-associated SNPs (single nucleotide polymorphisms) are more often found in noncoding regions of the displaying chromatin features associated with transcriptional...
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Research: Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis
- Catia Attanasio,
- Alex S. Nord,
- Yiwen Zhu,
- Matthew J. Blow,
- Simon C. Biddie,
- Eric M. Mendenhall,
- Jesse Dixon,
- Crystal Wright,
- Roya Hosseini,
- Jennifer A. Akiyama,
- Amy Holt,
- Ingrid Plajzer-Frick,
- Malak Shoukry,
- Veena Afzal,
- Bing Ren,
- Bradley E. Bernstein,
- Edward M. Rubin,
- Axel Visel,
- and Len A. Pennacchio
Genome Res. June 2014 24: 920-929; Published in Advance April 21, 2014, doi:10.1101/gr.168930.113
...with active enhancers, is associated with more complex tissue-specific regulatory chromatin states in vivo. To functionally stratify the nature of the SMARCA4-bound regions and gain insights into their role in gene regulation in vivo, we generated ChIP-seq data for both activating (H3K4me3, H3K4me1, H3K27ac...
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Research: Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
- Swann Floc'hlay,
- Emily S. Wong,
- Bingqing Zhao,
- Rebecca R. Viales,
- Morgane Thomas-Chollier,
- Denis Thieffry,
- David A. Garfield,
- and Eileen E.M. Furlong
Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
...embryonic development. We collected Drosophila F1 hybrid embryos from eight crosses and quantified allele-specific changes in TF occupancy (using open chromatin [ATAC-seq] as a proxy), enhancer and promoter activity (using H3K27ac or H3K4me3 and H3K27ac ChIP-seq as proxies, respectively), and gene...
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Research: Coding exons function as tissue-specific enhancers of nearby genes
- Ramon Y. Birnbaum,
- E. Josephine Clowney,
- Orly Agamy,
- Mee J. Kim,
- Jingjing Zhao,
- Takayuki Yamanaka,
- Zachary Pappalardo,
- Shoa L. Clarke,
- Aaron M. Wenger,
- Loan Nguyen,
- Fiorella Gurrieri,
- David B. Everman,
- Charles E. Schwartz,
- Ohad S. Birk,
- Gill Bejerano,
- Stavros Lomvardas,
- and Nadav Ahituv
Genome Res. June 2012 22: 1059-1068; Published in Advance March 22, 2012, doi:10.1101/gr.133546.111
...above the 1.02 Mb average length (N50) of a human–mouse– chicken syntenyblock in that study. These results further suggest that these eExons could be important forDLX5/6 andTWIST1 regulation. Dync1i1 eExon 15 is marked in the limb by an enhancer chromatin signature To examine the dual role of these...
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Research: Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
- J. Omar Yáñez-Cuna,
- Cosmas D. Arnold,
- Gerald Stampfel,
- Łukasz M. Boryń,
- Daniel Gerlach,
- Martina Rath,
- and Alexander Stark
Genome Res. July 2014 24: 1147-1156; Published in Advance April 8, 2014, doi:10.1101/gr.169243.113
...-specific enhancer activity STARR-seq measures the enhancer activity of defined DNA fragments in the constant sequence environment of a reporter plasmid (Fig. 2A) and thus is independent of the fragments’ genomic contexts and chromatin states (Arnold et al. 2013). We therefore hypothesized that all functional...
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Research: Restless Legs Syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon
- Derek Spieler,
- Maria Kaffe,
- Franziska Knauf,
- José Bessa,
- Juan J. Tena,
- Florian Giesert,
- Barbara Schormair,
- Erik Tilch,
- Heekyoung Lee,
- Marion Horsch,
- Darina Czamara,
- Nazanin Karbalai,
- Christine von Toerne,
- Melanie Waldenberger,
- Christian Gieger,
- Peter Lichtner,
- Melina Claussnitzer,
- Ronald Naumann,
- Bertram Müller-Myhsok,
- Miguel Torres,
- Lillian Garrett,
- Jan Rozman,
- Martin Klingenspor,
- Valérie Gailus-Durner,
- Helmut Fuchs,
- Martin Hrabě de Angelis,
- Johannes Beckers,
- Sabine M. Hölter,
- Thomas Meitinger,
- Stefanie M. Hauck,
- Helmut Laumen,
- Wolfgang Wurst,
- Fernando Casares,
- Jose Luis Gómez-Skarmeta,
- and Juliane Winkelmann
Genome Res. April 2014 24: 592-603; Published in Advance March 18, 2014, doi:10.1101/gr.166751.113
...embryonic ganglionic eminences (GE). CREB1 binds this enhancer and rs12469063 affects its binding in vitro. In addition, MEIS1 target genes suggest a role in the specification of neuronal progenitors in the GE, and heterozygous Meis1 -deficient mice exhibit hyperactivity, resembling the RLS phenotype. Thus...
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Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
...demonstrate increased selective pressure tomaintain regulatory activity in the vicinity of protein-coding genes. Multiple genomic features indicative of broad regulatory element activity were significantly associated with regulatory conservation. Promoters and enhancers overlapping regions of chromatin...
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Research: The genomic landscape of cohesin-associated chromatin interactions
- Laura E. DeMare,
- Jing Leng,
- Justin Cotney,
- Steven K. Reilly,
- Jun Yin,
- Richard Sarro,
- and James P. Noonan
Genome Res. August 2013 23: 1224-1234; Published in Advance May 23, 2013, doi:10.1101/gr.156570.113
...JP. 2012. Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.Genome Res22: 1069–1080. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, et al. 2010. Histone H3K27ac...
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Research: Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes
- Sakthi D. Moorthy,
- Scott Davidson,
- Virlana M. Shchuka,
- Gurdeep Singh,
- Nakisa Malek-Gilani,
- Lida Langroudi,
- Alexandre Martchenko,
- Vincent So,
- Neil N. Macpherson,
- and Jennifer A. Mitchell
Genome Res. February 2017 27: 246-258; Published in Advance November 28, 2016, doi:10.1101/gr.210930.116
...et al. 2013; Loven et al. 2013; Parker et al. 2013; Whyte et al. 2013). Stretch enhancers are regions of ≥3 kb which exhibit an enhancer chromatin state based on the ChromHMM algorithm (Ernst et al. 2011; Parker et al. 2013). Super-enhancers have been predicted in numerous cell types where...

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