Table of Contents

October 2013; 23 (10)

Research

  • Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation

    • Hélène Neyret-Kahn,
    • Moussa Benhamed,
    • Tao Ye,
    • Stéphanie Le Gras,
    • Jack-Christophe Cossec,
    • Pierre Lapaquette,
    • Oliver Bischof,
    • Maia Ouspenskaia,
    • Mary Dasso,
    • Jacob Seeler,
    • Irwin Davidson,
    • and Anne Dejean
    Genome Res. October 2013 23: 1563-1579; Published in Advance July 26, 2013, doi:10.1101/gr.154872.113

  • Lamin A/C-promoter interactions specify chromatin state–dependent transcription outcomes

    • Eivind Lund,
    • Anja R. Oldenburg,
    • Erwan Delbarre,
    • Christel T. Freberg,
    • Isabelle Duband-Goulet,
    • Ragnhild Eskeland,
    • Brigitte Buendia,
    • and Philippe Collas
    Genome Res. October 2013 23: 1580-1589; Published in Advance July 16, 2013, doi:10.1101/gr.159400.113

  • GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination

    • Paul A. Ginno,
    • Yoong Wearn Lim,
    • Paul L. Lott,
    • Ian Korf,
    • and Frédéric Chédin
    Genome Res. October 2013 23: 1590-1600; Published in Advance July 18, 2013, doi:10.1101/gr.158436.113

  • De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

    • Felix Schlesinger,
    • Andrew D. Smith,
    • Thomas R. Gingeras,
    • Gregory J. Hannon,
    • and Emily Hodges
    Genome Res. October 2013 23: 1601-1614; Published in Advance June 28, 2013, doi:10.1101/gr.157271.113

  • Frac-seq reveals isoform-specific recruitment to polyribosomes

    • Timothy Sterne-Weiler,
    • Rocio Teresa Martinez-Nunez,
    • Jonathan M. Howard,
    • Ivan Cvitovik,
    • Sol Katzman,
    • Muhammad A. Tariq,
    • Nader Pourmand,
    • and Jeremy R. Sanford
    Genome Res. October 2013 23: 1615-1623; Published in Advance June 19, 2013, doi:10.1101/gr.148585.112
    OPEN ACCESS ARTICLE

  • Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions

    • Adam R. Prickett,
    • Nikolaos Barkas,
    • Ruth B. McCole,
    • Siobhan Hughes,
    • Samuele M. Amante,
    • Reiner Schulz,
    • and Rebecca J. Oakey
    Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112

  • Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

    • Jessica A. Hurt,
    • Alex D. Robertson,
    • and Christopher B. Burge
    Genome Res. October 2013 23: 1636-1650; Published in Advance June 13, 2013, doi:10.1101/gr.157354.113

  • The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

    • Michael Regulski,
    • Zhenyuan Lu,
    • Jude Kendall,
    • Mark T.A. Donoghue,
    • Jon Reinders,
    • Victor Llaca,
    • Stephane Deschamps,
    • Andrew Smith,
    • Dan Levy,
    • W. Richard McCombie,
    • Scott Tingey,
    • Antoni Rafalski,
    • James Hicks,
    • Doreen Ware,
    • and Robert A. Martienssen
    Genome Res. October 2013 23: 1651-1662; Published in Advance June 5, 2013, doi:10.1101/gr.153510.112
    OPEN ACCESS ARTICLE

  • Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

    • Robert J. Schmitz,
    • Yupeng He,
    • Oswaldo Valdés-López,
    • Saad M. Khan,
    • Trupti Joshi,
    • Mark A. Urich,
    • Joseph R. Nery,
    • Brian Diers,
    • Dong Xu,
    • Gary Stacey,
    • and Joseph R. Ecker
    Genome Res. October 2013 23: 1663-1674; Published in Advance June 5, 2013, doi:10.1101/gr.152538.112

  • Multiple RNA recognition patterns during microRNA biogenesis in plants

    • Nicolás G. Bologna,
    • Arnaldo L. Schapire,
    • Jixian Zhai,
    • Uciel Chorostecki,
    • Jerome Boisbouvier,
    • Blake C. Meyers,
    • and Javier F. Palatnik
    Genome Res. October 2013 23: 1675-1689; Published in Advance August 29, 2013, doi:10.1101/gr.153387.112

  • DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast

    • Joel H. Graber,
    • Fathima I. Nazeer,
    • Pei-chun Yeh,
    • Jason N. Kuehner,
    • Sneha Borikar,
    • Derick Hoskinson,
    • and Claire L. Moore
    Genome Res. October 2013 23: 1690-1703; Published in Advance June 20, 2013, doi:10.1101/gr.144964.112
    OPEN ACCESS ARTICLE

  • Meta-analyses of studies of the human microbiota

    • Catherine A. Lozupone,
    • Jesse Stombaugh,
    • Antonio Gonzalez,
    • Gail Ackermann,
    • Doug Wendel,
    • Yoshiki Vázquez-Baeza,
    • Janet K. Jansson,
    • Jeffrey I. Gordon,
    • and Rob Knight
    Genome Res. October 2013 23: 1704-1714; Published in Advance July 16, 2013, doi:10.1101/gr.151803.112
    OPEN ACCESS ARTICLE

  • Sympatric chimpanzees and gorillas harbor convergent gut microbial communities

    • Andrew H. Moeller,
    • Martine Peeters,
    • Jean-Basco Ndjango,
    • Yingying Li,
    • Beatrice H. Hahn,
    • and Howard Ochman
    Genome Res. October 2013 23: 1715-1720; Published in Advance June 26, 2013, doi:10.1101/gr.154773.113

Methods

  • Pathoscope: Species identification and strain attribution with unassembled sequencing data

    • Owen E. Francis,
    • Matthew Bendall,
    • Solaiappan Manimaran,
    • Changjin Hong,
    • Nathan L. Clement,
    • Eduardo Castro-Nallar,
    • Quinn Snell,
    • G. Bruce Schaalje,
    • Mark J. Clement,
    • Keith A. Crandall,
    • and W. Evan Johnson
    Genome Res. October 2013 23: 1721-1729; Published in Advance July 10, 2013, doi:10.1101/gr.150151.112
    OPEN ACCESS ARTICLE

  • Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

    • Song Li,
    • Louisa M. Liberman,
    • Neelanjan Mukherjee,
    • Philip N. Benfey,
    • and Uwe Ohler
    Genome Res. October 2013 23: 1730-1739; Published in Advance July 1, 2013, doi:10.1101/gr.149310.112

Resources

  • Coelacanth genomes reveal signatures for evolutionary transition from water to land

    • Masato Nikaido,
    • Hideki Noguchi,
    • Hidenori Nishihara,
    • Atsushi Toyoda,
    • Yutaka Suzuki,
    • Rei Kajitani,
    • Hikoyu Suzuki,
    • Miki Okuno,
    • Mitsuto Aibara,
    • Benjamin P. Ngatunga,
    • Semvua I. Mzighani,
    • Hassan W.J. Kalombo,
    • Kawilarang W.A. Masengi,
    • Josef Tuda,
    • Sadao Nogami,
    • Ryuichiro Maeda,
    • Masamitsu Iwata,
    • Yoshitaka Abe,
    • Koji Fujimura,
    • Masataka Okabe,
    • Takanori Amano,
    • Akiteru Maeno,
    • Toshihiko Shiroishi,
    • Takehiko Itoh,
    • Sumio Sugano,
    • Yuji Kohara,
    • Asao Fujiyama,
    • and Norihiro Okada
    Genome Res. October 2013 23: 1740-1748; Published in Advance July 22, 2013, doi:10.1101/gr.158105.113
    OPEN ACCESS ARTICLE

  • The million mutation project: A new approach to genetics in Caenorhabditis elegans

    • Owen Thompson,
    • Mark Edgley,
    • Pnina Strasbourger,
    • Stephane Flibotte,
    • Brent Ewing,
    • Ryan Adair,
    • Vinci Au,
    • Iasha Chaudhry,
    • Lisa Fernando,
    • Harald Hutter,
    • Armelle Kieffer,
    • Joanne Lau,
    • Norris Lee,
    • Angela Miller,
    • Greta Raymant,
    • Bin Shen,
    • Jay Shendure,
    • Jon Taylor,
    • Emily H. Turner,
    • LaDeana W. Hillier,
    • Donald G. Moerman,
    • and Robert H. Waterston
    Genome Res. October 2013 23: 1749-1762; Published in Advance June 25, 2013, doi:10.1101/gr.157651.113
    OPEN ACCESS ARTICLE
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This Issue

October 2013; 23 (10)
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