Table of Contents

May 2016; 26 (5)

Research

  • Zygotes segregate entire parental genomes in distinct blastomere lineages causing cleavage-stage chimerism and mixoploidy

    • Aspasia Destouni,
    • Masoud Zamani Esteki,
    • Maaike Catteeuw,
    • Olga Tšuiko,
    • Eftychia Dimitriadou,
    • Katrien Smits,
    • Ants Kurg,
    • Andres Salumets,
    • Ann Van Soom,
    • Thierry Voet,
    • and Joris R. Vermeesch
    Genome Res. May 2016 26: 567-578; Published in Advance April 12, 2016, doi:10.1101/gr.200527.115

  • Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity

    • Yishay Pinto,
    • Orshay Gabay,
    • Leonardo Arbiza,
    • Aaron J. Sams,
    • Alon Keinan,
    • and Erez Y. Levanon
    Genome Res. May 2016 26: 579-587; Published in Advance April 7, 2016, doi:10.1101/gr.199240.115
    OPEN ACCESS ARTICLE

  • Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4

    • Kate Liddiard,
    • Brian Ruis,
    • Taylor Takasugi,
    • Adam Harvey,
    • Kevin E. Ashelford,
    • Eric A. Hendrickson,
    • and Duncan M. Baird
    Genome Res. May 2016 26: 588-600; Published in Advance March 3, 2016, doi:10.1101/gr.200840.115
    OPEN ACCESS ARTICLE

  • Enhancer methylation dynamics contribute to cancer plasticity and patient mortality

    • Rachel E. Bell,
    • Tamar Golan,
    • Danna Sheinboim,
    • Hagar Malcov,
    • David Amar,
    • Avi Salamon,
    • Tamar Liron,
    • Sahar Gelfman,
    • Yankel Gabet,
    • Ron Shamir,
    • and Carmit Levy
    Genome Res. May 2016 26: 601-611; Published in Advance February 23, 2016, doi:10.1101/gr.197194.115

  • Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

    • Vibhor Kumar,
    • Nirmala Arul Rayan,
    • Masafumi Muratani,
    • Stefan Lim,
    • Bavani Elanggovan,
    • Lixia Xin,
    • Tess Lu,
    • Harshyaa Makhija,
    • Jeremie Poschmann,
    • Thomas Lufkin,
    • Huck Hui Ng,
    • and Shyam Prabhakar
    Genome Res. May 2016 26: 612-623; Published in Advance March 8, 2016, doi:10.1101/gr.201038.115

  • Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest

    • Andrea Orioli,
    • Viviane Praz,
    • Philippe Lhôte,
    • and Nouria Hernandez
    Genome Res. May 2016 26: 624-635; Published in Advance March 3, 2016, doi:10.1101/gr.201400.115
    OPEN ACCESS ARTICLE

  • nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs

    • Valentina Gandin,
    • Laia Masvidal,
    • Laura Hulea,
    • Simon-Pierre Gravel,
    • Marie Cargnello,
    • Shannon McLaughlan,
    • Yutian Cai,
    • Preetika Balanathan,
    • Masahiro Morita,
    • Arjuna Rajakumar,
    • Luc Furic,
    • Michael Pollak,
    • John A. Porco, Jr.,
    • Julie St-Pierre,
    • Jerry Pelletier,
    • Ola Larsson,
    • and Ivan Topisirovic
    Genome Res. May 2016 26: 636-648; Published in Advance March 16, 2016, doi:10.1101/gr.197566.115
    OPEN ACCESS ARTICLE

  • Discovery of a new repeat family in the Callithrix jacchus genome

    • Miriam K. Konkel,
    • Brygg Ullmer,
    • Erika L. Arceneaux,
    • Sreeja Sanampudi,
    • Sarah A. Brantley,
    • Robert Hubley,
    • Arian F.A. Smit,
    • and Mark A. Batzer
    Genome Res. May 2016 26: 649-659; Published in Advance February 25, 2016, doi:10.1101/gr.199075.115

Methods

  • Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes

    • Li Zhao,
    • Yiyun Chen,
    • Amol Onkar Bajaj,
    • Aiden Eblimit,
    • Mingchu Xu,
    • Zachry T. Soens,
    • Feng Wang,
    • Zhongqi Ge,
    • Sung Yun Jung,
    • Feng He,
    • Yumei Li,
    • Theodore G. Wensel,
    • Jun Qin,
    • and Rui Chen
    Genome Res. May 2016 26: 660-669; Published in Advance February 24, 2016, doi:10.1101/gr.198911.115

  • An extended set of yeast-based functional assays accurately identifies human disease mutations

    • Song Sun,
    • Fan Yang,
    • Guihong Tan,
    • Michael Costanzo,
    • Rose Oughtred,
    • Jodi Hirschman,
    • Chandra L. Theesfeld,
    • Pritpal Bansal,
    • Nidhi Sahni,
    • Song Yi,
    • Analyn Yu,
    • Tanya Tyagi,
    • Cathy Tie,
    • David E. Hill,
    • Marc Vidal,
    • Brenda J. Andrews,
    • Charles Boone,
    • Kara Dolinski,
    • and Frederick P. Roth
    Genome Res. May 2016 26: 670-680; Published in Advance March 14, 2016, doi:10.1101/gr.192526.115
    OPEN ACCESS ARTICLE

  • 2C-Cas9: a versatile tool for clonal analysis of gene function

    • Vincenzo Di Donato,
    • Flavia De Santis,
    • Thomas O. Auer,
    • Noé Testa,
    • Héctor Sánchez-Iranzo,
    • Nadia Mercader,
    • Jean-Paul Concordet,
    • and Filippo Del Bene
    Genome Res. May 2016 26: 681-692; Published in Advance March 8, 2016, doi:10.1101/gr.196170.115

  • Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler

    • Jeffrey N. McKnight,
    • Toshio Tsukiyama,
    • and Gregory D. Bowman
    Genome Res. May 2016 26: 693-704; Published in Advance March 18, 2016, doi:10.1101/gr.199919.115

Resource

  • Improved definition of the mouse transcriptome via targeted RNA sequencing

    • Giovanni Bussotti,
    • Tommaso Leonardi,
    • Michael B. Clark,
    • Tim R. Mercer,
    • Joanna Crawford,
    • Lorenzo Malquori,
    • Cedric Notredame,
    • Marcel E. Dinger,
    • John S. Mattick,
    • and Anton J. Enright
    Genome Res. May 2016 26: 705-716; doi:10.1101/gr.199760.115
    OPEN ACCESS ARTICLE

Corrigenda

  • Corrigendum: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

    • PingHsun Hsieh,
    • August E. Woerner,
    • Jeffrey D. Wall,
    • Joseph Lachance,
    • Sarah A. Tishkoff,
    • Ryan N. Gutenkunst,
    • and Michael F. Hammer
    Genome Res. May 2016 26: 717.1; doi:10.1101/gr.206524.116
    OPEN ACCESS ARTICLE

  • Corrigendum: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

    • Young Seok Ju,
    • Jose M.C. Tubio,
    • William Mifsud,
    • Beiyuan Fu,
    • Helen R. Davies,
    • Manasa Ramakrishna,
    • Yilong Li,
    • Lucy Yates,
    • Gunes Gundem,
    • Patrick S. Tarpey,
    • Sam Behjati,
    • Elli Papaemmanuil,
    • Sancha Martin,
    • Anthony Fullam,
    • Moritz Gerstung,
    • ICGC Prostate Cancer Working Group,
    • ICGC Bone Cancer Working Group,
    • ICGC Breast Cancer Working Group,
    • Jyoti Nangalia,
    • Anthony R. Green,
    • Carlos Caldas,
    • Åke Borg,
    • Andrew Tutt,
    • Ming Ta Michael Lee,
    • Laura J. van't Veer,
    • Benita K.T. Tan,
    • Samuel Aparicio,
    • Paul N. Span,
    • John W.M. Martens,
    • Stian Knappskog,
    • Anne Vincent-Salomon,
    • Anne-Lise Børresen-Dale,
    • Jórunn Erla Eyfjörd,
    • Ola Myklebost,
    • Adrienne M. Flanagan,
    • Christopher Foster,
    • David E. Neal,
    • Colin Cooper,
    • Rosalind Eeles,
    • G. Steven Bova,
    • Sunil R. Lakhani,
    • Christine Desmedt,
    • Gilles Thomas,
    • Andrea L. Richardson,
    • Colin A. Purdie,
    • Alastair M. Thompson,
    • Ultan McDermott,
    • Fengtang Yang,
    • Serena Nik-Zainal,
    • Peter J. Campbell,
    • and Michael R. Stratton
    Genome Res. May 2016 26: 717.2; doi:10.1101/gr.206557.116
    OPEN ACCESS ARTICLE
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This Issue

May 2016; 26 (5)
Cover
  1. Research
  2. Methods
  3. Resource
  4. Corrigenda

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