Table of Contents

April 2019; 29 (4)

Research

  • Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans

    • Maria Zhivagui,
    • Alvin W.T. Ng,
    • Maude Ardin,
    • Mona I. Churchwell,
    • Manuraj Pandey,
    • Claire Renard,
    • Stephanie Villar,
    • Vincent Cahais,
    • Alexis Robitaille,
    • Liacine Bouaoun,
    • Adriana Heguy,
    • Kathryn Z. Guyton,
    • Martha R. Stampfer,
    • James McKay,
    • Monica Hollstein,
    • Magali Olivier,
    • Steven G. Rozen,
    • Frederick A. Beland,
    • Michael Korenjak,
    • and Jiri Zavadil
    Genome Res. April 2019 29: 521-531; Published in Advance March 7, 2019, doi:10.1101/gr.242453.118
    OPEN ACCESS ARTICLE

  • Coexpression patterns define epigenetic regulators associated with neurological dysfunction

    • Leandros Boukas,
    • James M. Havrilla,
    • Peter F. Hickey,
    • Aaron R. Quinlan,
    • Hans T. Bjornsson,
    • and Kasper D. Hansen
    Genome Res. April 2019 29: 532-542; Published in Advance March 11, 2019, doi:10.1101/gr.239442.118
    OPEN ACCESS ARTICLE

  • New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation

    • Le Li,
    • Yuwei Gao,
    • Qiong Wu,
    • Alfred S.L. Cheng,
    • and Kevin Y. Yip
    Genome Res. April 2019 29: 543-553; Published in Advance February 19, 2019, doi:10.1101/gr.240036.118

  • CG dinucleotides enhance promoter activity independent of DNA methylation

    • Dominik Hartl,
    • Arnaud R. Krebs,
    • Ralph S. Grand,
    • Tuncay Baubec,
    • Luke Isbel,
    • Christiane Wirbelauer,
    • Lukas Burger,
    • and Dirk Schübeler
    Genome Res. April 2019 29: 554-563; Published in Advance February 1, 2019, doi:10.1101/gr.241653.118
    OPEN ACCESS ARTICLE

  • TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells

    • Kasper D. Rasmussen,
    • Ivan Berest,
    • Sandra Keβler,
    • Koutarou Nishimura,
    • Lucía Simón-Carrasco,
    • George S. Vassiliou,
    • Marianne T. Pedersen,
    • Jesper Christensen,
    • Judith B. Zaugg,
    • and Kristian Helin
    Genome Res. April 2019 29: 564-575; Published in Advance February 22, 2019, doi:10.1101/gr.239277.118

  • Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

    • Marta Farré,
    • Jaebum Kim,
    • Anastasia A. Proskuryakova,
    • Yang Zhang,
    • Anastasia I. Kulemzina,
    • Qiye Li,
    • Yang Zhou,
    • Yingqi Xiong,
    • Jennifer L. Johnson,
    • Polina L. Perelman,
    • Warren E. Johnson,
    • Wesley C. Warren,
    • Anna V. Kukekova,
    • Guojie Zhang,
    • Stephen J. O'Brien,
    • Oliver A. Ryder,
    • Alexander S. Graphodatsky,
    • Jian Ma,
    • Harris A. Lewin,
    • and Denis M. Larkin
    Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118

  • The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

    • Drew R. Schield,
    • Daren C. Card,
    • Nicole R. Hales,
    • Blair W. Perry,
    • Giulia M. Pasquesi,
    • Heath Blackmon,
    • Richard H. Adams,
    • Andrew B. Corbin,
    • Cara F. Smith,
    • Balan Ramesh,
    • Jeffery P. Demuth,
    • Esther Betrán,
    • Marc Tollis,
    • Jesse M. Meik,
    • Stephen P. Mackessy,
    • and Todd A. Castoe
    Genome Res. April 2019 29: 590-601; Published in Advance March 21, 2019, doi:10.1101/gr.240952.118

  • Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila

    • Michelle Pherson,
    • Ziva Misulovin,
    • Maria Gause,
    • and Dale Dorsett
    Genome Res. April 2019 29: 602-612; Published in Advance February 22, 2019, doi:10.1101/gr.243832.118
    OPEN ACCESS ARTICLE

  • Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome

    • Keerthi T. Chathoth and
    • Nicolae Radu Zabet
    Genome Res. April 2019 29: 613-625; Published in Advance February 1, 2019, doi:10.1101/gr.246710.118
    OPEN ACCESS ARTICLE

  • Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

    • Theodore Gouliouris,
    • Kathy E. Raven,
    • Danesh Moradigaravand,
    • Catherine Ludden,
    • Francesc Coll,
    • Beth Blane,
    • Plamena Naydenova,
    • Carolyne Horner,
    • Nicholas M. Brown,
    • Jukka Corander,
    • Direk Limmathurotsakul,
    • Julian Parkhill,
    • and Sharon J. Peacock
    Genome Res. April 2019 29: 626-634; Published in Advance March 21, 2019, doi:10.1101/gr.232629.117
    OPEN ACCESS ARTICLE

Methods

  • Resolving the full spectrum of human genome variation using Linked-Reads

    • Patrick Marks,
    • Sarah Garcia,
    • Alvaro Martinez Barrio,
    • Kamila Belhocine,
    • Jorge Bernate,
    • Rajiv Bharadwaj,
    • Keith Bjornson,
    • Claudia Catalanotti,
    • Josh Delaney,
    • Adrian Fehr,
    • Ian T. Fiddes,
    • Brendan Galvin,
    • Haynes Heaton,
    • Jill Herschleb,
    • Christopher Hindson,
    • Esty Holt,
    • Cassandra B. Jabara,
    • Susanna Jett,
    • Nikka Keivanfar,
    • Sofia Kyriazopoulou-Panagiotopoulou,
    • Monkol Lek,
    • Bill Lin,
    • Adam Lowe,
    • Shazia Mahamdallie,
    • Shamoni Maheshwari,
    • Tony Makarewicz,
    • Jamie Marshall,
    • Francesca Meschi,
    • Christopher J. O'Keefe,
    • Heather Ordonez,
    • Pranav Patel,
    • Andrew Price,
    • Ariel Royall,
    • Elise Ruark,
    • Sheila Seal,
    • Michael Schnall-Levin,
    • Preyas Shah,
    • David Stafford,
    • Stephen Williams,
    • Indira Wu,
    • Andrew Wei Xu,
    • Nazneen Rahman,
    • Daniel MacArthur,
    • and Deanna M. Church
    Genome Res. April 2019 29: 635-645; Published in Advance March 20, 2019, doi:10.1101/gr.234443.118
    OPEN ACCESS ARTICLE

  • Long-read single-molecule maps of the functional methylome

    • Hila Sharim,
    • Assaf Grunwald,
    • Tslil Gabrieli,
    • Yael Michaeli,
    • Sapir Margalit,
    • Dmitry Torchinsky,
    • Rani Arielly,
    • Gil Nifker,
    • Matyas Juhasz,
    • Felix Gularek,
    • Miguel Almalvez,
    • Brandon Dufault,
    • Sreetama Sen Chandra,
    • Alexander Liu,
    • Surajit Bhattacharya,
    • Yi-Wen Chen,
    • Eric Vilain,
    • Kathryn R. Wagner,
    • Jonathan Pevsner,
    • Jeff Reifenberger,
    • Ernest T. Lam,
    • Alex R. Hastie,
    • Han Cao,
    • Hayk Barseghyan,
    • Elmar Weinhold,
    • and Yuval Ebenstein
    Genome Res. April 2019 29: 646-656; Published in Advance March 7, 2019, doi:10.1101/gr.240739.118
    OPEN ACCESS ARTICLE

  • Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression

    • Di Huang,
    • Hanna M. Petrykowska,
    • Brendan F. Miller,
    • Laura Elnitski,
    • and Ivan Ovcharenko
    Genome Res. April 2019 29: 657-667; Published in Advance March 18, 2019, doi:10.1101/gr.247007.118
    OPEN ACCESS ARTICLE

  • Improved discovery of genetic interactions using CRISPRiSeq across multiple environments

    • Mia Jaffe,
    • Adam Dziulko,
    • Justin D. Smith,
    • Robert P. St.Onge,
    • Sasha F. Levy,
    • and Gavin Sherlock
    Genome Res. April 2019 29: 668-681; Published in Advance February 19, 2019, doi:10.1101/gr.246603.118
    OPEN ACCESS ARTICLE

Resources

  • GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

    • Yi Shao,
    • Chunyan Chen,
    • Hao Shen,
    • Bin Z. He,
    • Daqi Yu,
    • Shuai Jiang,
    • Shilei Zhao,
    • Zhiqiang Gao,
    • Zhenglin Zhu,
    • Xi Chen,
    • Yan Fu,
    • Hua Chen,
    • Ge Gao,
    • Manyuan Long,
    • and Yong E. Zhang
    Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
    OPEN ACCESS ARTICLE

  • Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

    • Bérénice A. Benayoun,
    • Elizabeth A. Pollina,
    • Param Priya Singh,
    • Salah Mahmoudi,
    • Itamar Harel,
    • Kerriann M. Casey,
    • Ben W. Dulken,
    • Anshul Kundaje,
    • and Anne Brunet
    Genome Res. April 2019 29: 697-709; Published in Advance March 11, 2019, doi:10.1101/gr.240093.118
    OPEN ACCESS ARTICLE

Corrigenda

  • Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution

    • Amit Blumberg,
    • Edward J. Rice,
    • Anshul Kundaje,
    • Charles G. Danko,
    • and Dan Mishmar
    Genome Res. April 2019 29: 710.1; doi:10.1101/gr.248971.119
    OPEN ACCESS ARTICLE

  • Corrigendum: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells

    • Agustín F. Fernández,
    • Gustavo F. Bayón,
    • Rocío G. Urdinguio,
    • Estela G. Toraño,
    • María G. García,
    • Antonella Carella,
    • Sandra Petrus-Reurer,
    • Cecilia Ferrero,
    • Pablo Martinez-Camblor,
    • Isabel Cubillo,
    • Javier García-Castro,
    • Jesús Delgado-Calle,
    • Flor M. Pérez-Campo,
    • José A. Riancho,
    • Clara Bueno,
    • Pablo Menéndez,
    • Anouk Mentink,
    • Katia Mareschi,
    • Fabian Claire,
    • Corrado Fagnani,
    • Emanuela Medda,
    • Virgilia Toccaceli,
    • Sonia Brescianini,
    • Sebastián Moran,
    • Manel Esteller,
    • Alexandra Stolzing,
    • Jan de Boer,
    • Lorenza Nisticò,
    • Maria A. Stazi,
    • and Mario F. Fraga
    Genome Res. April 2019 29: 710.2; doi:10.1101/gr.249417.119
    OPEN ACCESS ARTICLE
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This Issue

April 2019; 29 (4)
Cover
  1. Research
  2. Methods
  3. Resources
  4. Corrigenda

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