Table of Contents

April 2015; 25 (4)

Research

  • A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    • Monika Karmin,
    • Lauri Saag,
    • Mário Vicente,
    • Melissa A. Wilson Sayres,
    • Mari Järve,
    • Ulvi Gerst Talas,
    • Siiri Rootsi,
    • Anne-Mai Ilumäe,
    • Reedik Mägi,
    • Mario Mitt,
    • Luca Pagani,
    • Tarmo Puurand,
    • Zuzana Faltyskova,
    • Florian Clemente,
    • Alexia Cardona,
    • Ene Metspalu,
    • Hovhannes Sahakyan,
    • Bayazit Yunusbayev,
    • Georgi Hudjashov,
    • Michael DeGiorgio,
    • Eva-Liis Loogväli,
    • Christina Eichstaedt,
    • Mikk Eelmets,
    • Gyaneshwer Chaubey,
    • Kristiina Tambets,
    • Sergei Litvinov,
    • Maru Mormina,
    • Yali Xue,
    • Qasim Ayub,
    • Grigor Zoraqi,
    • Thorfinn Sand Korneliussen,
    • Farida Akhatova,
    • Joseph Lachance,
    • Sarah Tishkoff,
    • Kuvat Momynaliev,
    • François-Xavier Ricaut,
    • Pradiptajati Kusuma,
    • Harilanto Razafindrazaka,
    • Denis Pierron,
    • Murray P. Cox,
    • Gazi Nurun Nahar Sultana,
    • Rane Willerslev,
    • Craig Muller,
    • Michael Westaway,
    • David Lambert,
    • Vedrana Skaro,
    • Lejla Kovačevic´,
    • Shahlo Turdikulova,
    • Dilbar Dalimova,
    • Rita Khusainova,
    • Natalya Trofimova,
    • Vita Akhmetova,
    • Irina Khidiyatova,
    • Daria V. Lichman,
    • Jainagul Isakova,
    • Elvira Pocheshkhova,
    • Zhaxylyk Sabitov,
    • Nikolay A. Barashkov,
    • Pagbajabyn Nymadawa,
    • Evelin Mihailov,
    • Joseph Wee Tien Seng,
    • Irina Evseeva,
    • Andrea Bamberg Migliano,
    • Syafiq Abdullah,
    • George Andriadze,
    • Dragan Primorac,
    • Lubov Atramentova,
    • Olga Utevska,
    • Levon Yepiskoposyan,
    • Damir Marjanovic´,
    • Alena Kushniarevich,
    • Doron M. Behar,
    • Christian Gilissen,
    • Lisenka Vissers,
    • Joris A. Veltman,
    • Elena Balanovska,
    • Miroslava Derenko,
    • Boris Malyarchuk,
    • Andres Metspalu,
    • Sardana Fedorova,
    • Anders Eriksson,
    • Andrea Manica,
    • Fernando L. Mendez,
    • Tatiana M. Karafet,
    • Krishna R. Veeramah,
    • Neil Bradman,
    • Michael F. Hammer,
    • Ludmila P. Osipova,
    • Oleg Balanovsky,
    • Elza K. Khusnutdinova,
    • Knut Johnsen,
    • Maido Remm,
    • Mark G. Thomas,
    • Chris Tyler-Smith,
    • Peter A. Underhill,
    • Eske Willerslev,
    • Rasmus Nielsen,
    • Mait Metspalu,
    • Richard Villems,
    • and Toomas Kivisild
    Genome Res. April 2015 25: 459-466; Published in Advance March 13, 2015, doi:10.1101/gr.186684.114

  • The role of DNA methylation in directing the functional organization of the cancer epigenome

    • Fides D. Lay,
    • Yaping Liu,
    • Theresa K. Kelly,
    • Heather Witt,
    • Peggy J. Farnham,
    • Peter A. Jones,
    • and Benjamin P. Berman
    Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
    OPEN ACCESS ARTICLE

  • Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers

    • Xabier Agirre,
    • Giancarlo Castellano,
    • Marien Pascual,
    • Simon Heath,
    • Marta Kulis,
    • Victor Segura,
    • Anke Bergmann,
    • Anna Esteve,
    • Angelika Merkel,
    • Emanuele Raineri,
    • Lidia Agueda,
    • Julie Blanc,
    • David Richardson,
    • Laura Clarke,
    • Avik Datta,
    • Nuria Russiñol,
    • Ana C. Queirós,
    • Renée Beekman,
    • Juan R. Rodríguez-Madoz,
    • Edurne San José-Enériz,
    • Fang Fang,
    • Norma C. Gutiérrez,
    • José M. García-Verdugo,
    • Michael I. Robson,
    • Eric C. Schirmer,
    • Elisabeth Guruceaga,
    • Joost H.A. Martens,
    • Marta Gut,
    • Maria J. Calasanz,
    • Paul Flicek,
    • Reiner Siebert,
    • Elías Campo,
    • Jesús F. San Miguel,
    • Ari Melnick,
    • Hendrik G. Stunnenberg,
    • Ivo G. Gut,
    • Felipe Prosper,
    • and José I. Martín-Subero
    Genome Res. April 2015 25: 478-487; Published in Advance February 2, 2015, doi:10.1101/gr.180240.114

  • The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer

    • Ronan Chaligné,
    • Tatiana Popova,
    • Marco-Antonio Mendoza-Parra,
    • Mohamed-Ashick M. Saleem,
    • David Gentien,
    • Kristen Ban,
    • Tristan Piolot,
    • Olivier Leroy,
    • Odette Mariani,
    • Hinrich Gronemeyer,
    • Anne Vincent-Salomon,
    • Marc-Henri Stern,
    • and Edith Heard
    Genome Res. April 2015 25: 488-503; Published in Advance February 4, 2015, doi:10.1101/gr.185926.114
    OPEN ACCESS ARTICLE

  • Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

    • Elizabeth Ing-Simmons,
    • Vlad C. Seitan,
    • Andre J. Faure,
    • Paul Flicek,
    • Thomas Carroll,
    • Job Dekker,
    • Amanda G. Fisher,
    • Boris Lenhard,
    • and Matthias Merkenschlager
    Genome Res. April 2015 25: 504-513; Published in Advance February 12, 2015, doi:10.1101/gr.184986.114

  • A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

    • Claus Schertel,
    • Monica Albarca,
    • Claudia Rockel-Bauer,
    • Nicholas W. Kelley,
    • Johannes Bischof,
    • Korneel Hens,
    • Erik van Nimwegen,
    • Konrad Basler,
    • and Bart Deplancke
    Genome Res. April 2015 25: 514-523; Published in Advance January 7, 2015, doi:10.1101/gr.181305.114

  • Origin and domestication of papaya Yh chromosome

    • Robert VanBuren,
    • Fanchang Zeng,
    • Cuixia Chen,
    • Jisen Zhang,
    • Ching Man Wai,
    • Jennifer Han,
    • Rishi Aryal,
    • Andrea R. Gschwend,
    • Jianping Wang,
    • Jong-Kuk Na,
    • Lixian Huang,
    • Lingmao Zhang,
    • Wenjing Miao,
    • Jiqing Gou,
    • Jie Arro,
    • Romain Guyot,
    • Richard C. Moore,
    • Ming-Li Wang,
    • Francis Zee,
    • Deborah Charlesworth,
    • Paul H. Moore,
    • Qingyi Yu,
    • and Ray Ming
    Genome Res. April 2015 25: 524-533; Published in Advance March 11, 2015, doi:10.1101/gr.183905.114

  • Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

    • Itai Sharon,
    • Michael Kertesz,
    • Laura A. Hug,
    • Dmitry Pushkarev,
    • Timothy A. Blauwkamp,
    • Cindy J. Castelle,
    • Mojgan Amirebrahimi,
    • Brian C. Thomas,
    • David Burstein,
    • Susannah G. Tringe,
    • Kenneth H. Williams,
    • and Jillian F. Banfield
    Genome Res. April 2015 25: 534-543; Published in Advance February 9, 2015, doi:10.1101/gr.183012.114

Methods

  • Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

    • Maxwell W. Libbrecht,
    • Ferhat Ay,
    • Michael M. Hoffman,
    • David M. Gilbert,
    • Jeffrey A. Bilmes,
    • and William Stafford Noble
    Genome Res. April 2015 25: 544-557; Published in Advance February 12, 2015, doi:10.1101/gr.184341.114

  • Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins

    • Dimiter Kunnev,
    • Amy Freeland,
    • Maochun Qin,
    • Robert W. Leach,
    • Jianmin Wang,
    • Rajani M. Shenoy,
    • and Steven C. Pruitt
    Genome Res. April 2015 25: 558-569; Published in Advance March 11, 2015, doi:10.1101/gr.176099.114

  • Single-cell-level spatial gene expression in the embryonic neural differentiation niche

    • Yi Huang,
    • Xiaoming Yu,
    • Na Sun,
    • Nan Qiao,
    • Yaqiang Cao,
    • Jerome D. Boyd-Kirkup,
    • Qin Shen,
    • and Jing-Dong J. Han
    Genome Res. April 2015 25: 570-581; Published in Advance January 9, 2015, doi:10.1101/gr.181966.114

Resources

  • The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

    • Stefan Schoenfelder,
    • Mayra Furlan-Magaril,
    • Borbala Mifsud,
    • Filipe Tavares-Cadete,
    • Robert Sugar,
    • Biola-Maria Javierre,
    • Takashi Nagano,
    • Yulia Katsman,
    • Moorthy Sakthidevi,
    • Steven W. Wingett,
    • Emilia Dimitrova,
    • Andrew Dimond,
    • Lucas B. Edelman,
    • Sarah Elderkin,
    • Kristina Tabbada,
    • Elodie Darbo,
    • Simon Andrews,
    • Bram Herman,
    • Andy Higgs,
    • Emily LeProust,
    • Cameron S. Osborne,
    • Jennifer A. Mitchell,
    • Nicholas M. Luscombe,
    • and Peter Fraser
    Genome Res. April 2015 25: 582-597; Published in Advance March 9, 2015, doi:10.1101/gr.185272.114
    OPEN ACCESS ARTICLE

  • A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines

    • David B. West,
    • Ravi K. Pasumarthi,
    • Brian Baridon,
    • Esi Djan,
    • Amanda Trainor,
    • Stephen M. Griffey,
    • Eric K. Engelhard,
    • Jared Rapp,
    • Bowen Li,
    • Pieter J. de Jong,
    • and K.C. Kent Lloyd
    Genome Res. April 2015 25: 598-607; Published in Advance January 15, 2015, doi:10.1101/gr.184184.114

Errata

  • Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

    • Tannistha Nandi,
    • Matthew T.G. Holden,
    • Xavier Didelot,
    • Kurosh Mehershahi,
    • Justin A. Boddey,
    • Ifor Beacham,
    • Ian Peak,
    • John Harting,
    • Primo Baybayan,
    • Yan Guo,
    • Susana Wang,
    • Lee Chee How,
    • Bernice Sim,
    • Angela Essex-Lopresti,
    • Mitali Sarkar-Tyson,
    • Michelle Nelson,
    • Sophie Smither,
    • Catherine Ong,
    • Lay Tin Aw,
    • Chua Hui Hoon,
    • Stephen Michell,
    • David J. Studholme,
    • Richard Titball,
    • Swaine L. Chen,
    • Julian Parkhill,
    • and Patrick Tan
    Genome Res. April 2015 25: 608
    OPEN ACCESS ARTICLE

  • BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies

    • Guntram Borck,
    • Friederike Hög,
    • Maria Lisa Dentici,
    • Perciliz L. Tan,
    • Nadine Sowada,
    • Ana Medeira,
    • Lucie Gueneau,
    • Holger Thiele,
    • Maria Kousi,
    • Francesca Lepri,
    • Larissa Wenzeck,
    • Ian Blumenthal,
    • Antonio Radicioni,
    • Tito Livio Schwarzenberg,
    • Barbara Mandriani,
    • Rita Fischetto,
    • Deborah J. Morris-Rosendahl,
    • Janine Altmüller,
    • Alexandre Reymond,
    • Peter Nürnberg,
    • Giuseppe Merla,
    • Bruno Dallapiccola,
    • Nicholas Katsanis,
    • Patrick Cramer,
    • and Christian Kubisch
    Genome Res. April 2015 25: 609
    OPEN ACCESS ARTICLE
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This Issue

April 2015; 25 (4)
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  1. Research
  2. Methods
  3. Resources
  4. Errata

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