Volume 25, Issue 4 | April 2015

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
    ...[+91 authors]...,
    Rasmus Nielsen
    Mait Metspalu
    Richard Villems
    Toomas Kivisild
    First Published March 13, 2015
  - The role of DNA methylation in directing the functional organization of the cancer epigenome
    Lay Fides D.
    Liu Yaping
    Kelly Theresa K.
    Witt Heather
    Farnham Peggy J.
    Jones Peter A.
    Berman Benjamin P.
    First Published March 6, 2015
  - Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers
    Agirre Xabier
    Castellano Giancarlo
    Pascual Marien
    Heath Simon
    Kulis Marta
    Segura Victor Bergmann Anke Esteve Anna Merkel Angelika Raineri Emanuele Agueda Lidia Blanc Julie Richardson David Clarke Laura Datta Avik Russiñol Nuria Queirós Ana C. Beekman Renée Rodríguez-Madoz Juan R. José-Enériz Edurne San Fang Fang Gutiérrez Norma C. García-Verdugo José M. Robson Michael I. Schirmer Eric C. Guruceaga Elisabeth Martens Joost H.A. Gut Marta Calasanz Maria J. Flicek Paul Siebert Reiner Campo Elías Miguel Jesús F. San Melnick Ari
    ...[+29 authors]...,
    Stunnenberg Hendrik G.
    Gut Ivo G.
    Prosper Felipe
    Martín-Subero José I.
    First Published February 2, 2015
  - 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
    ...[+4 authors]...,
    Hinrich Gronemeyer
    Anne Vincent-Salomon
    Marc-Henri Stern
    Edith Heard
    First Published February 4, 2015
  - 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
    Matthias Merkenschlager
    First Published February 12, 2015
  - 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
    Bart Deplancke
    First Published January 7, 2015
  - 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
    ...[+14 authors]...,
    Deborah Charlesworth
    Paul H. Moore
    Qingyi Yu
    Ray Ming
    First Published March 11, 2015
  - 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
    ...[+3 authors]...,
    David Burstein
    Susannah G. Tringe
    Kenneth H. Williams
    Jillian F. Banfield
    First Published February 9, 2015
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
    William Stafford Noble
    First Published February 12, 2015
  - 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
    Steven C. Pruitt
    First Published March 11, 2015
  - 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
    Jing-Dong J. Han
    First Published January 9, 2015
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
    ...[+15 authors]...,
    Cameron S. Osborne
    Jennifer A. Mitchell
    Nicholas M. Luscombe
    Peter Fraser
    First Published March 9, 2015
  - 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
    ...[+2 authors]...,
    Jared Rapp
    Bowen Li
    Pieter J. de Jong
    K.C. Kent Lloyd
    First Published January 15, 2015
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
    ...[+17 authors]...,
    Richard Titball
    Swaine L. Chen
    Julian Parkhill
    Patrick Tan
    First Published April 1, 2015
  - 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
    ...[+16 authors]...,
    Bruno Dallapiccola
    Nicholas Katsanis
    Patrick Cramer
    Christian Kubisch
    First Published April 1, 2015

Table of Contents

Volume 25, Issue 4 | April 2015

Research

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

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

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

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

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

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

Origin and domestication of papaya Yh chromosome

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

Methods

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

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

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

Resources

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

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

Errata

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

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

Table of Contents

Volume 25, Issue 4 | April 2015

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Research

Methods

Resources

Errata