Volume 50 Issue 1, January 2018

Volume 50 Issue 1

This issue features epigenetic analysis of cell commitment at many levels in mammalian genomes: during early embryonic development, in stem cells, and in cancer cells. These studies provide fundamental insight into the functional consequences of genome variation. On the cover: Red-tailed black cockatoo feathers (tonysartandnature.com).

See Editorial.

Image: Tony Cunningham. Cover Design: Erin Dewalt.

News & Views

  • News & Views |

    A new study illustrates the power of the human induced pluripotent stem cell (hiPSC) platform by studying hiPSC-derived sensory neurons from 107 individuals. In addition to identifying thousands of quantitative trait loci influencing gene expression, chromatin accessibility and RNA splicing, the work highlights several underappreciated challenges in the hiPSC field.

    • Gabriel E. Hoffman
    •  & Kristen J. Brennand
  • News & Views |

    What allows bacteria, both pathogens and mutualists alike, to survive in close association with a eukaryotic host? A new study performed a large-scale comparative genomics analysis to identify novel genetic and genomic traits that are enriched in plant-associated bacterial taxa.

    • Ryan A. Melnyk
    •  & Cara H. Haney
  • News & Views |

    H3K4me1 is enriched at active and primed enhancers. However, whether H3K4me1 controls or simply correlates with enhancer activity and function has remained unclear. Several recent reports, including two in Nature Genetics, provide major mechanistic and functional insights into the role of H3K4me1 at enhancers.

    • Alvaro Rada-Iglesias

Letters

  • Letter |

    Analysis of 329,000 individuals in the UK Biobank identifies 116 loci associated with neuroticism. Genes implicated are enriched in neuronal differentiation pathways, and genetic correlations between neuroticism and other mental health traits are elucidated.

    • Michelle Luciano
    • , Saskia P. Hagenaars
    • , Gail Davies
    • , W. David Hill
    • , Toni-Kim Clarke
    • , Masoud Shirali
    • , Sarah E. Harris
    • , Riccardo E. Marioni
    • , David C. Liewald
    • , Chloe Fawns-Ritchie
    • , Mark J. Adams
    • , David M. Howard
    • , Cathryn M. Lewis
    • , Catharine R. Gale
    • , Andrew M. McIntosh
    •  & Ian J. Deary

    Collection:

  • Letter |

    An analysis of single-cell DNA methylome sequencing data from human preimplantation embryos finds evidence for de novo methylation. Methylation reprogramming at this stage is a balance between global demethylation, which is faster in the paternal genome, and focused remethylation.

    • Ping Zhu
    • , Hongshan Guo
    • , Yixin Ren
    • , Yu Hou
    • , Ji Dong
    • , Rong Li
    • , Ying Lian
    • , Xiaoying Fan
    • , Boqiang Hu
    • , Yun Gao
    • , Xiaoye Wang
    • , Yuan Wei
    • , Ping Liu
    • , Jie Yan
    • , Xiulian Ren
    • , Peng Yuan
    • , Yifeng Yuan
    • , Zhiqiang Yan
    • , Lu Wen
    • , Liying Yan
    • , Jie Qiao
    •  & Fuchou Tang
  • Letter | | Open Access

    A reference-quality genome assembly of a Drosophila melanogaster strain allows for accurate mapping of structural variants through comparative analysis with the existing Drosophila genome. Previously hidden structural variation alters a larger fraction of the genome than SNPs and often affects candidate genes underlying complex traits.

    • Mahul Chakraborty
    • , Nicholas W. VanKuren
    • , Roy Zhao
    • , Xinwen Zhang
    • , Shannon Kalsow
    •  & J. J. Emerson

Articles

  • Article |

    Exome-wide analysis identifies rare and low-frequency coding variants associated with body mass index. Gene-based meta-analysis and functional studies implicate 13 genes, eight of which are novel, and neuronal pathways as factors in human obesity.

    • Valérie Turcot
    • , Yingchang Lu
    • , Heather M. Highland
    • , Claudia Schurmann
    • , Anne E. Justice
    • , Rebecca S. Fine
    • , Jonathan P. Bradfield
    • , Tõnu Esko
    • , Ayush Giri
    • , Mariaelisa Graff
    • , Xiuqing Guo
    • , Audrey E. Hendricks
    • , Tugce Karaderi
    • , Adelheid Lempradl
    • , Adam E. Locke
    • , Anubha Mahajan
    • , Eirini Marouli
    • , Suthesh Sivapalaratnam
    • , Kristin L. Young
    • , Tamuno Alfred
    • , Mary F. Feitosa
    • , Nicholas G. D. Masca
    • , Alisa K. Manning
    • , Carolina Medina-Gomez
    • , Poorva Mudgal
    • , Maggie C. Y. Ng
    • , Alex P. Reiner
    • , Sailaja Vedantam
    • , Sara M. Willems
    • , Thomas W. Winkler
    • , Gonçalo Abecasis
    • , Katja K. Aben
    • , Dewan S. Alam
    • , Sameer E. Alharthi
    • , Matthew Allison
    • , Philippe Amouyel
    • , Folkert W. Asselbergs
    • , Paul L. Auer
    • , Beverley Balkau
    • , Lia E. Bang
    • , Inês Barroso
    • , Lisa Bastarache
    • , Marianne Benn
    • , Sven Bergmann
    • , Lawrence F. Bielak
    • , Matthias Blüher
    • , Michael Boehnke
    • , Heiner Boeing
    • , Eric Boerwinkle
    • , Carsten A. Böger
    • , Jette Bork-Jensen
    • , Michiel L. Bots
    • , Erwin P. Bottinger
    • , Donald W. Bowden
    • , Ivan Brandslund
    • , Gerome Breen
    • , Murray H. Brilliant
    • , Linda Broer
    • , Marco Brumat
    • , Amber A. Burt
    • , Adam S. Butterworth
    • , Peter T. Campbell
    • , Stefania Cappellani
    • , David J. Carey
    • , Eulalia Catamo
    • , Mark J. Caulfield
    • , John C. Chambers
    • , Daniel I. Chasman
    • , Yii-Der I. Chen
    • , Rajiv Chowdhury
    • , Cramer Christensen
    • , Audrey Y. Chu
    • , Massimiliano Cocca
    • , Francis S. Collins
    • , James P. Cook
    • , Janie Corley
    • , Jordi Corominas Galbany
    • , Amanda J. Cox
    • , David S. Crosslin
    • , Gabriel Cuellar-Partida
    • , Angela D’Eustacchio
    • , John Danesh
    • , Gail Davies
    • , Paul I. W. Bakker
    • , Mark C. H. Groot
    • , Renée Mutsert
    • , Ian J. Deary
    • , George Dedoussis
    • , Ellen W. Demerath
    • , Martin Heijer
    • , Anneke I. Hollander
    • , Hester M. Ruijter
    • , Joe G. Dennis
    • , Josh C. Denny
    • , Emanuele Di Angelantonio
    • , Fotios Drenos
    • , Mengmeng Du
    • , Marie-Pierre Dubé
    • , Alison M. Dunning
    • , Douglas F. Easton
    • , Todd L. Edwards
    • , David Ellinghaus
    • , Patrick T. Ellinor
    • , Paul Elliott
    • , Evangelos Evangelou
    • , Aliki-Eleni Farmaki
    • , I. Sadaf Farooqi
    • , Jessica D. Faul
    • , Sascha Fauser
    • , Shuang Feng
    • , Ele Ferrannini
    • , Jean Ferrieres
    • , Jose C. Florez
    • , Ian Ford
    • , Myriam Fornage
    • , Oscar H. Franco
    • , Andre Franke
    • , Paul W. Franks
    • , Nele Friedrich
    • , Ruth Frikke-Schmidt
    • , Tessel E. Galesloot
    • , Wei Gan
    • , Ilaria Gandin
    • , Paolo Gasparini
    • , Jane Gibson
    • , Vilmantas Giedraitis
    • , Anette P. Gjesing
    • , Penny Gordon-Larsen
    • , Mathias Gorski
    • , Hans-Jörgen Grabe
    • , Struan F. A. Grant
    • , Niels Grarup
    • , Helen L. Griffiths
    • , Megan L. Grove
    • , Vilmundur Gudnason
    • , Stefan Gustafsson
    • , Jeff Haessler
    • , Hakon Hakonarson
    • , Anke R. Hammerschlag
    • , Torben Hansen
    • , Kathleen Mullan Harris
    • , Tamara B. Harris
    • , Andrew T. Hattersley
    • , Christian T. Have
    • , Caroline Hayward
    • , Liang He
    • , Nancy L. Heard-Costa
    • , Andrew C. Heath
    • , Iris M. Heid
    • , Øyvind Helgeland
    • , Jussi Hernesniemi
    • , Alex W. Hewitt
    • , Oddgeir L. Holmen
    • , G. Kees Hovingh
    • , Joanna M. M. Howson
    • , Yao Hu
    • , Paul L. Huang
    • , Jennifer E. Huffman
    • , M. Arfan Ikram
    • , Erik Ingelsson
    • , Anne U. Jackson
    • , Jan-Håkan Jansson
    • , Gail P. Jarvik
    • , Gorm B. Jensen
    • , Yucheng Jia
    • , Stefan Johansson
    • , Marit E. Jørgensen
    • , Torben Jørgensen
    • , J. Wouter Jukema
    • , Bratati Kahali
    • , René S. Kahn
    • , Mika Kähönen
    • , Pia R. Kamstrup
    • , Stavroula Kanoni
    • , Jaakko Kaprio
    • , Maria Karaleftheri
    • , Sharon L. R. Kardia
    • , Fredrik Karpe
    • , Sekar Kathiresan
    • , Frank Kee
    • , Lambertus A. Kiemeney
    • , Eric Kim
    • , Hidetoshi Kitajima
    • , Pirjo Komulainen
    • , Jaspal S. Kooner
    • , Charles Kooperberg
    • , Tellervo Korhonen
    • , Peter Kovacs
    • , Helena Kuivaniemi
    • , Zoltán Kutalik
    • , Kari Kuulasmaa
    • , Johanna Kuusisto
    • , Markku Laakso
    • , Timo A. Lakka
    • , David Lamparter
    • , Ethan M. Lange
    • , Leslie A. Lange
    • , Claudia Langenberg
    • , Eric B. Larson
    • , Nanette R. Lee
    • , Terho Lehtimäki
    • , Cora E. Lewis
    • , Huaixing Li
    • , Jin Li
    • , Ruifang Li-Gao
    • , Honghuang Lin
    • , Keng-Hung Lin
    • , Li-An Lin
    • , Xu Lin
    • , Lars Lind
    • , Jaana Lindström
    • , Allan Linneberg
    • , Ching-Ti Liu
    • , Dajiang J. Liu
    • , Yongmei Liu
    • , Ken S. Lo
    • , Artitaya Lophatananon
    • , Andrew J. Lotery
    • , Anu Loukola
    • , Jian’an Luan
    • , Steven A. Lubitz
    • , Leo-Pekka Lyytikäinen
    • , Satu Männistö
    • , Gaëlle Marenne
    • , Angela L. Mazul
    • , Mark I. McCarthy
    • , Roberta McKean-Cowdin
    • , Sarah E. Medland
    • , Karina Meidtner
    • , Lili Milani
    • , Vanisha Mistry
    • , Paul Mitchell
    • , Karen L. Mohlke
    • , Leena Moilanen
    • , Marie Moitry
    • , Grant W. Montgomery
    • , Dennis O. Mook-Kanamori
    • , Carmel Moore
    • , Trevor A. Mori
    • , Andrew D. Morris
    • , Andrew P. Morris
    • , Martina Müller-Nurasyid
    • , Patricia B. Munroe
    • , Mike A. Nalls
    • , Narisu Narisu
    • , Christopher P. Nelson
    • , Matt Neville
    • , Sune F. Nielsen
    • , Kjell Nikus
    • , Pål R. Njølstad
    • , Børge G. Nordestgaard
    • , Dale R. Nyholt
    • , Jeffrey R. O’Connel
    • , Michelle L. O’Donoghue
    • , Loes M. Olde Loohuis
    • , Roel A. Ophoff
    • , Katharine R. Owen
    • , Chris J. Packard
    • , Sandosh Padmanabhan
    • , Colin N. A. Palmer
    • , Nicholette D. Palmer
    • , Gerard Pasterkamp
    • , Aniruddh P. Patel
    • , Alison Pattie
    • , Oluf Pedersen
    • , Peggy L. Peissig
    • , Gina M. Peloso
    • , Craig E. Pennell
    • , Markus Perola
    • , James A. Perry
    • , John R. B. Perry
    • , Tune H. Pers
    • , Thomas N. Person
    • , Annette Peters
    • , Eva R. B. Petersen
    • , Patricia A. Peyser
    • , Ailith Pirie
    • , Ozren Polasek
    • , Tinca J. Polderman
    • , Hannu Puolijoki
    • , Olli T. Raitakari
    • , Asif Rasheed
    • , Rainer Rauramaa
    • , Dermot F. Reilly
    • , Frida Renström
    • , Myriam Rheinberger
    • , Paul M. Ridker
    • , John D. Rioux
    • , Manuel A. Rivas
    • , David J. Roberts
    • , Neil R. Robertson
    • , Antonietta Robino
    • , Olov Rolandsson
    • , Igor Rudan
    • , Katherine S. Ruth
    • , Danish Saleheen
    • , Veikko Salomaa
    • , Nilesh J. Samani
    • , Yadav Sapkota
    • , Naveed Sattar
    • , Robert E. Schoen
    • , Pamela J. Schreiner
    • , Matthias B. Schulze
    • , Robert A. Scott
    • , Marcelo P. Segura-Lepe
    • , Svati H. Shah
    • , Wayne H.-H. Sheu
    • , Xueling Sim
    • , Andrew J. Slater
    • , Kerrin S. Small
    • , Albert V. Smith
    • , Lorraine Southam
    • , Timothy D. Spector
    • , Elizabeth K. Speliotes
    • , John M. Starr
    • , Kari Stefansson
    • , Valgerdur Steinthorsdottir
    • , Kathleen E. Stirrups
    • , Konstantin Strauch
    • , Heather M. Stringham
    • , Michael Stumvoll
    • , Liang Sun
    • , Praveen Surendran
    • , Amy J. Swift
    • , Hayato Tada
    • , Katherine E. Tansey
    • , Jean-Claude Tardif
    • , Kent D. Taylor
    • , Alexander Teumer
    • , Deborah J. Thompson
    • , Gudmar Thorleifsson
    • , Unnur Thorsteinsdottir
    • , Betina H. Thuesen
    • , Anke Tönjes
    • , Gerard Tromp
    • , Stella Trompet
    • , Emmanouil Tsafantakis
    • , Jaakko Tuomilehto
    • , Anne Tybjaerg-Hansen
    • , Jonathan P. Tyrer
    • , Rudolf Uher
    • , André G. Uitterlinden
    • , Matti Uusitupa
    • , Sander W. Laan
    • , Cornelia M. Duijn
    • , Nienke Leeuwen
    • , Jessica van Setten
    • , Mauno Vanhala
    • , Anette Varbo
    • , Tibor V. Varga
    • , Rohit Varma
    • , Digna R. Velez Edwards
    • , Sita H. Vermeulen
    • , Giovanni Veronesi
    • , Henrik Vestergaard
    • , Veronique Vitart
    • , Thomas F. Vogt
    • , Uwe Völker
    • , Dragana Vuckovic
    • , Lynne E. Wagenknecht
    • , Mark Walker
    • , Lars Wallentin
    • , Feijie Wang
    • , Carol A. Wang
    • , Shuai Wang
    • , Yiqin Wang
    • , Erin B. Ware
    • , Nicholas J. Wareham
    • , Helen R. Warren
    • , Dawn M. Waterworth
    • , Jennifer Wessel
    • , Harvey D. White
    • , Cristen J. Willer
    • , James G. Wilson
    • , Daniel R. Witte
    • , Andrew R. Wood
    • , Ying Wu
    • , Hanieh Yaghootkar
    • , Jie Yao
    • , Pang Yao
    • , Laura M. Yerges-Armstrong
    • , Robin Young
    • , Eleftheria Zeggini
    • , Xiaowei Zhan
    • , Weihua Zhang
    • , Jing Hua Zhao
    • , Wei Zhao
    • , Wei Zhao
    • , Wei Zhou
    • , Krina T Zondervan
    • , Jerome I. Rotter
    • , John A. Pospisilik
    • , Fernando Rivadeneira
    • , Ingrid B. Borecki
    • , Panos Deloukas
    • , Timothy M. Frayling
    • , Guillaume Lettre
    • , Kari E. North
    • , Cecilia M. Lindgren
    • , Joel N. Hirschhorn
    •  & Ruth J. F. Loos
  • Article |

    The authors perform meta-analysis of GWAS studies for asthma from multiancestral cohorts. They identify five new loci and find that the asthma-associated loci are enriched near enhancer marks in immune cells.

    • Florence Demenais
    • , Patricia Margaritte-Jeannin
    • , Kathleen C. Barnes
    • , William O. C. Cookson
    • , Janine Altmüller
    • , Wei Ang
    • , R. Graham Barr
    • , Terri H. Beaty
    • , Allan B. Becker
    • , John Beilby
    • , Hans Bisgaard
    • , Unnur Steina Bjornsdottir
    • , Eugene Bleecker
    • , Klaus Bønnelykke
    • , Dorret I. Boomsma
    • , Emmanuelle Bouzigon
    • , Christopher E. Brightling
    • , Myriam Brossard
    • , Guy G. Brusselle
    • , Esteban Burchard
    • , Kristin M. Burkart
    • , Andrew Bush
    • , Moira Chan-Yeung
    • , Kian Fan Chung
    • , Alexessander Couto Alves
    • , John A. Curtin
    • , Adnan Custovic
    • , Denise Daley
    • , Johan C. de Jongste
    • , Blanca E. Del-Rio-Navarro
    • , Kathleen M. Donohue
    • , Liesbeth Duijts
    • , Celeste Eng
    • , Johan G. Eriksson
    • , Martin Farrall
    • , Yuliya Fedorova
    • , Bjarke Feenstra
    • , Manuel A. Ferreira
    • , Maxim B. Freidin
    • , Zofia Gajdos
    • , Jim Gauderman
    • , Ulrike Gehring
    • , Frank Geller
    • , Jon Genuneit
    • , Sina A. Gharib
    • , Frank Gilliland
    • , Raquel Granell
    • , Penelope E. Graves
    • , Daniel F. Gudbjartsson
    • , Tari Haahtela
    • , Susan R. Heckbert
    • , Dick Heederik
    • , Joachim Heinrich
    • , Markku Heliövaara
    • , John Henderson
    • , Blanca E. Himes
    • , Hiroshi Hirose
    • , Joel N. Hirschhorn
    • , Albert Hofman
    • , Patrick Holt
    • , Jouke Hottenga
    • , Thomas J. Hudson
    • , Jennie Hui
    • , Medea Imboden
    • , Vladimir Ivanov
    • , Vincent W. V. Jaddoe
    • , Alan James
    • , Christer Janson
    • , Marjo-Riitta Jarvelin
    • , Deborah Jarvis
    • , Graham Jones
    • , Ingileif Jonsdottir
    • , Pekka Jousilahti
    • , Michael Kabesch
    • , Mika Kähönen
    • , David B. Kantor
    • , Alexandra S. Karunas
    • , Elza Khusnutdinova
    • , Gerard H. Koppelman
    • , Anita L. Kozyrskyj
    • , Eskil Kreiner
    • , Michiaki Kubo
    • , Rajesh Kumar
    • , Ashish Kumar
    • , Mikko Kuokkanen
    • , Lies Lahousse
    • , Tarja Laitinen
    • , Catherine Laprise
    • , Mark Lathrop
    • , Susanne Lau
    • , Young-Ae Lee
    • , Terho Lehtimäki
    • , Sébastien Letort
    • , Albert M. Levin
    • , Guo Li
    • , Liming Liang
    • , Laura R. Loehr
    • , Stephanie J. London
    • , Daan W. Loth
    • , Ani Manichaikul
    • , Ingo Marenholz
    • , Fernando J. Martinez
    • , Melanie C. Matheson
    • , Rasika A. Mathias
    • , Kenji Matsumoto
    • , Hamdi Mbarek
    • , Wendy L. McArdle
    • , Mads Melbye
    • , Erik Melén
    • , Deborah Meyers
    • , Sven Michel
    • , Hamida Mohamdi
    • , Arthur W. Musk
    • , Rachel A. Myers
    • , Maartje A. E. Nieuwenhuis
    • , Emiko Noguchi
    • , George T. O’Connor
    • , Ludmila M. Ogorodova
    • , Cameron D. Palmer
    • , Aarno Palotie
    • , Julie E. Park
    • , Craig E. Pennell
    • , Göran Pershagen
    • , Alexey Polonikov
    • , Dirkje S. Postma
    • , Nicole Probst-Hensch
    • , Valery P. Puzyrev
    • , Benjamin A. Raby
    • , Olli T. Raitakari
    • , Adaikalavan Ramasamy
    • , Stephen S. Rich
    • , Colin F. Robertson
    • , Isabelle Romieu
    • , Muhammad T. Salam
    • , Veikko Salomaa
    • , Vivi Schlünssen
    • , Robert Scott
    • , Polina A. Selivanova
    • , Torben Sigsgaard
    • , Angela Simpson
    • , Valérie Siroux
    • , Lewis J. Smith
    • , Maria Solodilova
    • , Marie Standl
    • , Kari Stefansson
    • , David P. Strachan
    • , Bruno H. Stricker
    • , Atsushi Takahashi
    • , Philip J. Thompson
    • , Gudmar Thorleifsson
    • , Unnur Thorsteinsdottir
    • , Carla M. T. Tiesler
    • , Dara G. Torgerson
    • , Tatsuhiko Tsunoda
    • , André G. Uitterlinden
    • , Ralf J. P. van der Valk
    • , Amaury Vaysse
    • , Sailaja Vedantam
    • , Andrea von Berg
    • , Erika von Mutius
    • , Judith M. Vonk
    • , Johannes Waage
    • , Nick J. Wareham
    • , Scott T. Weiss
    • , Wendy B. White
    • , Magnus Wickman
    • , Elisabeth Widén
    • , Gonneke Willemsen
    • , L. Keoki Williams
    • , Inge M. Wouters
    • , James J. Yang
    • , Jing Hua Zhao
    • , Miriam F. Moffatt
    • , Carole Ober
    •  & Dan L. Nicolae
  • Article |

    This study identifies regulatory variants in sensory neurons derived from induced pluripotent stem cells. Despite differentiation-induced variability, an allele-specific method allowed detection of loci influencing gene expression, chromatin accessibility and RNA splicing.

    • Jeremy Schwartzentruber
    • , Stefanie Foskolou
    • , Helena Kilpinen
    • , Julia Rodrigues
    • , Kaur Alasoo
    • , Andrew J. Knights
    • , Minal Patel
    • , Angela Goncalves
    • , Rita Ferreira
    • , Caroline Louise Benn
    • , Anna Wilbrey
    • , Magda Bictash
    • , Emma Impey
    • , Lishuang Cao
    • , Sergio Lainez
    • , Alexandre Julien Loucif
    • , Paul John Whiting
    • , Alex Gutteridge
    •  & Daniel J. Gaffney
  • Article |

    This study uses human astrocytes and glioma tumorspheres to generate an atlas of mutant-IDH1-induced epigenomic reprogramming. The findings have implications for understanding mutant IDH function and for optimizing approaches to target IDH-mutant tumors.

    • Sevin Turcan
    • , Vladimir Makarov
    • , Julian Taranda
    • , Yuxiang Wang
    • , Armida W. M. Fabius
    • , Wei Wu
    • , Yupeng Zheng
    • , Nour El-Amine
    • , Sara Haddock
    • , Gouri Nanjangud
    • , H. Carl LeKaye
    • , Cameron Brennan
    • , Justin Cross
    • , Jason T. Huse
    • , Neil L. Kelleher
    • , Pavel Osten
    • , Craig B. Thompson
    •  & Timothy A. Chan
  • Article |

    The authors conduct mass spectrometry experiments identifying H3K4me1-associated proteins, including members of the BAF chromatin-remodeling complex. They show that H3K4me1 augments association of the BAF complex with enhancers in vivo and that H3K4me1-marked nucleosomes are more efficiently remodeled by the BAF complex in vitro.

    • Andrea Local
    • , Hui Huang
    • , Claudio P. Albuquerque
    • , Namit Singh
    • , Ah Young Lee
    • , Wei Wang
    • , Chaochen Wang
    • , Judy E. Hsia
    • , Andrew K. Shiau
    • , Kai Ge
    • , Kevin D. Corbett
    • , Dong Wang
    • , Huilin Zhou
    •  & Bing Ren
  • Article |

    TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit bivalent promoter hypermethylation without a corresponding decrease in gene expression in the undifferentiated state. However, PAX6 promoter hypermethylation in TKO hESCs impairs neural differentiation.

    • Nipun Verma
    • , Heng Pan
    • , Louis C. Doré
    • , Abhijit Shukla
    • , Qing V. Li
    • , Bobbie Pelham-Webb
    • , Virginia Teijeiro
    • , Federico González
    • , Andrei Krivtsov
    • , Chan-Jung Chang
    • , Eirini P. Papapetrou
    • , Chuan He
    • , Olivier Elemento
    •  & Danwei Huangfu
  • Article |

    Transcriptome, DNA methylome and Hi-C profiling of peri- and post-implantation mouse cell lineages identified allele- and lineage-specific methylation patterns. Global demethylation and remethylation correlate with megabase chromatin compartments.

    • Yu Zhang
    • , Yunlong Xiang
    • , Qiangzong Yin
    • , Zhenhai Du
    • , Xu Peng
    • , Qiujun Wang
    • , Miguel Fidalgo
    • , Weikun Xia
    • , Yuanyuan Li
    • , Zhen-ao Zhao
    • , Wenhao Zhang
    • , Jing Ma
    • , Feng Xu
    • , Jianlong Wang
    • , Lei Li
    •  & Wei Xie

    Collection:

  • Article |

    Rare cells resembling the 2-cell-stage embryo (2 C) arise in embryonic stem cell cultures. By performing single-cell analyses and an siRNA screen, the authors identify the intermediate cellular states and epigenetic regulators that underpin the transition to a 2C-like state.

    • Diego Rodriguez-Terrones
    • , Xavier Gaume
    • , Takashi Ishiuchi
    • , Amélie Weiss
    • , Arnaud Kopp
    • , Kai Kruse
    • , Audrey Penning
    • , Juan M. Vaquerizas
    • , Laurent Brino
    •  & Maria-Elena Torres-Padilla
  • Article |

    Ron Wevers and colleagues report that mutations in the methanethiol oxidase gene SELENBP1 cause chronic extraoral halitosis. They find that enzyme deficiency leads to increased levels of methanethiol and dimethylsulfide in the breath and that knockout mice have similar biochemical phenotypes.

    • Arjan Pol
    • , G. Herma Renkema
    • , Albert Tangerman
    • , Edwin G. Winkel
    • , Udo F. Engelke
    • , Arjan P. M. de Brouwer
    • , Kent C. Lloyd
    • , Renee S. Araiza
    • , Lambert van den Heuvel
    • , Heymut Omran
    • , Heike Olbrich
    • , Marijn Oude Elberink
    • , Christian Gilissen
    • , Richard J. Rodenburg
    • , Jörn Oliver Sass
    • , K. Otfried Schwab
    • , Hendrik Schäfer
    • , Hanka Venselaar
    • , J. Silvia Sequeira
    • , Huub J. M. Op den Camp
    •  & Ron A. Wevers
  • Article |

    RNA-directed DNA methylation (RdDM) in the Arabidopsis thaliana male sexual lineage is shown here to regulate gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene, thereby disrupting meiosis

    • James Walker
    • , Hongbo Gao
    • , Jingyi Zhang
    • , Billy Aldridge
    • , Martin Vickers
    • , James D. Higgins
    •  & Xiaoqi Feng
  • Article |

    Comparative genomic analysis of 3,837 bacterial genomes, including new sequences from 484 root-associated isolates, identifies plant-associated gene clusters and plant-mimicking domains.

    • Asaf Levy
    • , Isai Salas Gonzalez
    • , Maximilian Mittelviefhaus
    • , Scott Clingenpeel
    • , Sur Herrera Paredes
    • , Jiamin Miao
    • , Kunru Wang
    • , Giulia Devescovi
    • , Kyra Stillman
    • , Freddy Monteiro
    • , Bryan Rangel Alvarez
    • , Derek S. Lundberg
    • , Tse-Yuan Lu
    • , Sarah Lebeis
    • , Zhao Jin
    • , Meredith McDonald
    • , Andrew P. Klein
    • , Meghan E. Feltcher
    • , Tijana Glavina Rio
    • , Sarah R. Grant
    • , Sharon L. Doty
    • , Ruth E. Ley
    • , Bingyu Zhao
    • , Vittorio Venturi
    • , Dale A. Pelletier
    • , Julia A. Vorholt
    • , Susannah G. Tringe
    • , Tanja Woyke
    •  & Jeffery L. Dangl

Technical Reports

  • Technical Report |

    LeafCutter is a new tool that identifies variable intron splicing events from RNA-seq data for analysis of complex alternative splicing. The method does not require transcript annotation and can be used to map splicing quantitative trait loci.

    • Yang I. Li
    • , David A. Knowles
    • , Jack Humphrey
    • , Alvaro N. Barbeira
    • , Scott P. Dickinson
    • , Hae Kyung Im
    •  & Jonathan K. Pritchard