Genetics

  • Article
    | Open Access

    Genetic resources for livestock are valuable for understanding their demography and past selection, and may inform future breeding programs and agricultural improvement. Here, the authors present deep resequencing of 248 wild and domestic sheep, with associated data and analysis.

    • Xin Li
    • , Ji Yang
    • , Min Shen
    • , Xing-Long Xie
    • , Guang-Jian Liu
    • , Ya-Xi Xu
    • , Feng-Hua Lv
    • , Hua Yang
    • , Yong-Lin Yang
    • , Chang-Bin Liu
    • , Ping Zhou
    • , Peng-Cheng Wan
    • , Yun-Sheng Zhang
    • , Lei Gao
    • , Jing-Quan Yang
    • , Wen-Hui Pi
    • , Yan-Ling Ren
    • , Zhi-Qiang Shen
    • , Feng Wang
    • , Juan Deng
    • , Song-Song Xu
    • , Hosein Salehian-Dehkordi
    • , Eer Hehua
    • , Ali Esmailizadeh
    • , Mostafa Dehghani-Qanatqestani
    • , Ondřej Štěpánek
    • , Christina Weimann
    • , Georg Erhardt
    • , Agraw Amane
    • , Joram M. Mwacharo
    • , Jian-Lin Han
    • , Olivier Hanotte
    • , Johannes A. Lenstra
    • , Juha Kantanen
    • , David W. Coltman
    • , James W. Kijas
    • , Michael W. Bruford
    • , Kathiravan Periasamy
    • , Xin-Hua Wang
    •  & Meng-Hua Li
  • Article
    | Open Access

    Genetic variants at the RSPO3 locus are associated with waist-to-hip ratio (adjusted for BMI). Here, Loh et al. describe two independent RSPO3 signals that associate with body fat distribution, perform fine-mapping and explore the function of RSPO3 in human adipocyte biology and body fat distribution in zebrafish

    • Nellie Y. Loh
    • , James E. N. Minchin
    • , Katherine E. Pinnick
    • , Manu Verma
    • , Marijana Todorčević
    • , Nathan Denton
    • , Julia El-Sayed Moustafa
    • , John P. Kemp
    • , Celia L. Gregson
    • , David M. Evans
    • , Matt J. Neville
    • , Kerrin S. Small
    • , Mark I. McCarthy
    • , Anubha Mahajan
    • , John F. Rawls
    • , Fredrik Karpe
    •  & Constantinos Christodoulides
  • Article
    | Open Access

    Mediator is a multiprotein complex required to activate gene transcription by RNAPII. Here, the authors report that MED12 and MED13 are conditional positive regulators that facilitate the expression of genes depleted in active chromatin marks and the induction of gene expression in response to environmental stimuli in Arabidopsis.

    • Qikun Liu
    • , Sylvain Bischof
    • , C. Jake Harris
    • , Zhenhui Zhong
    • , Lingyu Zhan
    • , Calvin Nguyen
    • , Andrew Rashoff
    • , William D. Barshop
    • , Fei Sun
    • , Suhua Feng
    • , Magdalena Potok
    • , Javier Gallego-Bartolome
    • , Jixian Zhai
    • , James A. Wohlschlegel
    • , Michael F. Carey
    • , Jeffrey A. Long
    •  & Steven E. Jacobsen
  • Article
    | Open Access

    Age-associated metabolic changes include lipid accumulation. Here, the authors show that with replicative aging yeast accumulate lipid droplets which protect cells from cold stress and can be modulated through Biosynthesis of NAD+ 2 (BNA2).

    • Anthony O. Beas
    • , Patricia B. Gordon
    • , Clara L. Prentiss
    • , Carissa Perez Olsen
    • , Matthew A. Kukurugya
    • , Bryson D. Bennett
    • , Susan M. Parkhurst
    •  & Daniel E. Gottschling
  • Article
    | Open Access

    B chromosomes are supernumerary chromosomes exhibiting dramatic differences between different organs in same species. Here, the authors show programmed B chromosome elimination in goatgrass starts at the onset of embryo differentiation by nondisjunction of chromatids, anaphase lagging, and ends with the degradation of micronucleated DNA.

    • Alevtina Ruban
    • , Thomas Schmutzer
    • , Dan D. Wu
    • , Joerg Fuchs
    • , Anastassia Boudichevskaia
    • , Myroslava Rubtsova
    • , Klaus Pistrick
    • , Michael Melzer
    • , Axel Himmelbach
    • , Veit Schubert
    • , Uwe Scholz
    •  & Andreas Houben
  • Article
    | Open Access

    The impact of late Pleistocene climate change on ecosystems has been hard to assess. Here, the authors sequence ancient DNA from Hall’s Cave, Texas and find that both plant and vertebrate diversity decreased with cooling, and though plant diversity recovered with rewarming, megafauna went extinct.

    • Frederik V. Seersholm
    • , Daniel J. Werndly
    • , Alicia Grealy
    • , Taryn Johnson
    • , Erin M. Keenan Early
    • , Ernest L. Lundelius Jr.
    • , Barbara Winsborough
    • , Grayal Earle Farr
    • , Rickard Toomey
    • , Anders J. Hansen
    • , Beth Shapiro
    • , Michael R. Waters
    • , Gregory McDonald
    • , Anna Linderholm
    • , Thomas W. Stafford Jr.
    •  & Michael Bunce
  • Article
    | Open Access

    Northern China contains some of the world’s earliest farming societies. Here, authors use 55 ancient genomes to trace the genetic history of human migrations across northern China for the last 7500 years, and document genetic changes mirroring shifts in subsistence strategy.

    • Chao Ning
    • , Tianjiao Li
    • , Ke Wang
    • , Fan Zhang
    • , Tao Li
    • , Xiyan Wu
    • , Shizhu Gao
    • , Quanchao Zhang
    • , Hai Zhang
    • , Mark J. Hudson
    • , Guanghui Dong
    • , Sihao Wu
    • , Yanming Fang
    • , Chen Liu
    • , Chunyan Feng
    • , Wei Li
    • , Tao Han
    • , Ruo Li
    • , Jian Wei
    • , Yonggang Zhu
    • , Yawei Zhou
    • , Chuan-Chao Wang
    • , Shengying Fan
    • , Zenglong Xiong
    • , Zhouyong Sun
    • , Maolin Ye
    • , Lei Sun
    • , Xiaohong Wu
    • , Fawei Liang
    • , Yanpeng Cao
    • , Xingtao Wei
    • , Hong Zhu
    • , Hui Zhou
    • , Johannes Krause
    • , Martine Robbeets
    • , Choongwon Jeong
    •  & Yinqiu Cui
  • Article
    | Open Access

    There are more than 20 known melanoma susceptibility genes. Here, using a massively parallel reporter assay, the authors identify risk-associated variants that alter gene transcription, and demonstrate that expression of one such gene, MX2, leads to the promotion of melanoma in a zebrafish model.

    • Jiyeon Choi
    • , Tongwu Zhang
    • , Andrew Vu
    • , Julien Ablain
    • , Matthew M. Makowski
    • , Leandro M. Colli
    • , Mai Xu
    • , Rebecca C. Hennessey
    • , Jinhu Yin
    • , Harriet Rothschild
    • , Cathrin Gräwe
    • , Michael A. Kovacs
    • , Karen M. Funderburk
    • , Myriam Brossard
    • , John Taylor
    • , Bogdan Pasaniuc
    • , Raj Chari
    • , Stephen J. Chanock
    • , Clive J. Hoggart
    • , Florence Demenais
    • , Jennifer H. Barrett
    • , Matthew H. Law
    • , Mark M. Iles
    • , Kai Yu
    • , Michiel Vermeulen
    • , Leonard I. Zon
    •  & Kevin M. Brown
  • Article
    | Open Access

    ARID1A, which is often mutated in human endometrial cancer, is a component of the SWI/SNF chromatin remodelling complex. Here, the authors show that Arid1a mutations in the mouse endometrium and primary human endometrial epithelial cells cause widespread reprogramming of gene transcription and result in a loss of response to TGFβ.

    • Yohan Suryo Rahmanto
    • , Wenjing Shen
    • , Xu Shi
    • , Xi Chen
    • , Yu Yu
    • , Zheng-Cheng Yu
    • , Tsutomu Miyamoto
    • , Meng-Horng Lee
    • , Vivek Singh
    • , Ryoichi Asaka
    • , Geoffrey Shimberg
    • , Michele I. Vitolo
    • , Stuart S. Martin
    • , Denis Wirtz
    • , Ronny Drapkin
    • , Jianhua Xuan
    • , Tian-Li Wang
    •  & Ie-Ming Shih
  • Article
    | Open Access

    Sample index hopping results in various artefacts in multiplexed scRNA-seq experiments. Here, the authors introduce a statistical model to estimate sample index hopping rate in droplet-based scRNA-seq data and show that artifacts can be corrected by purging phantom molecules from the data.

    • Rick Farouni
    • , Haig Djambazian
    • , Lorenzo E. Ferri
    • , Jiannis Ragoussis
    •  & Hamed S. Najafabadi
  • Article
    | Open Access

    The relationship between regulatory elements, chromatin interactions and gene expression during development remains poorly understood. Here the authors present Tiled-C, a low-input 3C approach to study genome architecture at high resolution, and apply it to mouse erythroid differentiation in vivo, finding that enhancer-promoter interactions are formed gradually during differentiation, concomitant with progressive upregulation of gene activity.

    • A. Marieke Oudelaar
    • , Robert A. Beagrie
    • , Matthew Gosden
    • , Sara de Ornellas
    • , Emily Georgiades
    • , Jon Kerry
    • , Daniel Hidalgo
    • , Joana Carrelha
    • , Arun Shivalingam
    • , Afaf H. El-Sagheer
    • , Jelena M. Telenius
    • , Tom Brown
    • , Veronica J. Buckle
    • , Merav Socolovsky
    • , Douglas R. Higgs
    •  & Jim R. Hughes
  • Article
    | Open Access

    Obesity and type 2 diabetes (T2D) are metabolic disorders characterized by insulin resistance in skeletal muscle. Here, the authors map skeletal muscle enhancer elements dynamically regulated after exposure to free fatty acid palmitate or inflammatory cytokine TNFα and identify target genes involved in metabolic dysfunction in skeletal muscle.

    • Kristine Williams
    • , Lars R. Ingerslev
    • , Jette Bork-Jensen
    • , Martin Wohlwend
    • , Ann Normann Hansen
    • , Lewin Small
    • , Rasmus Ribel-Madsen
    • , Arne Astrup
    • , Oluf Pedersen
    • , Johan Auwerx
    • , Christopher T. Workman
    • , Niels Grarup
    • , Torben Hansen
    •  & Romain Barrès
  • Article
    | Open Access

    Numerous strategies exist to limit the off-target activity of CRISPR-Cas9 nucleases. Here the authors co-administer truncated gRNAs that block both Cas9 and high-fidelity Cas9 variants from cleaving at off-target sites.

    • John C. Rose
    • , Nicholas A. Popp
    • , Christopher D. Richardson
    • , Jason J. Stephany
    • , Julie Mathieu
    • , Cindy T. Wei
    • , Jacob E. Corn
    • , Dustin J. Maly
    •  & Douglas M. Fowler
  • Article
    | Open Access

    Phosphorylation plays an important role in the regulation of molecular circadian clocks. Here the authors utilize multi-omics data from flies to describe the circadian kinome and identify GASKET as a potentially important regulator within the circadian kinase network.

    • Chenwei Wang
    • , Ke Shui
    • , Shanshan Ma
    • , Shaofeng Lin
    • , Ying Zhang
    • , Bo Wen
    • , Wankun Deng
    • , Haodong Xu
    • , Hui Hu
    • , Anyuan Guo
    • , Yu Xue
    •  & Luoying Zhang
  • Article
    | Open Access

    Local activity of the DNA methylation machinery remains poorly understood. Here, the authors present a theoretical and experimental framework to infer methylation and demethylation rates at genome scale in mouse embryonic stem cells, finding that maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies.

    • Paul Adrian Ginno
    • , Dimos Gaidatzis
    • , Angelika Feldmann
    • , Leslie Hoerner
    • , Dilek Imanci
    • , Lukas Burger
    • , Frederic Zilbermann
    • , Antoine H. F. M. Peters
    • , Frank Edenhofer
    • , Sébastien A. Smallwood
    • , Arnaud R. Krebs
    •  & Dirk Schübeler
  • Article
    | Open Access

    The netrin receptor UNC-40/DCC is required to recruit GABAAR at neuromuscular junctions in C. elegans. Here, the authors show that UNC-40/DCC assembles an intracellular synaptic scaffold, regulating the content of GABAAR and inhibitory neurotransmission.

    • Xin Zhou
    • , Marine Gueydan
    • , Maelle Jospin
    • , Tingting Ji
    • , Aurore Valfort
    • , Bérangère Pinan-Lucarré
    •  & Jean-Louis Bessereau
  • Article
    | Open Access

    Multiple myeloma is characterised by frequent gene fusions. Here, the authors use data from the Multiple Myeloma Research Foundation CoMMpass Study to further investigate fusion genes in this disease and their clinical relevance.

    • Steven M. Foltz
    • , Qingsong Gao
    • , Christopher J. Yoon
    • , Hua Sun
    • , Lijun Yao
    • , Yize Li
    • , Reyka G. Jayasinghe
    • , Song Cao
    • , Justin King
    • , Daniel R. Kohnen
    • , Mark A. Fiala
    • , Li Ding
    •  & Ravi Vij
  • Article
    | Open Access

    Multi-nucleotide variants (MNV) are genetic variants in close proximity of each other on the same haplotype whose functional impact is difficult to predict if they reside in the same codon. Here, Wang et al. use the gnomAD dataset to assemble a catalogue of MNVs and estimate their global mutation rate.

    • Qingbo Wang
    • , Emma Pierce-Hoffman
    • , Beryl B. Cummings
    • , Jessica Alföldi
    • , Laurent C. Francioli
    • , Laura D. Gauthier
    • , Andrew J. Hill
    • , Anne H. O’Donnell-Luria
    • , Irina M. Armean
    • , Eric Banks
    • , Louis Bergelson
    • , Kristian Cibulskis
    • , Ryan L. Collins
    • , Kristen M. Connolly
    • , Miguel Covarrubias
    • , Mark J. Daly
    • , Stacey Donnelly
    • , Yossi Farjoun
    • , Steven Ferriera
    • , Stacey Gabriel
    • , Jeff Gentry
    • , Namrata Gupta
    • , Thibault Jeandet
    • , Diane Kaplan
    • , Kristen M. Laricchia
    • , Christopher Llanwarne
    • , Eric V. Minikel
    • , Ruchi Munshi
    • , Benjamin M. Neale
    • , Sam Novod
    • , Nikelle Petrillo
    • , Timothy Poterba
    • , David Roazen
    • , Valentin Ruano-Rubio
    • , Andrea Saltzman
    • , Kaitlin E. Samocha
    • , Molly Schleicher
    • , Cotton Seed
    • , Matthew Solomonson
    • , Jose Soto
    • , Grace Tiao
    • , Kathleen Tibbetts
    • , Charlotte Tolonen
    • , Christopher Vittal
    • , Gordon Wade
    • , Arcturus Wang
    • , James S. Ware
    • , Nicholas A. Watts
    • , Ben Weisburd
    • , Nicola Whiffin
    • , Carlos A. Aguilar Salinas
    • , Tariq Ahmad
    • , Christine M. Albert
    • , Diego Ardissino
    • , Gil Atzmon
    • , John Barnard
    • , Laurent Beaugerie
    • , Emelia J. Benjamin
    • , Michael Boehnke
    • , Lori L. Bonnycastle
    • , Erwin P. Bottinger
    • , Donald W. Bowden
    • , Matthew J. Bown
    • , John C. Chambers
    • , Juliana C. Chan
    • , Daniel Chasman
    • , Judy Cho
    • , Mina K. Chung
    • , Bruce Cohen
    • , Adolfo Correa
    • , Dana Dabelea
    • , Dawood Darbar
    • , Ravindranath Duggirala
    • , Josée Dupuis
    • , Patrick T. Ellinor
    • , Roberto Elosua
    • , Jeanette Erdmann
    • , Tõnu Esko
    • , Martti Färkkilä
    • , Jose Florez
    • , Andre Franke
    • , Gad Getz
    • , Benjamin Glaser
    • , Stephen J. Glatt
    • , David Goldstein
    • , Clicerio Gonzalez
    • , Leif Groop
    • , Christopher Haiman
    • , Craig Hanis
    • , Matthew Harms
    • , Mikko Hiltunen
    • , Matti M. Holi
    • , Christina M. Hultman
    • , Mikko Kallela
    • , Jaakko Kaprio
    • , Sekar Kathiresan
    • , Bong-Jo Kim
    • , Young Jin Kim
    • , George Kirov
    • , Jaspal Kooner
    • , Seppo Koskinen
    • , Harlan M. Krumholz
    • , Subra Kugathasan
    • , Soo Heon Kwak
    • , Markku Laakso
    • , Terho Lehtimäki
    • , Ruth J. F. Loos
    • , Steven A. Lubitz
    • , Ronald C. W. Ma
    • , Jaume Marrugat
    • , Kari M. Mattila
    • , Steven McCarroll
    • , Mark I. McCarthy
    • , Dermot McGovern
    • , Ruth McPherson
    • , James B. Meigs
    • , Olle Melander
    • , Andres Metspalu
    • , Peter M. Nilsson
    • , Michael C. O’Donovan
    • , Dost Ongur
    • , Lorena Orozco
    • , Michael J. Owen
    • , Colin N. A. Palmer
    • , Aarno Palotie
    • , Kyong Soo Park
    • , Carlos Pato
    • , Ann E. Pulver
    • , Nazneen Rahman
    • , Anne M. Remes
    • , John D. Rioux
    • , Samuli Ripatti
    • , Dan M. Roden
    • , Danish Saleheen
    • , Veikko Salomaa
    • , Nilesh J. Samani
    • , Jeremiah Scharf
    • , Heribert Schunkert
    • , Moore B. Shoemaker
    • , Pamela Sklar
    • , Hilkka Soininen
    • , Harry Sokol
    • , Tim Spector
    • , Patrick F. Sullivan
    • , Jaana Suvisaari
    • , E. Shyong Tai
    • , Yik Ying Teo
    • , Tuomi Tiinamaija
    • , Ming Tsuang
    • , Dan Turner
    • , Teresa Tusie-Luna
    • , Erkki Vartiainen
    • , Hugh Watkins
    • , Rinse K. Weersma
    • , Maija Wessman
    • , James G. Wilson
    • , Ramnik J. Xavier
    • , Konrad J. Karczewski
    •  & Daniel G. MacArthur
  • Article
    | Open Access

    The mechanisms regulating regeneration of the earthworm are unclear. Here, the authors use genomic and transcriptomic analysis of the earthworm Eisenia andrei together with Hi-C analysis to identify genes involved and show activation of LINE2 transposable elements on regeneration.

    • Yong Shao
    • , Xiao-Bo Wang
    • , Jin-Jin Zhang
    • , Ming-Li Li
    • , Shou-Song Wu
    • , Xi-Yao Ma
    • , Xue Wang
    • , Hui-Fang Zhao
    • , Yuan Li
    • , Helen He Zhu
    • , David M. Irwin
    • , De-Peng Wang
    • , Guo-Jie Zhang
    • , Jue Ruan
    •  & Dong-Dong Wu
  • Article
    | Open Access

    Upstream open reading frames (uORFs), located in 5’ untranslated regions, are regulators of downstream protein translation. Here, Whiffin et al. use the genomes of 15,708 individuals in the Genome Aggregation Database (gnomAD) to systematically assess the deleteriousness of variants creating or disrupting uORFs.

    • Nicola Whiffin
    • , Konrad J. Karczewski
    • , Xiaolei Zhang
    • , Sonia Chothani
    • , Miriam J. Smith
    • , D. Gareth Evans
    • , Angharad M. Roberts
    • , Nicholas M. Quaife
    • , Sebastian Schafer
    • , Owen Rackham
    • , Jessica Alföldi
    • , Anne H. O’Donnell-Luria
    • , Laurent C. Francioli
    • , Irina M. Armean
    • , Eric Banks
    • , Louis Bergelson
    • , Kristian Cibulskis
    • , Ryan L. Collins
    • , Kristen M. Connolly
    • , Miguel Covarrubias
    • , Beryl Cummings
    • , Mark J. Daly
    • , Stacey Donnelly
    • , Yossi Farjoun
    • , Steven Ferriera
    • , Stacey Gabriel
    • , Laura D. Gauthier
    • , Jeff Gentry
    • , Namrata Gupta
    • , Thibault Jeandet
    • , Diane Kaplan
    • , Kristen M. Laricchia
    • , Christopher Llanwarne
    • , Eric V. Minikel
    • , Ruchi Munshi
    • , Benjamin M. Neale
    • , Sam Novod
    • , Nikelle Petrillo
    • , Timothy Poterba
    • , David Roazen
    • , Valentin Ruano-Rubio
    • , Andrea Saltzman
    • , Kaitlin E. Samocha
    • , Molly Schleicher
    • , Cotton Seed
    • , Matthew Solomonson
    • , Jose Soto
    • , Grace Tiao
    • , Kathleen Tibbetts
    • , Charlotte Tolonen
    • , Christopher Vittal
    • , Gordon Wade
    • , Arcturus Wang
    • , Qingbo Wang
    • , Nicholas A. Watts
    • , Ben Weisburd
    • , Carlos A. Aguilar Salinas
    • , Tariq Ahmad
    • , Christine M. Albert
    • , Diego Ardissino
    • , Gil Atzmon
    • , John Barnard
    • , Laurent Beaugerie
    • , Emelia J. Benjamin
    • , Michael Boehnke
    • , Lori L. Bonnycastle
    • , Erwin P. Bottinger
    • , Donald W. Bowden
    • , Matthew J. Bown
    • , John C. Chambers
    • , Juliana C. Chan
    • , Daniel Chasman
    • , Judy Cho
    • , Mina K. Chung
    • , Bruce Cohen
    • , Adolfo Correa
    • , Dana Dabelea
    • , Mark J. Daly
    • , Dawood Darbar
    • , Ravindranath Duggirala
    • , Josée Dupuis
    • , Patrick T. Ellinor
    • , Roberto Elosua
    • , Jeanette Erdmann
    • , Tõnu Esko
    • , Martti Färkkilä
    • , Jose Florez
    • , Andre Franke
    • , Gad Getz
    • , Benjamin Glaser
    • , Stephen J. Glatt
    • , David Goldstein
    • , Clicerio Gonzalez
    • , Leif Groop
    • , Christopher Haiman
    • , Craig Hanis
    • , Matthew Harms
    • , Mikko Hiltunen
    • , Matti M. Holi
    • , Christina M. Hultman
    • , Mikko Kallela
    • , Jaakko Kaprio
    • , Sekar Kathiresan
    • , Bong-Jo Kim
    • , Young Jin Kim
    • , George Kirov
    • , Jaspal Kooner
    • , Seppo Koskinen
    • , Harlan M. Krumholz
    • , Subra Kugathasan
    • , Soo Heon Kwak
    • , Markku Laakso
    • , Terho Lehtimäki
    • , Ruth J. F. Loos
    • , Steven A. Lubitz
    • , Ronald C. W. Ma
    • , Jaume Marrugat
    • , Kari M. Mattila
    • , Steven McCarroll
    • , Mark I. McCarthy
    • , Dermot McGovern
    • , Ruth McPherson
    • , James B. Meigs
    • , Olle Melander
    • , Andres Metspalu
    • , Benjamin M. Neale
    • , Peter M. Nilsson
    • , Michael C. O’Donovan
    • , Dost Ongur
    • , Lorena Orozco
    • , Michael J. Owen
    • , Colin N. A. Palmer
    • , Aarno Palotie
    • , Kyong Soo Park
    • , Carlos Pato
    • , Ann E. Pulver
    • , Nazneen Rahman
    • , Anne M. Remes
    • , John D. Rioux
    • , Samuli Ripatti
    • , Dan M. Roden
    • , Danish Saleheen
    • , Veikko Salomaa
    • , Nilesh J. Samani
    • , Jeremiah Scharf
    • , Heribert Schunkert
    • , Moore B. Shoemaker
    • , Pamela Sklar
    • , Hilkka Soininen
    • , Harry Sokol
    • , Tim Spector
    • , Patrick F. Sullivan
    • , Jaana Suvisaari
    • , E. Shyong Tai
    • , Yik Ying Teo
    • , Tuomi Tiinamaija
    • , Ming Tsuang
    • , Dan Turner
    • , Teresa Tusie-Luna
    • , Erkki Vartiainen
    • , Hugh Watkins
    • , Rinse K. Weersma
    • , Maija Wessman
    • , James G. Wilson
    • , Ramnik J. Xavier
    • , Stuart A. Cook
    • , Paul J. R. Barton
    • , Daniel G. MacArthur
    •  & James S. Ware
  • Article
    | Open Access

    DNA methylation is an epigenetic marker in all domains of life. Here, Jeudy et al., using single-molecule realtime sequencing, determine DNA methylation patterns in giant viruses and evolutionary analysis of virus encoded DNA methyltransferases suggests that they affect viral fitness.

    • Sandra Jeudy
    • , Sofia Rigou
    • , Jean-Marie Alempic
    • , Jean-Michel Claverie
    • , Chantal Abergel
    •  & Matthieu Legendre
  • Article
    | Open Access

    Until now, the transcriptome of preimplantation mouse embryos has only been analysed by short-read sequencing. Here, the authors perform long-read sequencing to provide a more detailed transcriptome of the preimplantation mouse embryo, identifying various novel transcripts, for example Kdm4dl.

    • Yunbo Qiao
    • , Chao Ren
    • , Shisheng Huang
    • , Jie Yuan
    • , Xingchen Liu
    • , Jiao Fan
    • , Jianxiang Lin
    • , Susu Wu
    • , Qiuzhen Chen
    • , Xiaochen Bo
    • , Xiangyang Li
    • , Xingxu Huang
    • , Zhen Liu
    •  & Wenjie Shu
  • Article
    | Open Access

    Comprehensive epigenomic maps of various rice varieties are still unavailable. Here, the authors report the development of eChIP as a fast and low-input upgrade of regular plant ChIP-seq protocol for epigenome analysis of 20 rice varieties and annotate over 80% of the genome with different epigenome properties for transcriptional regulation.

    • Lun Zhao
    • , Liang Xie
    • , Qing Zhang
    • , Weizhi Ouyang
    • , Li Deng
    • , Pengpeng Guan
    • , Meng Ma
    • , Yue Li
    • , Ying Zhang
    • , Qin Xiao
    • , Jingwen Zhang
    • , Hongmeijuan Li
    • , Shunyao Wang
    • , Jiangwei Man
    • , Zhilin Cao
    • , Qinghua Zhang
    • , Qifa Zhang
    • , Guoliang Li
    •  & Xingwang Li
  • Article
    | Open Access

    Genomic studies of paleopteran insects, such as mayflies, are needed to reconstruct early insect evolution. Here, Almudi and colleagues present the genome of the mayfly Cloeon dipterum and use transcriptomics to characterize its adaptations to distinct habitats and the origin of insect wings.

    • Isabel Almudi
    • , Joel Vizueta
    • , Christopher D. R. Wyatt
    • , Alex de Mendoza
    • , Ferdinand Marlétaz
    • , Panos N. Firbas
    • , Roberto Feuda
    • , Giulio Masiero
    • , Patricia Medina
    • , Ana Alcaina-Caro
    • , Fernando Cruz
    • , Jessica Gómez-Garrido
    • , Marta Gut
    • , Tyler S. Alioto
    • , Carlos Vargas-Chavez
    • , Kristofer Davie
    • , Bernhard Misof
    • , Josefa González
    • , Stein Aerts
    • , Ryan Lister
    • , Jordi Paps
    • , Julio Rozas
    • , Alejandro Sánchez-Gracia
    • , Manuel Irimia
    • , Ignacio Maeso
    •  & Fernando Casares
  • Article
    | Open Access

    If left unrepaired, meiotic DSBs are toxic to mammalian cells, thus oocytes in which DSBs persist are eliminated by the DNA-damage checkpoint. Here the authors provide insights into the roles of PUMA, NOXA and BAX during DNA damage checkpoint that eliminates Dmc1−/− and Msh5−/− oocytes.

    • Elias ElInati
    • , Agata P. Zielinska
    • , Afshan McCarthy
    • , Nada Kubikova
    • , Valdone Maciulyte
    • , Shantha Mahadevaiah
    • , Mahesh N. Sangrithi
    • , Obah Ojarikre
    • , Dagan Wells
    • , Kathy K. Niakan
    • , Melina Schuh
    •  & James M. A. Turner
  • Article
    | Open Access

    While DNA methylation is thought to play a regulatory role, there are few examples where modification of a single CpG dinucleotide directly affects transcription factor binding. Here the authors show that methylation of a single CGATA element within the c-Kit gene inhibits binding and regulation by erythroid transcription factor GATA-1, both in cells and in mice, suggesting that methylation at this site plays an essential role in erythropoiesis.

    • Lu Yang
    • , Zhiliang Chen
    • , Elizabeth S. Stout
    • , Fabien Delerue
    • , Lars M. Ittner
    • , Marc R. Wilkins
    • , Kate G. R. Quinlan
    •  & Merlin Crossley
  • Article
    | Open Access

    Gene isoforms result from variable transcription start sites (TSSs) and polyadenylation sites (PASs) at the end of transcripts. Here, the authors perform transcript isoform sequencing and find widespread promoter- proximal transcriptional termination in Arabidopsis, suggesting this may represent a checkpoint that regulates plant gene expression.

    • Quentin Angelo Thomas
    • , Ryan Ard
    • , Jinghan Liu
    • , Bingnan Li
    • , Jingwen Wang
    • , Vicent Pelechano
    •  & Sebastian Marquardt
  • Article
    | Open Access

    Current machine learning classifiers have been applied to whole-genome sequencing data to identify determinants of antimicrobial resistance, but they lack interpretability. Here the authors present a metabolic machine learning classifier that uses flux balance analysis to estimate the biochemical effects of alleles.

    • Erol S. Kavvas
    • , Laurence Yang
    • , Jonathan M. Monk
    • , David Heckmann
    •  & Bernhard O. Palsson
  • Article
    | Open Access

    On the electrocardiogram, the PR interval reflects conduction from the atria to ventricles and also serves as risk indicator of cardiovascular morbidity and mortality. Here, the authors perform genome-wide meta-analyses for PR interval in multiple ancestries and identify 141 previously unreported genetic loci.

    • Ioanna Ntalla
    • , Lu-Chen Weng
    • , James H. Cartwright
    • , Amelia Weber Hall
    • , Gardar Sveinbjornsson
    • , Nathan R. Tucker
    • , Seung Hoan Choi
    • , Mark D. Chaffin
    • , Carolina Roselli
    • , Michael R. Barnes
    • , Borbala Mifsud
    • , Helen R. Warren
    • , Caroline Hayward
    • , Jonathan Marten
    • , James J. Cranley
    • , Maria Pina Concas
    • , Paolo Gasparini
    • , Thibaud Boutin
    • , Ivana Kolcic
    • , Ozren Polasek
    • , Igor Rudan
    • , Nathalia M. Araujo
    • , Maria Fernanda Lima-Costa
    • , Antonio Luiz P. Ribeiro
    • , Renan P. Souza
    • , Eduardo Tarazona-Santos
    • , Vilmantas Giedraitis
    • , Erik Ingelsson
    • , Anubha Mahajan
    • , Andrew P. Morris
    • , Fabiola Del Greco M
    • , Luisa Foco
    • , Martin Gögele
    • , Andrew A. Hicks
    • , James P. Cook
    • , Lars Lind
    • , Cecilia M. Lindgren
    • , Johan Sundström
    • , Christopher P. Nelson
    • , Muhammad B. Riaz
    • , Nilesh J. Samani
    • , Gianfranco Sinagra
    • , Sheila Ulivi
    • , Mika Kähönen
    • , Pashupati P. Mishra
    • , Nina Mononen
    • , Kjell Nikus
    • , Mark J. Caulfield
    • , Anna Dominiczak
    • , Sandosh Padmanabhan
    • , May E. Montasser
    • , Jeff R. O’Connell
    • , Kathleen Ryan
    • , Alan R. Shuldiner
    • , Stefanie Aeschbacher
    • , David Conen
    • , Lorenz Risch
    • , Sébastien Thériault
    • , Nina Hutri-Kähönen
    • , Terho Lehtimäki
    • , Leo-Pekka Lyytikäinen
    • , Olli T. Raitakari
    • , Catriona L. K. Barnes
    • , Harry Campbell
    • , Peter K. Joshi
    • , James F. Wilson
    • , Aaron Isaacs
    • , Jan A. Kors
    • , Cornelia M. van Duijn
    • , Paul L. Huang
    • , Vilmundur Gudnason
    • , Tamara B. Harris
    • , Lenore J. Launer
    • , Albert V. Smith
    • , Erwin P. Bottinger
    • , Ruth J. F. Loos
    • , Girish N. Nadkarni
    • , Michael H. Preuss
    • , Adolfo Correa
    • , Hao Mei
    • , James Wilson
    • , Thomas Meitinger
    • , Martina Müller-Nurasyid
    • , Annette Peters
    • , Melanie Waldenberger
    • , Massimo Mangino
    • , Timothy D. Spector
    • , Michiel Rienstra
    • , Yordi J. van de Vegte
    • , Pim van der Harst
    • , Niek Verweij
    • , Stefan Kääb
    • , Katharina Schramm
    • , Moritz F. Sinner
    • , Konstantin Strauch
    • , Michael J. Cutler
    • , Diane Fatkin
    • , Barry London
    • , Morten Olesen
    • , Dan M. Roden
    • , M. Benjamin Shoemaker
    • , J. Gustav Smith
    • , Mary L. Biggs
    • , Joshua C. Bis
    • , Jennifer A. Brody
    • , Bruce M. Psaty
    • , Kenneth Rice
    • , Nona Sotoodehnia
    • , Alessandro De Grandi
    • , Christian Fuchsberger
    • , Cristian Pattaro
    • , Peter P. Pramstaller
    • , Ian Ford
    • , J. Wouter Jukema
    • , Peter W. Macfarlane
    • , Stella Trompet
    • , Marcus Dörr
    • , Stephan B. Felix
    • , Uwe Völker
    • , Stefan Weiss
    • , Aki S. Havulinna
    • , Antti Jula
    • , Katri Sääksjärvi
    • , Veikko Salomaa
    • , Xiuqing Guo
    • , Susan R. Heckbert
    • , Henry J. Lin
    • , Jerome I. Rotter
    • , Kent D. Taylor
    • , Jie Yao
    • , Renée de Mutsert
    • , Arie C. Maan
    • , Dennis O. Mook-Kanamori
    • , Raymond Noordam
    • , Francesco Cucca
    • , Jun Ding
    • , Edward G. Lakatta
    • , Yong Qian
    • , Kirill V. Tarasov
    • , Daniel Levy
    • , Honghuang Lin
    • , Christopher H. Newton-Cheh
    • , Kathryn L. Lunetta
    • , Alison D. Murray
    • , David J. Porteous
    • , Blair H. Smith
    • , Bruno H. Stricker
    • , André Uitterlinden
    • , Marten E. van den Berg
    • , Jeffrey Haessler
    • , Rebecca D. Jackson
    • , Charles Kooperberg
    • , Ulrike Peters
    • , Alexander P. Reiner
    • , Eric A. Whitsel
    • , Alvaro Alonso
    • , Dan E. Arking
    • , Eric Boerwinkle
    • , Georg B. Ehret
    • , Elsayed Z. Soliman
    • , Christy L. Avery
    • , Stephanie M. Gogarten
    • , Kathleen F. Kerr
    • , Cathy C. Laurie
    • , Amanda A. Seyerle
    • , Adrienne Stilp
    • , Solmaz Assa
    • , M. Abdullah Said
    • , M. Yldau van der Ende
    • , Pier D. Lambiase
    • , Michele Orini
    • , Julia Ramirez
    • , Stefan Van Duijvenboden
    • , David O. Arnar
    • , Daniel F. Gudbjartsson
    • , Hilma Holm
    • , Patrick Sulem
    • , Gudmar Thorleifsson
    • , Rosa B. Thorolfsdottir
    • , Unnur Thorsteinsdottir
    • , Emelia J. Benjamin
    • , Andrew Tinker
    • , Kari Stefansson
    • , Patrick T. Ellinor
    • , Yalda Jamshidi
    • , Steven A. Lubitz
    •  & Patricia B. Munroe
  • Article
    | Open Access

    In tumors, hundreds of genes can undergo loss of heterozygosity (LOH). Here, the authors investigate the potential for this LOH as a class of non-driver cancer vulnerabilities.

    • Caitlin A. Nichols
    • , William J. Gibson
    • , Meredith S. Brown
    • , Jack A. Kosmicki
    • , John P. Busanovich
    • , Hope Wei
    • , Laura M. Urbanski
    • , Naomi Curimjee
    • , Ashton C. Berger
    • , Galen F. Gao
    • , Andrew D. Cherniack
    • , Sirano Dhe-Paganon
    • , Brenton R. Paolella
    •  & Rameen Beroukhim
  • Article
    | Open Access

    Pioneer factors direct cell fate through switching inaccessible chromatin to an accessible state at specific target enhancers. Here the authors show that HOX13 transcription factors have a pioneer activity which is required for the proper implementation of the distal limb developmental program.

    • Ines Desanlis
    • , Yacine Kherdjemil
    • , Alexandre Mayran
    • , Yasser Bouklouch
    • , Claudia Gentile
    • , Rushikesh Sheth
    • , Rolf Zeller
    • , Jacques Drouin
    •  & Marie Kmita
  • Article
    | Open Access

    The increasing amount of sequenced microbial genomes and metagenomes requires platforms for efficient integrated analysis. Here, Asnicar et al. present PhyloPhlAn 3.0, a pipeline allowing large-scale microbial genome characterization and phylogenetic contextualization at multiple levels of resolution.

    • Francesco Asnicar
    • , Andrew Maltez Thomas
    • , Francesco Beghini
    • , Claudia Mengoni
    • , Serena Manara
    • , Paolo Manghi
    • , Qiyun Zhu
    • , Mattia Bolzan
    • , Fabio Cumbo
    • , Uyen May
    • , Jon G. Sanders
    • , Moreno Zolfo
    • , Evguenia Kopylova
    • , Edoardo Pasolli
    • , Rob Knight
    • , Siavash Mirarab
    • , Curtis Huttenhower
    •  & Nicola Segata
  • Article
    | Open Access

    Alfalfa is an important forage crop, but genetic improvement is challenging due to the lack of a reference genome and an efficient genome editing protocol. Here, the authors report the chromosome-level assembly of the autotetraploid genome and a CRISPR/Cas9-based transgene-free genome editing protocol.

    • Haitao Chen
    • , Yan Zeng
    • , Yongzhi Yang
    • , Lingli Huang
    • , Bolin Tang
    • , He Zhang
    • , Fei Hao
    • , Wei Liu
    • , Youhan Li
    • , Yanbin Liu
    • , Xiaoshuang Zhang
    • , Ru Zhang
    • , Yesheng Zhang
    • , Yongxin Li
    • , Kun Wang
    • , Hua He
    • , Zhongkai Wang
    • , Guangyi Fan
    • , Hui Yang
    • , Aike Bao
    • , Zhanhuan Shang
    • , Jianghua Chen
    • , Wen Wang
    •  & Qiang Qiu
  • Article
    | Open Access

    Somatic and germline mutations are found at different densities across the genome. Here, the authors compare human somatic tumour mutations with the germline of humans, chimpanzees, and gorillas, and find that the mutation density of tumours correlates better with non-human great apes than with the human germline.

    • José María Heredia-Genestar
    • , Tomàs Marquès-Bonet
    • , David Juan
    •  & Arcadi Navarro
  • Article
    | Open Access

    Genetic changes acquired during in vitro culture pose a challenge to application of stem cells. Here the authors use whole genome sequencing to show that cultured human adult and pluripotent stem cells have a high mutational load caused by oxidative stress and reduced oxygen tension in culture lowers mutation rates.

    • Ewart Kuijk
    • , Myrthe Jager
    • , Bastiaan van der Roest
    • , Mauro D. Locati
    • , Arne Van Hoeck
    • , Jerome Korzelius
    • , Roel Janssen
    • , Nicolle Besselink
    • , Sander Boymans
    • , Ruben van Boxtel
    •  & Edwin Cuppen
  • Article
    | Open Access

    The genetic basis of prolactinomas remains poorly understood. Here, the authors find a recurrent hotspot somatic mutation in the splicing factor 3 subunit B1 (SF3B1R625H) in prolactinomas, and show that this mutation causes aberrant splicing of ESRRG mRNA leading to up-regulation of prolactin.

    • Chuzhong Li
    • , Weiyan Xie
    • , Jared S. Rosenblum
    • , Jianyu Zhou
    • , Jing Guo
    • , Yazhou Miao
    • , Yutao Shen
    • , Hongyun Wang
    • , Lei Gong
    • , Mingxuan Li
    • , Sida Zhao
    • , Sen Cheng
    • , Haibo Zhu
    • , Tao Jiang
    • , Shiying Ling
    • , Fei Wang
    • , Hongwei Zhang
    • , Mingshan Zhang
    • , Yanming Qu
    • , Qi Zhang
    • , Guilin Li
    • , Junmei Wang
    • , Jun Ma
    • , Zhengping Zhuang
    •  & Yazhuo Zhang
  • Article
    | Open Access

    Characterization of the distance over which TF binding influences gene expression is important for inferring target genes. Here the authors study this relationship using thousands of genomic data sets, finding two classes of TFs with distinct ranges of regulatory influence modulated by chromatin states of topologically associated domains.

    • Chen-Hao Chen
    • , Rongbin Zheng
    • , Collin Tokheim
    • , Xin Dong
    • , Jingyu Fan
    • , Changxin Wan
    • , Qin Tang
    • , Myles Brown
    • , Jun S. Liu
    • , Clifford A. Meyer
    •  & X. Shirley Liu
  • Article
    | Open Access

    TRANSPARENT TESTA19 (TT19) encodes a glutathione S-transferase which functions in anthocyanin stabilization and vacuolar transport. Here, by tt19 suppressor screening, the authors show that RDR6/SGS3/DCL4 siRNA pathway constituents synergistically interact with components of the flavonoid pathway to control carbon metabolism.

    • Nan Jiang
    • , Aimer Gutierrez-Diaz
    • , Eric Mukundi
    • , Yun Sun Lee
    • , Blake C. Meyers
    • , Marisa S. Otegui
    •  & Erich Grotewold
  • Article
    | Open Access

    In fission yeast, several lncRNAs act in cis to regulate expression of adjacent genes. Here, the authors show that the conserved Pir2ARS2 protein is targeted, along with splicing factors, to cryptic introns in lncRNAs and recruits effectors, including RNAi machinery, for gene repression.

    • Gobi Thillainadesan
    • , Hua Xiao
    • , Sahana Holla
    • , Jothy Dhakshnamoorthy
    • , Lisa M. Miller Jenkins
    • , David Wheeler
    •  & Shiv I. S. Grewal
  • Article
    | Open Access

    Most human protein-coding genes are expressed as multiple isoforms. Here the authors present ORF Capture-seq that uses cloned ORFs as probes to capture and sequence full length transcript sequences. This enables highly sensitive characterization of eukaryotic transcriptomes.

    • Gloria M. Sheynkman
    • , Katharine S. Tuttle
    • , Florent Laval
    • , Elizabeth Tseng
    • , Jason G. Underwood
    • , Liang Yu
    • , Da Dong
    • , Melissa L. Smith
    • , Robert Sebra
    • , Luc Willems
    • , Tong Hao
    • , Michael A. Calderwood
    • , David E. Hill
    •  & Marc Vidal
  • Article
    | Open Access

    In lung cancer, relatively few germline mutations are known to impact risk. Here the authors looked at rare variants in 39,146 individuals and find novel germline mutations associated with risk, as well as implicating ATM and a new candidate gene for lung cancer risk.

    • Xuemei Ji
    • , Semanti Mukherjee
    • , Maria Teresa Landi
    • , Yohan Bosse
    • , Philippe Joubert
    • , Dakai Zhu
    • , Ivan Gorlov
    • , Xiangjun Xiao
    • , Younghun Han
    • , Olga Gorlova
    • , Rayjean J. Hung
    • , Yonathan Brhane
    • , Robert Carreras-Torres
    • , David C. Christiani
    • , Neil Caporaso
    • , Mattias Johansson
    • , Geoffrey Liu
    • , Stig E. Bojesen
    • , Loic Le Marchand
    • , Demetrios Albanes
    • , Heike Bickeböller
    • , Melinda C. Aldrich
    • , William S. Bush
    • , Adonina Tardon
    • , Gad Rennert
    • , Chu Chen
    • , Jinyoung Byun
    • , Konstantin H. Dragnev
    • , John K. Field
    • , Lambertus FA. Kiemeney
    • , Philip Lazarus
    • , Shan Zienolddiny
    • , Stephen Lam
    • , Matthew B. Schabath
    • , Angeline S. Andrew
    • , Pier A. Bertazzi
    • , Angela C. Pesatori
    • , Nancy Diao
    • , Li Su
    • , Lei Song
    • , Ruyang Zhang
    • , Natasha Leighl
    • , Jakob S. Johansen
    • , Anders Mellemgaard
    • , Walid Saliba
    • , Christopher Haiman
    • , Lynne Wilkens
    • , Ana Fernandez-Somoano
    • , Guillermo Fernandez-Tardon
    • , Erik H. F. M. van der Heijden
    • , Jin Hee Kim
    • , Michael P. A. Davies
    • , Michael W. Marcus
    • , Hans Brunnström
    • , Jonas Manjer
    • , Olle Melander
    • , David C. Muller
    • , Kim Overvad
    • , Antonia Trichopoulou
    • , Rosario Tumino
    • , Gary E. Goodman
    • , Angela Cox
    • , Fiona Taylor
    • , Penella Woll
    • , Erich Wichmann
    • , Thomas Muley
    • , Angela Risch
    • , Albert Rosenberger
    • , Kjell Grankvist
    • , Mikael Johansson
    • , Frances Shepherd
    • , Ming-Sound Tsao
    • , Susanne M. Arnold
    • , Eric B. Haura
    • , Ciprian Bolca
    • , Ivana Holcatova
    • , Vladimir Janout
    • , Milica Kontic
    • , Jolanta Lissowska
    • , Anush Mukeria
    • , Simona Ognjanovic
    • , Tadeusz M. Orlowski
    • , Ghislaine Scelo
    • , Beata Swiatkowska
    • , David Zaridze
    • , Per Bakke
    • , Vidar Skaug
    • , Lesley M. Butler
    • , Kenneth Offit
    • , Preethi Srinivasan
    • , Chaitanya Bandlamudi
    • , Matthew D. Hellmann
    • , David B. Solit
    • , Mark E. Robson
    • , Charles M. Rudin
    • , Zsofia K. Stadler
    • , Barry S. Taylor
    • , Michael F. Berger
    • , Richard Houlston
    • , John McLaughlin
    • , Victoria Stevens
    • , David C. Nickle
    • , Ma’en Obeidat
    • , Wim Timens
    • , María Soler Artigas
    • , Sanjay Shete
    • , Hermann Brenner
    • , Stephen Chanock
    • , Paul Brennan
    • , James D. McKay
    •  & Christopher I. Amos
  • Article
    | Open Access

    Horseshoe crabs have been morphologically stable across evolutionary time. Here, the authors generate a chromosome-level assembly for the mangrove horseshoe crab, with implications for innate immunity, and challenging assumptions about the role of genome duplication in adaptive radiation.

    • Prashant Shingate
    • , Vydianathan Ravi
    • , Aravind Prasad
    • , Boon-Hui Tay
    • , Kritika M. Garg
    • , Balaji Chattopadhyay
    • , Laura-Marie Yap
    • , Frank E. Rheindt
    •  & Byrappa Venkatesh
  • Article
    | Open Access

    Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.

    • Shujun Ou
    • , Jianing Liu
    • , Kapeel M. Chougule
    • , Arkarachai Fungtammasan
    • , Arun S. Seetharam
    • , Joshua C. Stein
    • , Victor Llaca
    • , Nancy Manchanda
    • , Amanda M. Gilbert
    • , Sharon Wei
    • , Chen-Shan Chin
    • , David E. Hufnagel
    • , Sarah Pedersen
    • , Samantha J. Snodgrass
    • , Kevin Fengler
    • , Margaret Woodhouse
    • , Brian P. Walenz
    • , Sergey Koren
    • , Adam M. Phillippy
    • , Brett T. Hannigan
    • , R. Kelly Dawe
    • , Candice N. Hirsch
    • , Matthew B. Hufford
    •  & Doreen Ware
  • Article
    | Open Access

    Depression is correlated with many brain-related traits. Here, Shen et al. perform phenome-wide association studies of a depression polygenic risk score (PRS) and find associations with 51 behavioural and 26 neuroimaging traits which are further followed up on using Mendelian randomization and mediation analyses.

    • Xueyi Shen
    • , David M. Howard
    • , Mark J. Adams
    • , W. David Hill
    • , Toni-Kim Clarke
    • , Mark J. Adams
    • , Toni-Kim Clarke
    • , Andrew M. McIntosh
    • , Ian J. Deary
    • , Naomi R. Wray
    • , Stephan Ripke
    • , Manuel Mattheisen
    • , Maciej Trzaskowski
    • , Enda M. Byrne
    • , Abdel Abdellaoui
    • , Esben Agerbo
    • , Tracy M. Air
    • , Till F. M. Andlauer
    • , Silviu-Alin Bacanu
    • , Marie Bækvad-Hansen
    • , Aartjan T. F. Beekman
    • , Tim B. Bigdeli
    • , Elisabeth B. Binder
    • , Julien Bryois
    • , Henriette N. Buttenschøn
    • , Jonas Bybjerg-Grauholm
    • , Na Cai
    • , Enrique Castelao
    • , Jane Hvarregaard Christensen
    • , Jonathan R. I. Coleman
    • , Lucía Colodro-Conde
    • , Baptiste Couvy-Duchesne
    • , Nick Craddock
    • , Gregory E. Crawford
    • , Gail Davies
    • , Franziska Degenhardt
    • , Eske M. Derks
    • , Nese Direk
    • , Conor V. Dolan
    • , Erin C. Dunn
    • , Thalia C. Eley
    • , Valentina Escott-Price
    • , Farnush Farhadi Hassan Kiadeh
    • , Hilary K. Finucane
    • , Jerome C. Foo
    • , Andreas J. Forstner
    • , Josef Frank
    • , Héléna A. Gaspar
    • , Michael Gill
    • , Fernando S. Goes
    • , Scott D. Gordon
    • , Jakob Grove
    • , Lynsey S. Hall
    • , Christine Søholm Hansen
    • , Thomas F. Hansen
    • , Stefan Herms
    • , Ian B. Hickie
    • , Per Hoffmann
    • , Georg Homuth
    • , Carsten Horn
    • , Jouke-Jan Hottenga
    • , David M. Hougaard
    • , David M. Howard
    • , Marcus Ising
    • , Rick Jansen
    • , Ian Jones
    • , Lisa A. Jones
    • , Eric Jorgenson
    • , James A. Knowles
    • , Isaac S. Kohane
    • , Julia Kraft
    • , Warren W. Kretzschmar
    • , Zoltán Kutalik
    • , Yihan Li
    • , Penelope A. Lind
    • , Donald J. MacIntyre
    • , Dean F. MacKinnon
    • , Robert M. Maier
    • , Wolfgang Maier
    • , Jonathan Marchini
    • , Hamdi Mbarek
    • , Patrick McGrath
    • , Peter McGuffin
    • , Sarah E. Medland
    • , Divya Mehta
    • , Christel M. Middeldorp
    • , Evelin Mihailov
    • , Yuri Milaneschi
    • , Lili Milani
    • , Francis M. Mondimore
    • , Grant W. Montgomery
    • , Sara Mostafavi
    • , Niamh Mullins
    • , Matthias Nauck
    • , Bernard Ng
    • , Michel G. Nivard
    • , Dale R. Nyholt
    • , Paul F. O’Reilly
    • , Hogni Oskarsson
    • , Michael J. Owen
    • , Jodie N. Painter
    • , Carsten Bøcker Pedersen
    • , Marianne Giørtz Pedersen
    • , Roseann E. Peterson
    • , Erik Pettersson
    • , Wouter J. Peyrot
    • , Giorgio Pistis
    • , Danielle Posthuma
    • , Jorge A. Quiroz
    • , Per Qvist
    • , John P. Rice
    • , Brien P. Riley
    • , Margarita Rivera
    • , Saira Saeed Mirza
    • , Robert Schoevers
    • , Eva C. Schulte
    • , Ling Shen
    • , Jianxin Shi
    • , Stanley I. Shyn
    • , Engilbert Sigurdsson
    • , Grant C. B. Sinnamon
    • , Johannes H. Smit
    • , Daniel J. Smith
    • , Hreinn Stefansson
    • , Stacy Steinberg
    • , Fabian Streit
    • , Jana Strohmaier
    • , Katherine E. Tansey
    • , Henning Teismann
    • , Alexander Teumer
    • , Wesley Thompson
    • , Pippa A. Thomson
    • , Thorgeir E. Thorgeirsson
    • , Matthew Traylor
    • , Jens Treutlein
    • , Vassily Trubetskoy
    • , Andrés G. Uitterlinden
    • , Daniel Umbricht
    • , Sandra Van der Auwera
    • , Albert M. van Hemert
    • , Alexander Viktorin
    • , Peter M. Visscher
    • , Yunpeng Wang
    • , Bradley T. Webb
    • , Shantel Marie Weinsheimer
    • , Jürgen Wellmann
    • , Gonneke Willemsen
    • , Stephanie H. Witt
    • , Yang Wu
    • , Hualin S. Xi
    • , Jian Yang
    • , Futao Zhang
    • , Volker Arolt
    • , Bernhard T. Baune
    • , Klaus Berger
    • , Dorret I. Boomsma
    • , Sven Cichon
    • , Udo Dannlowski
    • , E. J. C. de Geus
    • , J. Raymond DePaulo
    • , Enrico Domenici
    • , Katharina Domschke
    • , Tõnu Esko
    • , Hans J. Grabe
    • , Steven P. Hamilton
    • , Caroline Hayward
    • , Andrew C. Heath
    • , Kenneth S. Kendler
    • , Stefan Kloiber
    • , Glyn Lewis
    • , Qingqin S. Li
    • , Susanne Lucae
    • , Pamela A. F. Madden
    • , Patrik K. Magnusson
    • , Nicholas G. Martin
    • , Andres Metspalu
    • , Ole Mors
    • , Preben Bo Mortensen
    • , Bertram Müller-Myhsok
    • , Merete Nordentoft
    • , Markus M. Nöthen
    • , Michael C. O’Donovan
    • , Sara A. Paciga
    • , Nancy L. Pedersen
    • , Brenda W. J. H. Penninx
    • , Roy H. Perlis
    • , David J. Porteous
    • , James B. Potash
    • , Martin Preisig
    • , Marcella Rietschel
    • , Catherine Schaefer
    • , Thomas G. Schulze
    • , Jordan W. Smoller
    • , Kari Stefansson
    • , Henning Tiemeier
    • , Rudolf Uher
    • , Henry Völzke
    • , Myrna M. Weissman
    • , Thomas Werge
    • , Cathryn M. Lewis
    • , Douglas F. Levinson
    • , Gerome Breen
    • , Anders D. Børglum
    • , Patrick F. Sullivan
    • , Ian J. Deary
    • , Heather C. Whalley
    •  & Andrew M. McIntosh
  • Article
    | Open Access

    The diamondback moth, Plutella xylostella is a cosmopolitan agricultural pest. By analyzing 532 genomes from 114 populations around the world, the authors find evidence supporting a South American origin of this moth, and look for signatures of positive selection.

    • Minsheng You
    • , Fushi Ke
    • , Shijun You
    • , Zhangyan Wu
    • , Qingfeng Liu
    • , Weiyi He
    • , Simon W. Baxter
    • , Zhiguang Yuchi
    • , Liette Vasseur
    • , Geoff M. Gurr
    • , Christopher M. Ward
    • , Hugo Cerda
    • , Guang Yang
    • , Lu Peng
    • , Yuanchun Jin
    • , Miao Xie
    • , Lijun Cai
    • , Carl J. Douglas
    • , Murray B. Isman
    • , Mark S. Goettel
    • , Qisheng Song
    • , Qinghai Fan
    • , Gefu Wang-Pruski
    • , David C. Lees
    • , Zhen Yue
    • , Jianlin Bai
    • , Tiansheng Liu
    • , Lianyun Lin
    • , Yunkai Zheng
    • , Zhaohua Zeng
    • , Sheng Lin
    • , Yue Wang
    • , Qian Zhao
    • , Xiaofeng Xia
    • , Wenbin Chen
    • , Lilin Chen
    • , Mingmin Zou
    • , Jinying Liao
    • , Qiang Gao
    • , Xiaodong Fang
    • , Ye Yin
    • , Huanming Yang
    • , Jian Wang
    • , Liwei Han
    • , Yingjun Lin
    • , Yanping Lu
    •  & Mousheng Zhuang
  • Article
    | Open Access

    The DNA methyltransferase DNMT3A plays an important role in establishing the DNA methylation patterns during development and deregulation of DNMT3A is associated with hematological cancers, with the R882H mutation the most frequently occurring DNMT3A missense mutation in acute myeloid leukemia. Here, the authors present the crystal structures of wild-type and R882H DNMT3A in complex with different DNA substrates and explain why the R882H mutation compromises the enzymatic activity of DNMT3A.

    • Hiwot Anteneh
    • , Jian Fang
    •  & Jikui Song
  • Article
    | Open Access

    The shattering of chromosomes is a dramatic early event in tumourigenesis and is termed chromothripsis. Here, the authors examine chromothripsis across 28 tumour types and show that 49% of cancers exhibit features of chromothripsis.

    • Natalia Voronina
    • , John K. L. Wong
    • , Daniel Hübschmann
    • , Mario Hlevnjak
    • , Sebastian Uhrig
    • , Christoph E. Heilig
    • , Peter Horak
    • , Simon Kreutzfeldt
    • , Andreas Mock
    • , Albrecht Stenzinger
    • , Barbara Hutter
    • , Martina Fröhlich
    • , Benedikt Brors
    • , Arne Jahn
    • , Barbara Klink
    • , Laura Gieldon
    • , Lina Sieverling
    • , Lars Feuerbach
    • , Priya Chudasama
    • , Katja Beck
    • , Matthias Kroiss
    • , Christoph Heining
    • , Lino Möhrmann
    • , Andrea Fischer
    • , Evelin Schröck
    • , Hanno Glimm
    • , Marc Zapatka
    • , Peter Lichter
    • , Stefan Fröhling
    •  & Aurélie Ernst
  • Article
    | Open Access

    The MOF acetyltransferase-containing Non-Specific Lethal (NSL) complex is a broad transcription regulator and haploinsufficiency of its KANSL1 subunit results in the Koolen-de Vries syndrome in humans. Here, the authors identify the BET protein BRD4 as evolutionary conserved co-factor of the NSL complex and provide evidence that NSL-deposited histone acetylation induces BRD4 recruitment for transcription of constitutively active genes.

    • Aline Gaub
    • , Bilal N. Sheikh
    • , M. Felicia Basilicata
    • , Marie Vincent
    • , Mathilde Nizon
    • , Cindy Colson
    • , Matthew J. Bird
    • , James E. Bradner
    • , Julien Thevenon
    • , Michael Boutros
    •  & Asifa Akhtar
  • Article
    | Open Access

    Structural changes to the left ventricle are characteristic of dilated cardiomyopathy (DCM), a disease for which many rare genetic variants are known. Here, Pirruccello et al. report GWAS of seven cardiac MRI measurements in the left ventricle and describe shared loci and polygenic association with DCM.

    • James P. Pirruccello
    • , Alexander Bick
    • , Minxian Wang
    • , Mark Chaffin
    • , Samuel Friedman
    • , Jie Yao
    • , Xiuqing Guo
    • , Bharath Ambale Venkatesh
    • , Kent D. Taylor
    • , Wendy S. Post
    • , Stephen Rich
    • , Joao A. C. Lima
    • , Jerome I. Rotter
    • , Anthony Philippakis
    • , Steven A. Lubitz
    • , Patrick T. Ellinor
    • , Amit V. Khera
    • , Sekar Kathiresan
    •  & Krishna G. Aragam