Browse Articles

  • Editorial |

    Gene nomenclature can be complicated, and the official naming of genes requires rational standards to avoid confusion and to maximize clarity. The HUGO Gene Nomenclature Committee has released updated guidelines for the naming of human genes, and we encourage the community to adopt these recommendations.

  • Comment |

    Standardized gene naming is crucial for effective communication about genes, and as genomics becomes increasingly important in health care, the need for a consistent language to refer to human genes becomes ever more essential. Here, we present the current HUGO Gene Nomenclature Committee (HGNC) guidelines for naming not only protein-coding genes but also RNA genes and pseudogenes, and we outline the changes in approach and ethos that have resulted from the discoveries of the past few decades.

    • Elspeth A. Bruford
    • , Bryony Braschi
    • , Paul Denny
    • , Tamsin E. M. Jones
    • , Ruth L. Seal
    •  & Susan Tweedie
  • News & Views |

    Genomes are highly organized in space and time. Compartments, topologically associating domains (TADs) and loops are three dimensional (3D) genome features that have been extensively studied. Among these three levels of organization, TADs have sparked the most debate. New microscopy data shed light on how TADs and their leaky borders contribute to gene regulation.

    • Irene Farabella
    •  & Marc A. Marti-Renom
  • Article |

    Genomic analysis of 118 cervical tumors from Ugandan individuals identifies HPV-clade-specific differences in tumor DNA methylation, regulatory-region-associated histone marks, gene expression and pathway dysregulation.

    • Alessia Gagliardi
    • , Vanessa L. Porter
    • , Zusheng Zong
    • , Reanne Bowlby
    • , Emma Titmuss
    • , Constance Namirembe
    • , Nicholas B. Griner
    • , Hilary Petrello
    • , Jay Bowen
    • , Simon K. Chan
    • , Luka Culibrk
    • , Teresa M. Darragh
    • , Mark H. Stoler
    • , Thomas C. Wright
    • , Patee Gesuwan
    • , Maureen A. Dyer
    • , Yussanne Ma
    • , Karen L. Mungall
    • , Steven J. M. Jones
    • , Carolyn Nakisige
    • , Karen Novik
    • , Jackson Orem
    • , Martin Origa
    • , Julie M. Gastier-Foster
    • , Robert Yarchoan
    • , Corey Casper
    • , Gordon B. Mills
    • , Janet S. Rader
    • , Akinyemi I. Ojesina
    • , Daniela S. Gerhard
    • , Andrew J. Mungall
    •  & Marco A. Marra
  • Letter |

    Quantitative ChIP–seq analysis maps G-quadruplex (G4) DNA structures in breast cancer patient-derived tumor xenograft (PDTX) models. G4-based subtypes highlight additional tumor heterogeneity in the integrative cluster (IC) system.

    • Robert Hänsel-Hertsch
    • , Angela Simeone
    • , Abigail Shea
    • , Winnie W. I. Hui
    • , Katherine G. Zyner
    • , Giovanni Marsico
    • , Oscar M. Rueda
    • , Alejandra Bruna
    • , Alistair Martin
    • , Xiaoyun Zhang
    • , Santosh Adhikari
    • , David Tannahill
    • , Carlos Caldas
    •  & Shankar Balasubramanian
  • Article
    | Open Access

    De novo genome assemblies of four European flint maize lines and comparison with two US Corn Belt genomes provide insights into the dynamics of intraspecies variation in repeat and gene content in maize genomes.

    • Georg Haberer
    • , Nadia Kamal
    • , Eva Bauer
    • , Heidrun Gundlach
    • , Iris Fischer
    • , Michael A. Seidel
    • , Manuel Spannagl
    • , Caroline Marcon
    • , Alevtina Ruban
    • , Claude Urbany
    • , Adnane Nemri
    • , Frank Hochholdinger
    • , Milena Ouzunova
    • , Andreas Houben
    • , Chris-Carolin Schön
    •  & Klaus F. X. Mayer
  • Letter |

    Nucleic acid processing by the cytoplasmic exonuclease TREX1 and cytosine editing by APOBEC3B drive chromothripsis and kataegis during telomere crisis.

    • John Maciejowski
    • , Aikaterini Chatzipli
    • , Alexandra Dananberg
    • , Kevan Chu
    • , Eleonore Toufektchan
    • , Leszek J. Klimczak
    • , Dmitry A. Gordenin
    • , Peter J. Campbell
    •  & Titia de Lange
  • Article |

    Genome-wide analysis of 3D chromatin topologies across gastric cancers suggests that Epstein–Barr virus infection may induce the epigenetic rewiring of EBV-positive tumors through human–viral chromatin interactions, a phenomenon termed ‘enhancer infestation’.

    • Atsushi Okabe
    • , Kie Kyon Huang
    • , Keisuke Matsusaka
    • , Masaki Fukuyo
    • , Manjie Xing
    • , Xuewen Ong
    • , Takayuki Hoshii
    • , Genki Usui
    • , Motoaki Seki
    • , Yasunobu Mano
    • , Bahityar Rahmutulla
    • , Teru Kanda
    • , Takayoshi Suzuki
    • , Sun Young Rha
    • , Tetsuo Ushiku
    • , Masashi Fukayama
    • , Patrick Tan
    •  & Atsushi Kaneda
  • Perspective |

    This Perspective discusses the need for mechanistic and quantitative understanding of the ecological and evolutionary dynamics of tumor growth to inform strategies for earlier detection, diagnosis and treatment of cancer.

    • Nastaran Zahir
    • , Ruping Sun
    • , Daniel Gallahan
    • , Robert A. Gatenby
    •  & Christina Curtis
  • Article |

    Analyses of epigenomic datasets spanning transitions from normal prostate epithelium to localized prostate cancer to metastases show that latent developmental programs are reactivated in metastatic disease and that prostate lineage-specific regulatory elements are strongly enriched for prostate cancer risk heritability.

    • Mark M. Pomerantz
    • , Xintao Qiu
    • , Yanyun Zhu
    • , David Y. Takeda
    • , Wenting Pan
    • , Sylvan C. Baca
    • , Alexander Gusev
    • , Keegan D. Korthauer
    • , Tesa M. Severson
    • , Gavin Ha
    • , Srinivas R. Viswanathan
    • , Ji-Heui Seo
    • , Holly M. Nguyen
    • , Baohui Zhang
    • , Bogdan Pasaniuc
    • , Claudia Giambartolomei
    • , Sarah A. Alaiwi
    • , Connor A. Bell
    • , Edward P. O’Connor
    • , Matthew S. Chabot
    • , David R. Stillman
    • , Rosina Lis
    • , Alba Font-Tello
    • , Lewyn Li
    • , Paloma Cejas
    • , Andries M. Bergman
    • , Joyce Sanders
    • , Henk G. van der Poel
    • , Simon A. Gayther
    • , Kate Lawrenson
    • , Marcos A. S. Fonseca
    • , Jessica Reddy
    • , Rosario I. Corona
    • , Gleb Martovetsky
    • , Brian Egan
    • , Toni Choueiri
    • , Leigh Ellis
    • , Isla P. Garraway
    • , Gwo-Shu Mary Lee
    • , Eva Corey
    • , Henry W. Long
    • , Wilbert Zwart
    •  & Matthew L. Freedman
  • Article |

    Cells lacking TET proteins and DNMT3A and DNMT3B show that DNMT1 has imprecise maintenance activity and weak de novo activity leading to spontaneous ‘epimutations’. These epimutations can be corrected through a neighbor-guided mechanism.

    • Qiujun Wang
    • , Guang Yu
    • , Xuan Ming
    • , Weikun Xia
    • , Xiguang Xu
    • , Yu Zhang
    • , Wenhao Zhang
    • , Yuanyuan Li
    • , Chunyi Huang
    • , Hehuang Xie
    • , Bing Zhu
    •  & Wei Xie
  • Article |

    Whole-genome bisulfite sequencing along with whole-genome and transcriptome sequencing of 100 prostate cancer metastases identifies genomic regions that are differentially methylated during disease progression and a novel epigenomic subtype.

    • Shuang G. Zhao
    • , William S. Chen
    • , Haolong Li
    • , Adam Foye
    • , Meng Zhang
    • , Martin Sjöström
    • , Rahul Aggarwal
    • , Denise Playdle
    • , Arnold Liao
    • , Joshi J. Alumkal
    • , Rajdeep Das
    • , Jonathan Chou
    • , Junjie T. Hua
    • , Travis J. Barnard
    • , Adina M. Bailey
    • , Eric D. Chow
    • , Marc D. Perry
    • , Ha X. Dang
    • , Rendong Yang
    • , Ruhollah Moussavi-Baygi
    • , Li Zhang
    • , Mohammed Alshalalfa
    • , S. Laura Chang
    • , Kathleen E. Houlahan
    • , Yu-Jia Shiah
    • , Tomasz M. Beer
    • , George Thomas
    • , Kim N. Chi
    • , Martin Gleave
    • , Amina Zoubeidi
    • , Robert E. Reiter
    • , Matthew B. Rettig
    • , Owen Witte
    • , M. Yvonne Kim
    • , Lawrence Fong
    • , Daniel E. Spratt
    • , Todd M. Morgan
    • , Rohit Bose
    • , Franklin W. Huang
    • , Hui Li
    • , Lisa Chesner
    • , Tanushree Shenoy
    • , Hani Goodarzi
    • , Irfan A. Asangani
    • , Shahneen Sandhu
    • , Joshua M. Lang
    • , Nupam P. Mahajan
    • , Primo N. Lara
    • , Christopher P. Evans
    • , Phillip Febbo
    • , Serafim Batzoglou
    • , Karen E. Knudsen
    • , Housheng H. He
    • , Jiaoti Huang
    • , Wilbert Zwart
    • , Joseph F. Costello
    • , Jianhua Luo
    • , Scott A. Tomlins
    • , Alexander W. Wyatt
    • , Scott M. Dehm
    • , Alan Ashworth
    • , Luke A. Gilbert
    • , Paul C. Boutros
    • , Kyle Farh
    • , Arul M. Chinnaiyan
    • , Christopher A. Maher
    • , Eric J. Small
    • , David A. Quigley
    •  & Felix Y. Feng
  • Editorial |

    When the status quo in science continues to perpetuate ingrained systems of discrimination, inequality and racism, the beneficiaries of these systems must not only reexamine their collective practices but also redress historical injustices through consequential, concrete actions that will lead to change. We cannot focus only on the first steps of listening and learning to build a better, fairer scientific community. We at Nature Genetics fully commit to pledging our energy and efforts toward long-term goals explicitly designed to fundamentally transform how science and its dissemination are conducted.

  • News & Views |

    How ‘difficult’ is it for somatic evolution to produce a cell that is capable of leaving the primary tumor and growing in a distant organ? In this issue, Reiter et al. assess genetic diversity across metastatic lesions and identify a tight selective bottleneck preceding distant metastasis.

    • Trevor A. Graham
    •  & Darryl Shibata
  • Article |

    A new computational method integrates whole-genome sequencing and transcriptomic data to identify regulatory noncoding variants in an individual cancer genome.

    • Yu Liu
    • , Chunliang Li
    • , Shuhong Shen
    • , Xiaolong Chen
    • , Karol Szlachta
    • , Michael N. Edmonson
    • , Ying Shao
    • , Xiaotu Ma
    • , Judith Hyle
    • , Shaela Wright
    • , Bensheng Ju
    • , Michael C. Rusch
    • , Yanling Liu
    • , Benshang Li
    • , Michael Macias
    • , Liqing Tian
    • , John Easton
    • , Maoxiang Qian
    • , Jun J. Yang
    • , Shaoyan Hu
    • , A. Thomas Look
    •  & Jinghui Zhang
  • News & Views |

    Pachytene Piwi-interacting RNAs (piRNAs) are abundant small non-coding RNAs expressed in mammalian germ lines. A new study indicates that, among the diverse pool of piRNA sequences, a small number act as highly selective guides that induce cleavage of coding and non-coding transcripts, thus promoting piRNA generation and regulating gene expression.

    • Alexei A. Aravin
  • Review Article |

    This review discusses major privacy threats relevant to collection and analysis of genomic data in the context of direct-to-consumer applications and provides suggestions for improving the design of privacy-protecting approaches.

    • Luca Bonomi
    • , Yingxiang Huang
    •  & Lucila Ohno-Machado
  • Article |

    Quantitative trait locus (QTL) mapping of N6-methyladenosine (m6A) in human cells highlights the role of RNA-binding proteins, RNA secondary structure and context-dependent m6A effects. m6A QTLs are enriched in loci associated with immune and blood-related traits.

    • Zijie Zhang
    • , Kaixuan Luo
    • , Zhongyu Zou
    • , Maguanyun Qiu
    • , Jiakun Tian
    • , Laura Sieh
    • , Hailing Shi
    • , Yuxin Zou
    • , Gao Wang
    • , Jean Morrison
    • , Allen C. Zhu
    • , Min Qiao
    • , Zhongshan Li
    • , Matthew Stephens
    • , Xin He
    •  & Chuan He
  • Article |

    Computational analyses integrating whole-genome sequencing, cardiac epigenomic data and RNA-binding-protein data identify a role for noncoding de novo mutations in congenital heart disease.

    • Felix Richter
    • , Sarah U. Morton
    • , Seong Won Kim
    • , Alexander Kitaygorodsky
    • , Lauren K. Wasson
    • , Kathleen M. Chen
    • , Jian Zhou
    • , Hongjian Qi
    • , Nihir Patel
    • , Steven R. DePalma
    • , Michael Parfenov
    • , Jason Homsy
    • , Joshua M. Gorham
    • , Kathryn B. Manheimer
    • , Matthew Velinder
    • , Andrew Farrell
    • , Gabor Marth
    • , Eric E. Schadt
    • , Jonathan R. Kaltman
    • , Jane W. Newburger
    • , Alessandro Giardini
    • , Elizabeth Goldmuntz
    • , Martina Brueckner
    • , Richard Kim
    • , George A. Porter Jr.
    • , Daniel Bernstein
    • , Wendy K. Chung
    • , Deepak Srivastava
    • , Martin Tristani-Firouzi
    • , Olga G. Troyanskaya
    • , Diane E. Dickel
    • , Yufeng Shen
    • , Jonathan G. Seidman
    • , Christine E. Seidman
    •  & Bruce D. Gelb
  • Article |

    A combination of super-resolution microscopy and Oligopaint technology shows that TAD boundaries are variable at the single-cell level. Loss of cohesin, in contrast to WAPL or CTCF depletion, reduces interactions across boundaries and alters transcriptional bursting of genes near boundaries.

    • Jennifer M. Luppino
    • , Daniel S. Park
    • , Son C. Nguyen
    • , Yemin Lan
    • , Zhuxuan Xu
    • , Rebecca Yunker
    •  & Eric F. Joyce
  • Article |

    Genome-wide detection of inversions in great ape genomes by using long-read sequencing and single-cell DNA template strand sequencing (Strand-seq) expands the number of known ape inversions and identifies several regions that have recurrently toggled between a direct and an inverted state during primate evolution.

    • David Porubsky
    • , Ashley D. Sanders
    • , Wolfram Höps
    • , PingHsun Hsieh
    • , Arvis Sulovari
    • , Ruiyang Li
    • , Ludovica Mercuri
    • , Melanie Sorensen
    • , Shwetha C. Murali
    • , David Gordon
    • , Stuart Cantsilieris
    • , Alex A. Pollen
    • , Mario Ventura
    • , Francesca Antonacci
    • , Tobias Marschall
    • , Jan O. Korbel
    •  & Evan E. Eichler
  • Article |

    Genome-wide association meta-analyses among 1.4 million individuals identify 318 new risk loci for type 2 diabetes and provide insight into the contribution of these risk variants to diabetes-related vascular outcomes.

    • Marijana Vujkovic
    • , Jacob M. Keaton
    • , Julie A. Lynch
    • , Donald R. Miller
    • , Jin Zhou
    • , Catherine Tcheandjieu
    • , Jennifer E. Huffman
    • , Themistocles L. Assimes
    • , Kimberly Lorenz
    • , Xiang Zhu
    • , Austin T. Hilliard
    • , Renae L. Judy
    • , Jie Huang
    • , Kyung M. Lee
    • , Derek Klarin
    • , Saiju Pyarajan
    • , John Danesh
    • , Olle Melander
    • , Asif Rasheed
    • , Nadeem H. Mallick
    • , Shahid Hameed
    • , Irshad H. Qureshi
    • , Muhammad Naeem Afzal
    • , Uzma Malik
    • , Anjum Jalal
    • , Shahid Abbas
    • , Xin Sheng
    • , Long Gao
    • , Klaus H. Kaestner
    • , Katalin Susztak
    • , Yan V. Sun
    • , Scott L. DuVall
    • , Kelly Cho
    • , Jennifer S. Lee
    • , J. Michael Gaziano
    • , Lawrence S. Phillips
    • , James B. Meigs
    • , Peter D. Reaven
    • , Peter W. Wilson
    • , Todd L. Edwards
    • , Daniel J. Rader
    • , Scott M. Damrauer
    • , Christopher J. O’Donnell
    • , Philip S. Tsao
    • , Mark A. Atkinson
    • , Al C. Powers
    • , Ali Naji
    • , Klaus H. Kaestner
    • , Goncalo R. Abecasis
    • , Aris Baras
    • , Michael N. Cantor
    • , Giovanni Coppola
    • , Aris N. Economides
    • , Luca A. Lotta
    • , John D. Overton
    • , Jeffrey G. Reid
    • , Alan R. Shuldiner
    • , Christina Beechert
    • , Caitlin Forsythe
    • , Erin D. Fuller
    • , Zhenhua Gu
    • , Michael Lattari
    • , Alexander E. Lopez
    • , Thomas D. Schleicher
    • , Maria Sotiropoulos Padilla
    • , Karina Toledo
    • , Louis Widom
    • , Sarah E. Wolf
    • , Manasi Pradhan
    • , Kia Manoochehri
    • , Ricardo H. Ulloa
    • , Xiaodong Bai
    • , Suganthi Balasubramanian
    • , Leland Barnard
    • , Andrew L. Blumenfeld
    • , Gisu Eom
    • , Lukas Habegger
    • , Alicia Hawes
    • , Shareef Khalid
    • , Evan K. Maxwell
    • , William J. Salerno
    • , Jeffrey C. Staples
    • , Ashish Yadav
    • , Marcus B. Jones
    • , Lyndon J. Mitnaul
    • , Samuel M. Aguayo
    • , Sunil K. Ahuja
    • , Zuhair K. Ballas
    • , Sujata Bhushan
    • , Edward J. Boyko
    • , David M. Cohen
    • , John Concato
    • , Joseph I. Constans
    • , Louis J. Dellitalia
    • , Joseph M. Fayad
    • , Ronald S. Fernando
    • , Hermes J. Florez
    • , Melinda A. Gaddy
    • , Saib S. Gappy
    • , Gretchen Gibson
    • , Michael Godschalk
    • , Jennifer A. Greco
    • , Samir Gupta
    • , Salvador Gutierrez
    • , Kimberly D. Hammer
    • , Mark B. Hamner
    • , John B. Harley
    • , Adriana M. Hung
    • , Mostaqul Huq
    • , Robin A. Hurley
    • , Pran R. Iruvanti
    • , Douglas J. Ivins
    • , Frank J. Jacono
    • , Darshana N. Jhala
    • , Laurence S. Kaminsky
    • , Scott Kinlay
    • , Jon B. Klein
    • , Suthat Liangpunsakul
    • , Jack H. Lichy
    • , Stephen M. Mastorides
    • , Roy O. Mathew
    • , Kristin M. Mattocks
    • , Rachel McArdle
    • , Paul N. Meyer
    • , Laurence J. Meyer
    • , Jonathan P. Moorman
    • , Timothy R. Morgan
    • , Maureen Murdoch
    • , Xuan-Mai T. Nguyen
    • , Olaoluwa O. Okusaga
    • , Kris-Ann K. Oursler
    • , Nora R. Ratcliffe
    • , Michael I. Rauchman
    • , R. Brooks Robey
    • , George W. Ross
    • , Richard J. Servatius
    • , Satish C. Sharma
    • , Scott E. Sherman
    • , Elif Sonel
    • , Peruvemba Sriram
    • , Todd Stapley
    • , Robert T. Striker
    • , Neeraj Tandon
    • , Gerardo Villareal
    • , Agnes S. Wallbom
    • , John M. Wells
    • , Jeffrey C. Whittle
    • , Mary A. Whooley
    • , Junzhe Xu
    • , Shing-Shing Yeh
    • , Michaela Aslan
    • , Jessica V. Brewer
    • , Mary T. Brophy
    • , Todd Connor
    • , Dean P. Argyres
    • , Nhan V. Do
    • , Elizabeth R. Hauser
    • , Donald E. Humphries
    • , Luis E. Selva
    • , Shahpoor Shayan
    • , Brady Stephens
    • , Stacey B. Whitbourne
    • , Hongyu Zhao
    • , Jennifer Moser
    • , Jean C. Beckham
    • , Jim L. Breeling
    • , J. P. Casas Romero
    • , Grant D. Huang
    • , Rachel B. Ramoni
    • , Saiju Pyarajan
    • , Yan V. Sun
    • , Kelly Cho
    • , Peter W. Wilson
    • , Christopher J. O’Donnell
    • , Philip S. Tsao
    • , Kyong-Mi Chang
    • , J. Michael Gaziano
    • , Sumitra Muralidhar
    • , Kyong-Mi Chang
    • , Benjamin F. Voight
    •  & Danish Saleheen
  • Article |

    Whole-genome bisulfite sequencing analysis of human embryonic stem cells shows that DNMT3 deficiency leads to global and local demethylation, which depends on TET activity. Dynamic loci overlap with putative somatic enhancers that are highly methylated in ESCs.

    • Jocelyn Charlton
    • , Eunmi J. Jung
    • , Alexandra L. Mattei
    • , Nina Bailly
    • , Jing Liao
    • , Eric J. Martin
    • , Pay Giesselmann
    • , Björn Brändl
    • , Elena K. Stamenova
    • , Franz-Josef Müller
    • , Evangelos Kiskinis
    • , Andreas Gnirke
    • , Zachary D. Smith
    •  & Alexander Meissner
  • Letter |

    Genome-wide analysis in 212,453 Japanese individuals identifies loci associated with 42 diseases. Comparative analysis with European populations identifies East Asian–specific associations.

    • Kazuyoshi Ishigaki
    • , Masato Akiyama
    • , Masahiro Kanai
    • , Atsushi Takahashi
    • , Eiryo Kawakami
    • , Hiroki Sugishita
    • , Saori Sakaue
    • , Nana Matoba
    • , Siew-Kee Low
    • , Yukinori Okada
    • , Chikashi Terao
    • , Tiffany Amariuta
    • , Steven Gazal
    • , Yuta Kochi
    • , Momoko Horikoshi
    • , Ken Suzuki
    • , Kaoru Ito
    • , Satoshi Koyama
    • , Kouichi Ozaki
    • , Shumpei Niida
    • , Yasushi Sakata
    • , Yasuhiko Sakata
    • , Takashi Kohno
    • , Kouya Shiraishi
    • , Yukihide Momozawa
    • , Makoto Hirata
    • , Koichi Matsuda
    • , Masashi Ikeda
    • , Nakao Iwata
    • , Shiro Ikegawa
    • , Ikuyo Kou
    • , Toshihiro Tanaka
    • , Hidewaki Nakagawa
    • , Akari Suzuki
    • , Tomomitsu Hirota
    • , Mayumi Tamari
    • , Kazuaki Chayama
    • , Daiki Miki
    • , Masaki Mori
    • , Satoshi Nagayama
    • , Yataro Daigo
    • , Yoshio Miki
    • , Toyomasa Katagiri
    • , Osamu Ogawa
    • , Wataru Obara
    • , Hidemi Ito
    • , Teruhiko Yoshida
    • , Issei Imoto
    • , Takashi Takahashi
    • , Chizu Tanikawa
    • , Takao Suzuki
    • , Nobuaki Sinozaki
    • , Shiro Minami
    • , Hiroki Yamaguchi
    • , Satoshi Asai
    • , Yasuo Takahashi
    • , Ken Yamaji
    • , Kazuhisa Takahashi
    • , Tomoaki Fujioka
    • , Ryo Takata
    • , Hideki Yanai
    • , Akihide Masumoto
    • , Yukihiro Koretsune
    • , Hiromu Kutsumi
    • , Masahiko Higashiyama
    • , Shigeo Murayama
    • , Naoko Minegishi
    • , Kichiya Suzuki
    • , Kozo Tanno
    • , Atsushi Shimizu
    • , Taiki Yamaji
    • , Motoki Iwasaki
    • , Norie Sawada
    • , Hirokazu Uemura
    • , Keitaro Tanaka
    • , Mariko Naito
    • , Makoto Sasaki
    • , Kenji Wakai
    • , Shoichiro Tsugane
    • , Masayuki Yamamoto
    • , Kazuhiko Yamamoto
    • , Yoshinori Murakami
    • , Yusuke Nakamura
    • , Soumya Raychaudhuri
    • , Johji Inazawa
    • , Toshimasa Yamauchi
    • , Takashi Kadowaki
    • , Michiaki Kubo
    •  & Yoichiro Kamatani
  • Letter |

    CTCF is dispensable for transdifferentiation of B cells into induced macrophages despite widespread loss of topologically associating domains. CTCF depletion impairs upregulation of inflammatory genes after endotoxin exposure by destabilizing promoter–enhancer interactions.

    • Grégoire Stik
    • , Enrique Vidal
    • , Mercedes Barrero
    • , Sergi Cuartero
    • , Maria Vila-Casadesús
    • , Julen Mendieta-Esteban
    • , Tian V. Tian
    • , Jinmi Choi
    • , Clara Berenguer
    • , Amaya Abad
    • , Beatrice Borsari
    • , François le Dily
    • , Patrick Cramer
    • , Marc A. Marti-Renom
    • , Ralph Stadhouders
    •  & Thomas Graf
  • News & Views |

    TET2 and DNMT3A mutations lead to similar long-term outcomes in blood cancers despite the antagonistic biochemical functions of their encoded proteins. A new study highlights the opposing effects of TET2 and DNMT3A mutations in shaping the early erythroid or myeloid bias of hematopoietic progenitors.

    • Isaac F. López-Moyado
    •  & Anjana Rao
  • Editorial |

    One of the many consequences of the global COVID-19 pandemic is the need for the scientific community to adapt to the cancellation of conferences and events because of travel restrictions and social-distancing guidelines. We have seen a very swift conversion to online meetings, which have allowed for this established form of science communication to continue and opened new avenues for innovation in the reporting of research and discussion of ideas.

  • Article |

    Analysis with alleles encoding pharmacologically degradable Mediator subunits shows that Mediator acts as a global coactivator that facilitates transcription globally but is acutely required for cell-type-specific gene regulatory circuits.

    • Martin G. Jaeger
    • , Björn Schwalb
    • , Sebastian D. Mackowiak
    • , Taras Velychko
    • , Alexander Hanzl
    • , Hana Imrichova
    • , Matthias Brand
    • , Benedikt Agerer
    • , Someth Chorn
    • , Behnam Nabet
    • , Fleur M. Ferguson
    • , André C. Müller
    • , Andreas Bergthaler
    • , Nathanael S. Gray
    • , James E. Bradner
    • , Christoph Bock
    • , Denes Hnisz
    • , Patrick Cramer
    •  & Georg E. Winter
  • Article |

    Immunogenomic analyses of advanced high-grade serous ovarian cancer samples before and after neoadjuvant chemotherapy show that the tumor–immune microenvironment is intrinsically heterogeneous and that chemotherapy induces local immune activation.

    • Alejandro Jiménez-Sánchez
    • , Paulina Cybulska
    • , Katherine LaVigne Mager
    • , Simon Koplev
    • , Oliver Cast
    • , Dominique-Laurent Couturier
    • , Danish Memon
    • , Pier Selenica
    • , Ines Nikolovski
    • , Yousef Mazaheri
    • , Yonina Bykov
    • , Felipe C. Geyer
    • , Geoff Macintyre
    • , Lena Morrill Gavarró
    • , Ruben M. Drews
    • , Michael B. Gill
    • , Anastasios D. Papanastasiou
    • , Ramon E. Sosa
    • , Robert A. Soslow
    • , Tyler Walther
    • , Ronglai Shen
    • , Dennis S. Chi
    • , Kay J. Park
    • , Travis Hollmann
    • , Jorge S. Reis-Filho
    • , Florian Markowetz
    • , Pedro Beltrao
    • , Hebert Alberto Vargas
    • , Dmitriy Zamarin
    • , James D. Brenton
    • , Alexandra Snyder
    • , Britta Weigelt
    • , Evis Sala
    •  & Martin L. Miller
  • Author Correction |

    • Andrea Cortese
    • , Yi Zhu
    • , Adriana P. Rebelo
    • , Sara Negri
    • , Steve Courel
    • , Lisa Abreu
    • , Chelsea J. Bacon
    • , Yunhong Bai
    • , Dana M. Bis-Brewer
    • , Enrico Bugiardini
    • , Elena Buglo
    • , Matt C. Danzi
    • , Shawna M. E. Feely
    • , Alkyoni Athanasiou-Fragkouli
    • , Nourelhoda A. Haridy
    • , Aixa Rodriguez
    • , Alexa Bacha
    • , Ashley Kosikowski
    • , Beth Wood
    • , Brett McCray
    • , Brianna Blume
    • , Carly Siskind
    • , Charlotte Sumner
    • , Daniela Calabrese
    • , David Walk
    • , Dragan Vujovic
    • , Eun Park
    • , Francesco Muntoni
    • , Gabrielle Donlevy
    • , Gyula Acsadi
    • , John Day
    • , Joshua Burns
    • , Jun Li
    • , Karen Krajewski
    • , Kate Eichinger
    • , Kayla Cornett
    • , Krista Mullen
    • , Perez Quiros Laura
    • , Laurie Gutmann
    • , Maria Barrett
    • , Mario Saporta
    • , Mariola Skorupinska
    • , Natalie Grant
    • , Paula Bray
    • , Reza Seyedsadjadi
    • , Riccardo Zuccarino
    • , Richard Finkel
    • , Richard Lewis
    • , Sabrina Yum
    • , Sarah Hilbert
    • , Simone Thomas
    • , Steffen Behrens-Spraggins
    • , Tara Jones
    • , Thomas Lloyd
    • , Tiffany Grider
    • , Tim Estilow
    • , Vera Fridman
    • , Rosario Isasi
    • , Alaa Khan
    • , Matilde Laurà
    • , Stefania Magri
    • , Menelaos Pipis
    • , Chiara Pisciotta
    • , Eric Powell
    • , Alexander M. Rossor
    • , Paola Saveri
    • , Janet E. Sowden
    • , Stefano Tozza
    • , Jana Vandrovcova
    • , Julia Dallman
    • , Elena Grignani
    • , Enrico Marchioni
    • , Steven S. Scherer
    • , Beisha Tang
    • , Zhiqiang Lin
    • , Abdullah Al-Ajmi
    • , Rebecca Schüle
    • , Matthis Synofzik
    • , Thierry Maisonobe
    • , Tanya Stojkovic
    • , Michaela Auer-Grumbach
    • , Mohamed A. Abdelhamed
    • , Sherifa A. Hamed
    • , Ruxu Zhang
    • , Fiore Manganelli
    • , Lucio Santoro
    • , Franco Taroni
    • , Davide Pareyson
    • , Henry Houlden
    • , David N. Herrmann
    • , Mary M. Reilly
    • , Michael E. Shy
    • , R. Grace Zhai
    •  & Stephan Zuchner
  • Article |

    Analysis of metastases using a mathematical framework and multi-region sampling data shows that lymph node metastases have higher levels of intratumor heterogeneity than distant metastases, and that these form via different evolutionary mechanisms.

    • Johannes G. Reiter
    • , Wei-Ting Hung
    • , I-Hsiu Lee
    • , Shriya Nagpal
    • , Peter Giunta
    • , Sebastian Degner
    • , Gang Liu
    • , Emma C. E. Wassenaar
    • , William R. Jeck
    • , Martin S. Taylor
    • , Alexander A. Farahani
    • , Hetal D. Marble
    • , Simon Knott
    • , Onno Kranenburg
    • , Jochen K. Lennerz
    •  & Kamila Naxerova
  • Article |

    Single-cell RNA sequencing of colorectal tumors highlights associations between lineage-related gene expression signatures and specific stromal and immune cell populations.

    • Hae-Ock Lee
    • , Yourae Hong
    • , Hakki Emre Etlioglu
    • , Yong Beom Cho
    • , Valentina Pomella
    • , Ben Van den Bosch
    • , Jasper Vanhecke
    • , Sara Verbandt
    • , Hyekyung Hong
    • , Jae-Woong Min
    • , Nayoung Kim
    • , Hye Hyeon Eum
    • , Junbin Qian
    • , Bram Boeckx
    • , Diether Lambrechts
    • , Petros Tsantoulis
    • , Gert De Hertogh
    • , Woosung Chung
    • , Taeseob Lee
    • , Minae An
    • , Hyun-Tae Shin
    • , Je-Gun Joung
    • , Min-Hyeok Jung
    • , Gunhwan Ko
    • , Pratyaksha Wirapati
    • , Seok Hyung Kim
    • , Hee Cheol Kim
    • , Seong Hyeon Yun
    • , Iain Bee Huat Tan
    • , Bobby Ranjan
    • , Woo Yong Lee
    • , Tae-You Kim
    • , Jung Kyoon Choi
    • , Young-Joon Kim
    • , Shyam Prabhakar
    • , Sabine Tejpar
    •  & Woong-Yang Park
  • News & Views |

    Many normal tissues are populated by clonal expansions that compete for space. Colom et al. now show that mutant clones keep other mutant clones in check by effectively annulling one another’s advantages.

    • Kamila Naxerova
  • Letter |

    Genome-wide analysis identifies 32 loci associated with breast cancer susceptibility, accounting for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade.

    • Haoyu Zhang
    • , Thomas U. Ahearn
    • , Julie Lecarpentier
    • , Daniel Barnes
    • , Jonathan Beesley
    • , Guanghao Qi
    • , Xia Jiang
    • , Tracy A. O’Mara
    • , Ni Zhao
    • , Manjeet K. Bolla
    • , Alison M. Dunning
    • , Joe Dennis
    • , Qin Wang
    • , Zumuruda Abu Ful
    • , Kristiina Aittomäki
    • , Irene L. Andrulis
    • , Hoda Anton-Culver
    • , Volker Arndt
    • , Kristan J. Aronson
    • , Banu K. Arun
    • , Paul L. Auer
    • , Jacopo Azzollini
    • , Daniel Barrowdale
    • , Heiko Becher
    • , Matthias W. Beckmann
    • , Sabine Behrens
    • , Javier Benitez
    • , Marina Bermisheva
    • , Katarzyna Bialkowska
    • , Ana Blanco
    • , Carl Blomqvist
    • , Natalia V. Bogdanova
    • , Stig E. Bojesen
    • , Bernardo Bonanni
    • , Davide Bondavalli
    • , Ake Borg
    • , Hiltrud Brauch
    • , Hermann Brenner
    • , Ignacio Briceno
    • , Annegien Broeks
    • , Sara Y. Brucker
    • , Thomas Brüning
    • , Barbara Burwinkel
    • , Saundra S. Buys
    • , Helen Byers
    • , Trinidad Caldés
    • , Maria A. Caligo
    • , Mariarosaria Calvello
    • , Daniele Campa
    • , Jose E. Castelao
    • , Jenny Chang-Claude
    • , Stephen J. Chanock
    • , Melissa Christiaens
    • , Hans Christiansen
    • , Wendy K. Chung
    • , Kathleen B. M. Claes
    • , Christine L. Clarke
    • , Sten Cornelissen
    • , Fergus J. Couch
    • , Angela Cox
    • , Simon S. Cross
    • , Kamila Czene
    • , Mary B. Daly
    • , Peter Devilee
    • , Orland Diez
    • , Susan M. Domchek
    • , Thilo Dörk
    • , Miriam Dwek
    • , Diana M. Eccles
    • , Arif B. Ekici
    • , D. Gareth Evans
    • , Peter A. Fasching
    • , Jonine Figueroa
    • , Lenka Foretova
    • , Florentia Fostira
    • , Eitan Friedman
    • , Debra Frost
    • , Manuela Gago-Dominguez
    • , Susan M. Gapstur
    • , Judy Garber
    • , José A. García-Sáenz
    • , Mia M. Gaudet
    • , Simon A. Gayther
    • , Graham G. Giles
    • , Andrew K. Godwin
    • , Mark S. Goldberg
    • , David E. Goldgar
    • , Anna González-Neira
    • , Mark H. Greene
    • , Jacek Gronwald
    • , Pascal Guénel
    • , Lothar Häberle
    • , Eric Hahnen
    • , Christopher A. Haiman
    • , Christopher R. Hake
    • , Per Hall
    • , Ute Hamann
    • , Elaine F. Harkness
    • , Bernadette A. M. Heemskerk-Gerritsen
    • , Peter Hillemanns
    • , Frans B. L. Hogervorst
    • , Bernd Holleczek
    • , Antoinette Hollestelle
    • , Maartje J. Hooning
    • , Robert N. Hoover
    • , John L. Hopper
    • , Anthony Howell
    • , Hanna Huebner
    • , Peter J. Hulick
    • , Evgeny N. Imyanitov
    • , Claudine Isaacs
    • , Louise Izatt
    • , Agnes Jager
    • , Milena Jakimovska
    • , Anna Jakubowska
    • , Paul James
    • , Ramunas Janavicius
    • , Wolfgang Janni
    • , Esther M. John
    • , Michael E. Jones
    • , Audrey Jung
    • , Rudolf Kaaks
    • , Pooja Middha Kapoor
    • , Beth Y. Karlan
    • , Renske Keeman
    • , Sofia Khan
    • , Elza Khusnutdinova
    • , Cari M. Kitahara
    • , Yon-Dschun Ko
    • , Irene Konstantopoulou
    • , Linetta B. Koppert
    • , Stella Koutros
    • , Vessela N. Kristensen
    • , Anne-Vibeke Laenkholm
    • , Diether Lambrechts
    • , Susanna C. Larsson
    • , Pierre Laurent-Puig
    • , Conxi Lazaro
    • , Emilija Lazarova
    • , Flavio Lejbkowicz
    • , Goska Leslie
    • , Fabienne Lesueur
    • , Annika Lindblom
    • , Jolanta Lissowska
    • , Wing-Yee Lo
    • , Jennifer T. Loud
    • , Jan Lubinski
    • , Alicja Lukomska
    • , Robert J. MacInnis
    • , Arto Mannermaa
    • , Mehdi Manoochehri
    • , Siranoush Manoukian
    • , Sara Margolin
    • , Maria Elena Martinez
    • , Laura Matricardi
    • , Lesley McGuffog
    • , Catriona McLean
    • , Noura Mebirouk
    • , Alfons Meindl
    • , Usha Menon
    • , Austin Miller
    • , Elvira Mingazheva
    • , Marco Montagna
    • , Anna Marie Mulligan
    • , Claire Mulot
    • , Taru A. Muranen
    • , Katherine L. Nathanson
    • , Susan L. Neuhausen
    • , Heli Nevanlinna
    • , Patrick Neven
    • , William G. Newman
    • , Finn C. Nielsen
    • , Liene Nikitina-Zake
    • , Jesse Nodora
    • , Kenneth Offit
    • , Edith Olah
    • , Olufunmilayo I. Olopade
    • , Håkan Olsson
    • , Nick Orr
    • , Laura Papi
    • , Janos Papp
    • , Tjoung-Won Park-Simon
    • , Michael T. Parsons
    • , Bernard Peissel
    • , Ana Peixoto
    • , Beth Peshkin
    • , Paolo Peterlongo
    • , Julian Peto
    • , Kelly-Anne Phillips
    • , Marion Piedmonte
    • , Dijana Plaseska-Karanfilska
    • , Karolina Prajzendanc
    • , Ross Prentice
    • , Darya Prokofyeva
    • , Brigitte Rack
    • , Paolo Radice
    • , Susan J. Ramus
    • , Johanna Rantala
    • , Muhammad U. Rashid
    • , Gad Rennert
    • , Hedy S. Rennert
    • , Harvey A. Risch
    • , Atocha Romero
    • , Matti A. Rookus
    • , Matthias Rübner
    • , Thomas Rüdiger
    • , Emmanouil Saloustros
    • , Sarah Sampson
    • , Dale P. Sandler
    • , Elinor J. Sawyer
    • , Maren T. Scheuner
    • , Rita K. Schmutzler
    • , Andreas Schneeweiss
    • , Minouk J. Schoemaker
    • , Ben Schöttker
    • , Peter Schürmann
    • , Leigha Senter
    • , Priyanka Sharma
    • , Mark E. Sherman
    • , Xiao-Ou Shu
    • , Christian F. Singer
    • , Snezhana Smichkoska
    • , Penny Soucy
    • , Melissa C. Southey
    • , John J. Spinelli
    • , Jennifer Stone
    • , Dominique Stoppa-Lyonnet
    • , Anthony J. Swerdlow
    • , Csilla I. Szabo
    • , Rulla M. Tamimi
    • , William J. Tapper
    • , Jack A. Taylor
    • , Manuel R. Teixeira
    • , MaryBeth Terry
    • , Mads Thomassen
    • , Darcy L. Thull
    • , Marc Tischkowitz
    • , Amanda E. Toland
    • , Rob A. E. M. Tollenaar
    • , Ian Tomlinson
    • , Diana Torres
    • , Melissa A. Troester
    • , Thérèse Truong
    • , Nadine Tung
    • , Michael Untch
    • , Celine M. Vachon
    • , Ans M. W. van den Ouweland
    • , Lizet E. van der Kolk
    • , Elke M. van Veen
    • , Elizabeth J. vanRensburg
    • , Ana Vega
    • , Barbara Wappenschmidt
    • , Clarice R. Weinberg
    • , Jeffrey N. Weitzel
    • , Hans Wildiers
    • , Robert Winqvist
    • , Alicja Wolk
    • , Xiaohong R. Yang
    • , Drakoulis Yannoukakos
    • , Wei Zheng
    • , Kristin K. Zorn
    • , Roger L. Milne
    • , Peter Kraft
    • , Jacques Simard
    • , Paul D. P. Pharoah
    • , Kyriaki Michailidou
    • , Antonis C. Antoniou
    • , Marjanka K. Schmidt
    • , Georgia Chenevix-Trench
    • , Douglas F. Easton
    • , Nilanjan Chatterjee
    •  & Montserrat García-Closas
  • Letter |

    Cas9 expression induces DNA damage and activates the p53 pathway, and it can lead to the selection of cells with p53-inactivating mutations. Cas9 is less active in wild-type TP53 cell lines than in TP53-mutant cell lines.

    • Oana M. Enache
    • , Veronica Rendo
    • , Mai Abdusamad
    • , Daniel Lam
    • , Desiree Davison
    • , Sangita Pal
    • , Naomi Currimjee
    • , Julian Hess
    • , Sasha Pantel
    • , Anwesha Nag
    • , Aaron R. Thorner
    • , John G. Doench
    • , Francisca Vazquez
    • , Rameen Beroukhim
    • , Todd R. Golub
    •  & Uri Ben-David
  • Technical Report |

    SAIGE-GENE is a scalable generalized mixed-model region-based association test that can analyze large datasets while accounting for sample relatedness and unbalanced case–control ratios for binary traits.

    • Wei Zhou
    • , Zhangchen Zhao
    • , Jonas B. Nielsen
    • , Lars G. Fritsche
    • , Jonathon LeFaive
    • , Sarah A. Gagliano Taliun
    • , Wenjian Bi
    • , Maiken E. Gabrielsen
    • , Mark J. Daly
    • , Benjamin M. Neale
    • , Kristian Hveem
    • , Goncalo R. Abecasis
    • , Cristen J. Willer
    •  & Seunggeun Lee
  • Article |

    Deep sequencing and lineage tracing analysis of esophageal epithelium of mutagen-treated aging mice leads to a model in which the proliferative advantage of positively selected mutations depends on the competitive fitness of neighboring cells.

    • Bartomeu Colom
    • , Maria P. Alcolea
    • , Gabriel Piedrafita
    • , Michael W. J. Hall
    • , Agnieszka Wabik
    • , Stefan C. Dentro
    • , Joanna C. Fowler
    • , Albert Herms
    • , Charlotte King
    • , Swee Hoe Ong
    • , Roshan K. Sood
    • , Moritz Gerstung
    • , Inigo Martincorena
    • , Benjamin A. Hall
    •  & Philip H. Jones
  • Publisher Correction |

    • Isidro Cortés-Ciriano
    • , Jake June-Koo Lee
    • , Ruibin Xi
    • , Dhawal Jain
    • , Youngsook L. Jung
    • , Lixing Yang
    • , Dmitry Gordenin
    • , Leszek J. Klimczak
    • , Cheng-Zhong Zhang
    • , David S. Pellman
    • , Kadir C. Akdemir
    • , Eva G. Alvarez
    • , Adrian Baez-Ortega
    • , Rameen Beroukhim
    • , Paul C. Boutros
    • , David D. L. Bowtell
    • , Benedikt Brors
    • , Kathleen H. Burns
    • , Peter J. Campbell
    • , Kin Chan
    • , Ken Chen
    • , Isidro Cortés-Ciriano
    • , Ana Dueso-Barroso
    • , Andrew J. Dunford
    • , Paul A. Edwards
    • , Xavier Estivill
    • , Dariush Etemadmoghadam
    • , Lars Feuerbach
    • , J. Lynn Fink
    • , Milana Frenkel-Morgenstern
    • , Dale W. Garsed
    • , Mark Gerstein
    • , Dmitry A. Gordenin
    • , David Haan
    • , James E. Haber
    • , Julian M. Hess
    • , Barbara Hutter
    • , Marcin Imielinski
    • , David T. W. Jones
    • , Young Seok Ju
    • , Marat D. Kazanov
    • , Leszek J. Klimczak
    • , Youngil Koh
    • , Jan O. Korbel
    • , Kiran Kumar
    • , Eunjung Alice Lee
    • , Jake June-Koo Lee
    • , Yilong Li
    • , Andy G. Lynch
    • , Geoff Macintyre
    • , Florian Markowetz
    • , Iñigo Martincorena
    • , Alexander Martinez-Fundichely
    • , Satoru Miyano
    • , Hidewaki Nakagawa
    • , Fabio C. P. Navarro
    • , Stephan Ossowski
    • , Peter J. Park
    • , John V. Pearson
    • , Montserrat Puiggròs
    • , Karsten Rippe
    • , Nicola D. Roberts
    • , Steven A. Roberts
    • , Bernardo Rodriguez-Martin
    • , Steven E. Schumacher
    • , Ralph Scully
    • , Mark Shackleton
    • , Nikos Sidiropoulos
    • , Lina Sieverling
    • , Chip Stewart
    • , David Torrents
    • , Jose M. C. Tubio
    • , Izar Villasante
    • , Nicola Waddell
    • , Jeremiah A. Wala
    • , Joachim Weischenfeldt
    • , Lixing Yang
    • , Xiaotong Yao
    • , Sung-Soo Yoon
    • , Jorge Zamora
    • , Cheng-Zhong Zhang
    •  & Peter J. Park