Browse Articles

  • World View |

    Given an opportunity to chronicle the experience of traversing America as a Black man, I elect to convey a less frequently told vantage point. This is the perspective of the ‘accomplished’ bootless.

    • Russell J. Ledet
  • News & Views |

    Patterns of co-occurring and mutually exclusive mutations reveal synergistic interactions among cancer driver genes. A new study functionally confirms these interactions and builds the pairwise relationships into networks of pathway disruption that have better predictive power than specific mutations alone.

    • Martin S. Taylor
  • News & Views |

    In a classical view of carcinogenesis, carcinogens directly cause mutations. In this issue, Riva et al. explore the effects of 20 known or suspected human carcinogens and find discernible mutational signatures for only three of them.

    • Nuria Lopez-Bigas
    •  & Abel Gonzalez-Perez
  • Technical Report |

    PolyGembler, a method for grouping and ordering contigs into complete pseudomolecules by combining long-read sequencing and genotype information from an outbred mapping population, improves the accuracy for assembly of polyploidy plant genomes.

    • Chenxi Zhou
    • , Bode Olukolu
    • , Dorcus C. Gemenet
    • , Shan Wu
    • , Wolfgang Gruneberg
    • , Minh Duc Cao
    • , Zhangjun Fei
    • , Zhao-Bang Zeng
    • , Andrew W. George
    • , Awais Khan
    • , G. Craig Yencho
    •  & Lachlan J. M. Coin
  • Article |

    Single-cell RNA-seq of a collection of 200 cancer cell lines finds common, recurrent heterogeneous expression programs, which also are found in patient samples and are linked to cell state and drug sensitivity.

    • Gabriela S. Kinker
    • , Alissa C. Greenwald
    • , Rotem Tal
    • , Zhanna Orlova
    • , Michael S. Cuoco
    • , James M. McFarland
    • , Allison Warren
    • , Christopher Rodman
    • , Jennifer A. Roth
    • , Samantha A. Bender
    • , Bhavna Kumar
    • , James W. Rocco
    • , Pedro A. C. M. Fernandes
    • , Christopher C. Mader
    • , Hadas Keren-Shaul
    • , Alexander Plotnikov
    • , Haim Barr
    • , Aviad Tsherniak
    • , Orit Rozenblatt-Rosen
    • , Valery Krizhanovsky
    • , Sidharth V. Puram
    • , Aviv Regev
    •  & Itay Tirosh
  • Article |

    Environmental exposures shape patterns of selection for mutations in clonal hematopoiesis. Cancer therapies promote the growth of clones with mutations that are strongly enriched in treatment-related myeloid neoplasms.

    • Kelly L. Bolton
    • , Ryan N. Ptashkin
    • , Teng Gao
    • , Lior Braunstein
    • , Sean M. Devlin
    • , Daniel Kelly
    • , Minal Patel
    • , Antonin Berthon
    • , Aijazuddin Syed
    • , Mariko Yabe
    • , Catherine C. Coombs
    • , Nicole M. Caltabellotta
    • , Mike Walsh
    • , Kenneth Offit
    • , Zsofia Stadler
    • , Diana Mandelker
    • , Jessica Schulman
    • , Akshar Patel
    • , John Philip
    • , Elsa Bernard
    • , Gunes Gundem
    • , Juan E. Arango Ossa
    • , Max Levine
    • , Juan S. Medina Martinez
    • , Noushin Farnoud
    • , Dominik Glodzik
    • , Sonya Li
    • , Mark E. Robson
    • , Choonsik Lee
    • , Paul D. P. Pharoah
    • , Konrad H. Stopsack
    • , Barbara Spitzer
    • , Simon Mantha
    • , James Fagin
    • , Laura Boucai
    • , Christopher J. Gibson
    • , Benjamin L. Ebert
    • , Andrew L. Young
    • , Todd Druley
    • , Koichi Takahashi
    • , Nancy Gillis
    • , Markus Ball
    • , Eric Padron
    • , David M. Hyman
    • , Jose Baselga
    • , Larry Norton
    • , Stuart Gardos
    • , Virginia M. Klimek
    • , Howard Scher
    • , Dean Bajorin
    • , Eder Paraiso
    • , Ryma Benayed
    • , Maria E. Arcila
    • , Marc Ladanyi
    • , David B. Solit
    • , Michael F. Berger
    • , Martin Tallman
    • , Montserrat Garcia-Closas
    • , Nilanjan Chatterjee
    • , Luis A. Diaz Jr
    • , Ross L. Levine
    • , Lindsay M. Morton
    • , Ahmet Zehir
    •  & Elli Papaemmanuil
  • Article |

    Whole-genome sequencing of wheat populations from 25 subspecies within the genera Triticum and Aegilops provides insights into the role of evolutionary constraints in shaping the adaptive landscape of bread wheat.

    • Yao Zhou
    • , Xuebo Zhao
    • , Yiwen Li
    • , Jun Xu
    • , Aoyue Bi
    • , Lipeng Kang
    • , Daxing Xu
    • , Haofeng Chen
    • , Ying Wang
    • , Yuan-ge Wang
    • , Sanyang Liu
    • , Chengzhi Jiao
    • , Hongfeng Lu
    • , Jing Wang
    • , Changbin Yin
    • , Yuling Jiao
    •  & Fei Lu
  • Article |

    Single-cell chromatin profiling of different brain regions identifies cell-type-specific regulatory elements, and helps to predict functional SNPs for Alzheimer’s and Parkinson’s diseases.

    • M. Ryan Corces
    • , Anna Shcherbina
    • , Soumya Kundu
    • , Michael J. Gloudemans
    • , Laure Frésard
    • , Jeffrey M. Granja
    • , Bryan H. Louie
    • , Tiffany Eulalio
    • , Shadi Shams
    • , S. Tansu Bagdatli
    • , Maxwell R. Mumbach
    • , Boxiang Liu
    • , Kathleen S. Montine
    • , William J. Greenleaf
    • , Anshul Kundaje
    • , Stephen B. Montgomery
    • , Howard Y. Chang
    •  & Thomas J. Montine
  • Article |

    dACE2 is a newly identified isoform of ACE2 that is unable to bind the SARS-CoV-2 spike protein. Truncated dACE2, but not full-length ACE2, is induced by interferons and viruses, thus suggesting that such conditions are unlikely to increase cellular entry of SARS-CoV-2.

    • Olusegun O. Onabajo
    • , A. Rouf Banday
    • , Megan L. Stanifer
    • , Wusheng Yan
    • , Adeola Obajemu
    • , Deanna M. Santer
    • , Oscar Florez-Vargas
    • , Helen Piontkivska
    • , Joselin M. Vargas
    • , Timothy J. Ring
    • , Carmon Kee
    • , Patricio Doldan
    • , D. Lorne Tyrrell
    • , Juan L. Mendoza
    • , Steeve Boulant
    •  & Ludmila Prokunina-Olsson
  • Article |

    A truncated angiotensin-converting enzyme 2 (ACE2) isoform that lacks domains required for severe acute respiratory syndrome coronavirus 2 binding exhibits tissue-specific expression patterns and is responsive to interferon stimulation, in contrast to full-length ACE2, which is unresponsive to interferons.

    • Kevin W. Ng
    • , Jan Attig
    • , William Bolland
    • , George R. Young
    • , Jack Major
    • , Antoni G. Wrobel
    • , Steve Gamblin
    • , Andreas Wack
    •  & George Kassiotis
  • Letter |

    Super-resolution microscopy identifies sub-topologically associating domain (TAD) nanodomains and intercellular heterogeneity in TAD conformation and insulation. Cohesin or CTCF depletion regulates distinct types of chromatin contacts at the TAD but not nanodomain level.

    • Quentin Szabo
    • , Axelle Donjon
    • , Ivana Jerković
    • , Giorgio L. Papadopoulos
    • , Thierry Cheutin
    • , Boyan Bonev
    • , Elphège P. Nora
    • , Benoit G. Bruneau
    • , Frédéric Bantignies
    •  & Giacomo Cavalli
  • Letter |

    Analysis of two independent cohorts of patients with Bardet–Biedl syndrome (BBS) with known recessive biallelic pathogenic mutations in one of 17 BBS genes shows an enrichment of rare nonsynonymous secondary variants in the same gene set, with significant over-representation of secondary alleles in chaperonin-encoding genes.

    • Maria Kousi
    • , Onuralp Söylemez
    • , Aysegül Ozanturk
    • , Niki Mourtzi
    • , Sebastian Akle
    • , Irwin Jungreis
    • , Jean Muller
    • , Christopher A. Cassa
    • , Harrison Brand
    • , Jill Anne Mokry
    • , Maxim Y. Wolf
    • , Azita Sadeghpour
    • , Kelsey McFadden
    • , Richard A. Lewis
    • , Michael E. Talkowski
    • , Hélène Dollfus
    • , Manolis Kellis
    • , Erica E. Davis
    • , Shamil R. Sunyaev
    •  & Nicholas Katsanis
  • Article |

    Genome-wide association analyses in the Japanese population and trans-ancestry meta-analyses identify new risk loci for coronary artery disease. A polygenic risk score derived from these findings identifies individuals with increased risk of long-term cardiovascular mortality.

    • Satoshi Koyama
    • , Kaoru Ito
    • , Chikashi Terao
    • , Masato Akiyama
    • , Momoko Horikoshi
    • , Yukihide Momozawa
    • , Hiroshi Matsunaga
    • , Hirotaka Ieki
    • , Kouichi Ozaki
    • , Yoshihiro Onouchi
    • , Atsushi Takahashi
    • , Seitaro Nomura
    • , Hiroyuki Morita
    • , Hiroshi Akazawa
    • , Changhoon Kim
    • , Jeong-sun Seo
    • , Koichiro Higasa
    • , Motoki Iwasaki
    • , Taiki Yamaji
    • , Norie Sawada
    • , Shoichiro Tsugane
    • , Teruhide Koyama
    • , Hiroaki Ikezaki
    • , Naoyuki Takashima
    • , Keitaro Tanaka
    • , Kokichi Arisawa
    • , Kiyonori Kuriki
    • , Mariko Naito
    • , Kenji Wakai
    • , Shinichiro Suna
    • , Yasuhiko Sakata
    • , Hiroshi Sato
    • , Masatsugu Hori
    • , Yasushi Sakata
    • , Koichi Matsuda
    • , Yoshinori Murakami
    • , Hiroyuki Aburatani
    • , Michiaki Kubo
    • , Fumihiko Matsuda
    • , Yoichiro Kamatani
    •  & Issei Komuro
  • Article |

    Somatic mutational loads in cancer genomes change with chromatin domain boundaries. Different mutational processes lead to distinct somatic mutation distributions in active versus inactive domains, including during tumor evolution.

    • Kadir C. Akdemir
    • , Victoria T. Le
    • , Justin M. Kim
    • , Sarah Killcoyne
    • , Devin A. King
    • , Ya-Ping Lin
    • , Yanyan Tian
    • , Akira Inoue
    • , Samirkumar B. Amin
    • , Frederick S. Robinson
    • , Manjunath Nimmakayalu
    • , Rafael E. Herrera
    • , Erica J. Lynn
    • , Kin Chan
    • , Sahil Seth
    • , Leszek J. Klimczak
    • , Moritz Gerstung
    • , Dmitry A. Gordenin
    • , John O’Brien
    • , Lei Li
    • , Yonathan Lissanu Deribe
    • , Roel G. Verhaak
    • , Peter J. Campbell
    • , Rebecca Fitzgerald
    • , Ashby J. Morrison
    • , Jesse R. Dixon
    •  & P. Andrew Futreal
  • Article |

    High-throughput chromosome conformation enhancer capture identifies dynamic enhancer networks that regulate differentiation of human mesenchymal stem cells. Transcription factors (TFs) at baited enhancers appear to stabilize TF binding at target enhancers.

    • Jesper G. S. Madsen
    • , Maria S. Madsen
    • , Alexander Rauch
    • , Sofie Traynor
    • , Elvira L. Van Hauwaert
    • , Anders K. Haakonsson
    • , Biola M. Javierre
    • , Mette Hyldahl
    • , Peter Fraser
    •  & Susanne Mandrup
  • Editorial |

    Genetic tools can help uncover evolutionary histories, migration patterns and admixture events of domesticated animals and their wild ancestors. The genetic window into the past can help shape breeding strategies and inform animal agricultural practices that should lead to a more resilient and sustainable future.

  • News & Views |

    FOXA1 is a key pioneer factor in androgen-receptor activity but has been an elusive drug target. A new study shows that inhibition of the associated cofactor LSD1 modifies the methylation state of FOXA1, thus resulting in chromatin dissociation and tumor inhibition, even in models of treatment-resistant prostate cancer.

    • Soleilmane Omarjee
    •  & Jason S. Carroll
  • News & Views |

    How do boundary elements divide chromosomes into domains? A new study uses random genomic insertions to show how small genomic fragments can shape chromatin folding through the interplay of loop extrusion and compartmentalization. Spoiler: context matters.

    • Erika C. Anderson
    •  & Elphège P. Nora
  • Article |

    Whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds identifies 16 loci linked to environmental adaptations among crossbred animals, including a highly divergent locus in African taurine cattle putatively linked to trypanotolerance.

    • Kwondo Kim
    • , Taehyung Kwon
    • , Tadelle Dessie
    • , DongAhn Yoo
    • , Okeyo Ally Mwai
    • , Jisung Jang
    • , Samsun Sung
    • , SaetByeol Lee
    • , Bashir Salim
    • , Jaehoon Jung
    • , Heesu Jeong
    • , Getinet Mekuriaw Tarekegn
    • , Abdulfatai Tijjani
    • , Dajeong Lim
    • , Seoae Cho
    • , Sung Jong Oh
    • , Hak-Kyo Lee
    • , Jaemin Kim
    • , Choongwon Jeong
    • , Stephen Kemp
    • , Olivier Hanotte
    •  & Heebal Kim
  • Letter
    | Open Access

    Haplotype-resolved assembly of a heterozygous diploid potato, RH89-039-16, and identification of deleterious mutations provide insights into the genome organization and breeding of a clonally propagated diploid species.

    • Qian Zhou
    • , Dié Tang
    • , Wu Huang
    • , Zhongmin Yang
    • , Yu Zhang
    • , John P. Hamilton
    • , Richard G. F. Visser
    • , Christian W. B. Bachem
    • , C. Robin Buell
    • , Zhonghua Zhang
    • , Chunzhi Zhang
    •  & Sanwen Huang
  • Article |

    A genomic analysis of tumors in mice caused by known or suspected carcinogens shows that most carcinogens do not generate distinct mutational signatures.

    • Laura Riva
    • , Arun R. Pandiri
    • , Yun Rose Li
    • , Alastair Droop
    • , James Hewinson
    • , Michael A. Quail
    • , Vivek Iyer
    • , Rebecca Shepherd
    • , Ronald A. Herbert
    • , Peter J. Campbell
    • , Robert C. Sills
    • , Ludmil B. Alexandrov
    • , Allan Balmain
    •  & David J. Adams
  • Article |

    Whole-exome sequencing of 250 parent–offspring trios identifies an enrichment of rare damaging de novo mutations in individuals with cerebral palsy and implicates genetically mediated dysregulation of early neuronal connectivity in the etiology of this disorder.

    • Sheng Chih Jin
    • , Sara A. Lewis
    • , Somayeh Bakhtiari
    • , Xue Zeng
    • , Michael C. Sierant
    • , Sheetal Shetty
    • , Sandra M. Nordlie
    • , Aureliane Elie
    • , Mark A. Corbett
    • , Bethany Y. Norton
    • , Clare L. van Eyk
    • , Shozeb Haider
    • , Brandon S. Guida
    • , Helen Magee
    • , James Liu
    • , Stephen Pastore
    • , John B. Vincent
    • , Janice Brunstrom-Hernandez
    • , Antigone Papavasileiou
    • , Michael C. Fahey
    • , Jesia G. Berry
    • , Kelly Harper
    • , Chongchen Zhou
    • , Junhui Zhang
    • , Boyang Li
    • , Jennifer Heim
    • , Dani L. Webber
    • , Mahalia S. B. Frank
    • , Lei Xia
    • , Yiran Xu
    • , Dengna Zhu
    • , Bohao Zhang
    • , Amar H. Sheth
    • , James R. Knight
    • , Christopher Castaldi
    • , Irina R. Tikhonova
    • , Francesc López-Giráldez
    • , Boris Keren
    • , Sandra Whalen
    • , Julien Buratti
    • , Diane Doummar
    • , Megan Cho
    • , Kyle Retterer
    • , Francisca Millan
    • , Yangong Wang
    • , Jeff L. Waugh
    • , Lance Rodan
    • , Julie S. Cohen
    • , Ali Fatemi
    • , Angela E. Lin
    • , John P. Phillips
    • , Timothy Feyma
    • , Suzanna C. MacLennan
    • , Spencer Vaughan
    • , Kylie E. Crompton
    • , Susan M. Reid
    • , Dinah S. Reddihough
    • , Qing Shang
    • , Chao Gao
    • , Iona Novak
    • , Nadia Badawi
    • , Yana A. Wilson
    • , Sarah J. McIntyre
    • , Shrikant M. Mane
    • , Xiaoyang Wang
    • , David J. Amor
    • , Daniela C. Zarnescu
    • , Qiongshi Lu
    • , Qinghe Xing
    • , Changlian Zhu
    • , Kaya Bilguvar
    • , Sergio Padilla-Lopez
    • , Richard P. Lifton
    • , Jozef Gecz
    • , Alastair H. MacLennan
    •  & Michael C. Kruer
  • Article |

    Computational analysis of over 9,000 cancer genomes, coupled with functional validation in cell lines, highlights combinations of mutations required for tumor progression. This integrated approach provides a framework to stratify patients on the basis of interdependent genetic aberrations.

    • Marco Mina
    • , Arvind Iyer
    • , Daniele Tavernari
    • , Franck Raynaud
    •  & Giovanni Ciriello
  • Article |

    A study of 580 tomato lines resulting from a cross between a wild desert-adapted species and a domesticated cultivar elucidates the genetic basis of gene expression and metabolite variation associated with fruit traits and defense against pathogens.

    • Jędrzej Szymański
    • , Samuel Bocobza
    • , Sayantan Panda
    • , Prashant Sonawane
    • , Pablo D. Cárdenas
    • , Justin Lashbrooke
    • , Avinash Kamble
    • , Nir Shahaf
    • , Sagit Meir
    • , Arnaud Bovy
    • , Jules Beekwilder
    • , Yury Tikunov
    • , Irene Romero de la Fuente
    • , Dani Zamir
    • , Ilana Rogachev
    •  & Asaph Aharoni
  • Article |

    Multi-omic profiling of brain tissue from patients with Alzheimer’s disease (AD) identifies gains in H3K27ac and H3K9ac linked to transcription and disease pathways. Increasing H3K27ac and H3K9ac in a fly model of AD exacerbates neurodegeneration.

    • Raffaella Nativio
    • , Yemin Lan
    • , Greg Donahue
    • , Simone Sidoli
    • , Amit Berson
    • , Ananth R. Srinivasan
    • , Oksana Shcherbakova
    • , Alexandre Amlie-Wolf
    • , Ji Nie
    • , Xiaolong Cui
    • , Chuan He
    • , Li-San Wang
    • , Benjamin A. Garcia
    • , John Q. Trojanowski
    • , Nancy M. Bonini
    •  & Shelley L. Berger
  • Article |

    A massively parallel reporter assay (eSTARR-seq) shows that gene-distal transcription start sites can delineate active enhancers with higher resolution than histone modifications.

    • Nathaniel D. Tippens
    • , Jin Liang
    • , Alden King-Yung Leung
    • , Shayne D. Wierbowski
    • , Abdullah Ozer
    • , James G. Booth
    • , John T. Lis
    •  & Haiyuan Yu
  • Author Correction |

    • Valeria Orrù
    • , Maristella Steri
    • , Carlo Sidore
    • , Michele Marongiu
    • , Valentina Serra
    • , Stefania Olla
    • , Gabriella Sole
    • , Sandra Lai
    • , Mariano Dei
    • , Antonella Mulas
    • , Francesca Virdis
    • , Maria Grazia Piras
    • , Monia Lobina
    • , Mara Marongiu
    • , Maristella Pitzalis
    • , Francesca Deidda
    • , Annalisa Loizedda
    • , Stefano Onano
    • , Magdalena Zoledziewska
    • , Stephen Sawcer
    • , Marcella Devoto
    • , Myriam Gorospe
    • , Gonçalo R. Abecasis
    • , Matteo Floris
    • , Mauro Pala
    • , David Schlessinger
    • , Edoardo Fiorillo
    •  & Francesco Cucca
  • Perspective |

    This Perspective discusses important aspects of data generation, infrastructure and management that affect how the research community uses medical data, including genetic and genomic information.

    • Amalio Telenti
    •  & Xiaoqian Jiang
  • Article |

    An analysis of 3,757 Sardinian genomes identifies 122 association signals for 459 immune cell traits at 69 loci. Some variants are associated with autoimmune disorders.

    • Valeria Orrù
    • , Maristella Steri
    • , Carlo Sidore
    • , Michele Marongiu
    • , Valentina Serra
    • , Stefania Olla
    • , Gabriella Sole
    • , Sandra Lai
    • , Mariano Dei
    • , Antonella Mulas
    • , Francesca Virdis
    • , Maria Grazia Piras
    • , Monia Lobina
    • , Mara Marongiu
    • , Maristella Pitzalis
    • , Francesca Deidda
    • , Annalisa Loizedda
    • , Stefano Onano
    • , Magdalena Zoledziewska
    • , Stephen Sawcer
    • , Marcella Devoto
    • , Myriam Gorospe
    • , Gonçalo R. Abecasis
    • , Matteo Floris
    • , Mauro Pala
    • , David Schlessinger
    • , Edoardo Fiorillo
    •  & Francesco Cucca
  • Article |

    Mathematical modeling of evolutionary dynamics of neoantigens and immune escape in growing tumors shows that strong negative selection for neoantigens inhibits tumor growth but also provides a strong selective pressure for the evolution of immune escape.

    • Eszter Lakatos
    • , Marc J. Williams
    • , Ryan O. Schenck
    • , William C. H. Cross
    • , Jacob Househam
    • , Luis Zapata
    • , Benjamin Werner
    • , Chandler Gatenbee
    • , Mark Robertson-Tessi
    • , Chris P. Barnes
    • , Alexander R. A. Anderson
    • , Andrea Sottoriva
    •  & Trevor A. Graham
  • Author Correction |

    • Anton G. Henssen
    • , Richard Koche
    • , Jiali Zhuang
    • , Eileen Jiang
    • , Casie Reed
    • , Amy Eisenberg
    • , Eric Still
    • , Ian C. MacArthur
    • , Elias Rodríguez-Fos
    • , Santiago Gonzalez
    • , Montserrat Puiggròs
    • , Andrew N. Blackford
    • , Christopher E. Mason
    • , Elisa de Stanchina
    • , Mithat Gönen
    • , Anne-Katrin Emde
    • , Minita Shah
    • , Kanika Arora
    • , Catherine Reeves
    • , Nicholas D. Socci
    • , Elizabeth Perlman
    • , Cristina R. Antonescu
    • , Charles W. M. Roberts
    • , Hanno Steen
    • , Elizabeth Mullen
    • , Stephen P. Jackson
    • , David Torrents
    • , Zhiping Weng
    • , Scott A. Armstrong
    •  & Alex Kentsis
  • Comment |

    The emergence of the COVID-19 pandemic has spurred a global rush to uncover basic biological mechanisms to inform effective vaccine and drug development. Despite the novelty of the virus, global sequencing efforts have already identified genomic variation across isolates. To enable easy exploration and spatial visualization of the potential implications of SARS-CoV-2 mutations in infection, host immunity and drug development, we have developed COVID-3D ( http://biosig.unimelb.edu.au/covid3d/ ).

    • Stephanie Portelli
    • , Moshe Olshansky
    • , Carlos H. M. Rodrigues
    • , Elston N. D’Souza
    • , Yoochan Myung
    • , Michael Silk
    • , Azadeh Alavi
    • , Douglas E. V. Pires
    •  & David B. Ascher
  • Comment |

    The WashU Virus Genome Browser is a web-based portal for efficient visualization of viral ‘omics’ data in the context of a variety of annotation tracks and host infection responses. The browser features both a phylogenetic-tree-based view and a genomic-coordinate, track-based view in which users can analyze the sequence features of viral genomes, sequence diversity among viral strains, genomic sites of diagnostic tests, predicted immunogenic epitopes and a continuously updated repository of publicly available genomic datasets.

    • Jennifer A. Flynn
    • , Deepak Purushotham
    • , Mayank N. K. Choudhary
    • , Xiaoyu Zhuo
    • , Changxu Fan
    • , Gavriel Matt
    • , Daofeng Li
    •  & Ting Wang
  • Comment |

    The UCSC SARS-CoV-2 Genome Browser ( https://genome.ucsc.edu/covid19.html ) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar viruses, immune epitopes, RT–PCR and sequencing primers and CRISPR guides. We invite all investigators to contribute to this resource to accelerate research and development activities globally.

    • Jason D. Fernandes
    • , Angie S. Hinrichs
    • , Hiram Clawson
    • , Jairo Navarro Gonzalez
    • , Brian T. Lee
    • , Luis R. Nassar
    • , Brian J. Raney
    • , Kate R. Rosenbloom
    • , Santrupti Nerli
    • , Arjun A. Rao
    • , Daniel Schmelter
    • , Alastair Fyfe
    • , Nathan Maulding
    • , Ann S. Zweig
    • , Todd M. Lowe
    • , Manuel Ares Jr
    • , Russ Corbet-Detig
    • , W. James Kent
    • , David Haussler
    •  & Maximilian Haeussler
  • Analysis |

    Mendelian randomization (MR) and colocalization analyses are used to estimate causal effects of 1,002 plasma proteins on 225 phenotypes. Evidence from drug developmental programs shows that target-indication pairs with MR and colocalization support were more likely to be approved, highlighting the value of this approach for prioritizing therapeutic targets.

    • Jie Zheng
    • , Valeriia Haberland
    • , Denis Baird
    • , Venexia Walker
    • , Philip C. Haycock
    • , Mark R. Hurle
    • , Alex Gutteridge
    • , Pau Erola
    • , Yi Liu
    • , Shan Luo
    • , Jamie Robinson
    • , Tom G. Richardson
    • , James R. Staley
    • , Benjamin Elsworth
    • , Stephen Burgess
    • , Benjamin B. Sun
    • , John Danesh
    • , Heiko Runz
    • , Joseph C. Maranville
    • , Hannah M. Martin
    • , James Yarmolinsky
    • , Charles Laurin
    • , Michael V. Holmes
    • , Jimmy Z. Liu
    • , Karol Estrada
    • , Rita Santos
    • , Linda McCarthy
    • , Dawn Waterworth
    • , Matthew R. Nelson
    • , George Davey Smith
    • , Adam S. Butterworth
    • , Gibran Hemani
    • , Robert A. Scott
    •  & Tom R. Gaunt
  • Author Correction |

    • Andrea Lunardi
    • , Ugo Ala
    • , Mirjam T. Epping
    • , Leonardo Salmena
    • , John G. Clohessy
    • , Kaitlyn A. Webster
    • , Guocan Wang
    • , Roberta Mazzucchelli
    • , Maristella Bianconi
    • , Edward C. Stack
    • , Rosina Lis
    • , Akash Patnaik
    • , Lewis C. Cantley
    • , Glenn Bubley
    • , Carlos Cordon-Cardo
    • , William L. Gerald
    • , Rodolfo Montironi
    • , Sabina Signoretti
    • , Massimo Loda
    • , Caterina Nardella
    •  & Pier Paolo Pandolfi
  • News & Views |

    The role of N6-methyladenosine (m6A) is still not fully understood. Two new studies advance understanding of this RNA modification. One shows that m6A modification of nascent messenger RNA promotes transcription by recruiting the histone H3 K9 demethylase KDM3B. Another study identifies genetic variants that affect m6A deposition and human disease.

    • Dalen Chan
    •  & Pedro J. Batista
  • News & Views |

    Binding of RNA to the gene expression regulator Polycomb repressive complex 2 (PRC2) has been proposed to antagonize PRC2’s chromatin recruitment. A new study now shows that RNA is in fact critical for correct recruitment of PRC2 at its target genes in human pluripotent stem cells and suggests that interplay of PRC2 and RNA can fine-tune PRC2’s regulatory role.

    • Ivano Mocavini
    •  & Luciano Di Croce
  • Editorial |

    Increasing amounts of crop genomic resources, along with new technical achievements in genome analysis, can facilitate basic and translational research in agriculture, and expand the ability to meet the global challenge of food production and security.

  • Article |

    MOBSTER is an approach for subclonal reconstruction of tumors from cancer genomics data on the basis of models that combine machine learning with evolutionary theory, thus leading to more accurate evolutionary histories of tumors.

    • Giulio Caravagna
    • , Timon Heide
    • , Marc J. Williams
    • , Luis Zapata
    • , Daniel Nichol
    • , Ketevan Chkhaidze
    • , William Cross
    • , George D. Cresswell
    • , Benjamin Werner
    • , Ahmet Acar
    • , Louis Chesler
    • , Chris P. Barnes
    • , Guido Sanguinetti
    • , Trevor A. Graham
    •  & Andrea Sottoriva
  • Article |

    Insertion of a tissue-invariant chromatin domain boundary into 16 ectopic loci leads to various structural phenotypes, which depend on local chromatin features, CTCF binding and transcriptional status.

    • Di Zhang
    • , Peng Huang
    • , Malini Sharma
    • , Cheryl A. Keller
    • , Belinda Giardine
    • , Haoyue Zhang
    • , Thomas G. Gilgenast
    • , Jennifer E. Phillips-Cremins
    • , Ross C. Hardison
    •  & Gerd A. Blobel