Genomics

  • Article
    | Open Access

    Somatic mutations in MED12 have been implicated as the causal genetic lesion in the majority of uterine leiomyomas. Here, the authors profile the chromatin landscape of matched normal and leiomyoma tissues and find that changes in enhancer acetylation, enhancer-promoter interaction strength, differential enhancer usage and transcription factor AP-1 occupancy are significant drivers of transcriptional dysregulation in MED12 mutant leiomyomas.

    • Mthabisi B. Moyo
    • , J. Brandon Parker
    •  & Debabrata Chakravarti
  • Article
    | Open Access

    Ancient DNA analysis of early European farmers has found a high level of genetic affinity with present-day Sardinians. Here, the authors generate genome-wide capture data for 70 individuals from Sardinia spanning the Middle Neolithic to Medieval period to reveal relationships with mainland European populations shifting over time.

    • Joseph H. Marcus
    • , Cosimo Posth
    • , Harald Ringbauer
    • , Luca Lai
    • , Robin Skeates
    • , Carlo Sidore
    • , Jessica Beckett
    • , Anja Furtwängler
    • , Anna Olivieri
    • , Charleston W. K. Chiang
    • , Hussein Al-Asadi
    • , Kushal Dey
    • , Tyler A. Joseph
    • , Chi-Chun Liu
    • , Clio Der Sarkissian
    • , Rita Radzevičiūtė
    • , Megan Michel
    • , Maria Giuseppina Gradoli
    • , Patrizia Marongiu
    • , Salvatore Rubino
    • , Vittorio Mazzarello
    • , Daniela Rovina
    • , Alessandra La Fragola
    • , Rita Maria Serra
    • , Pasquale Bandiera
    • , Raffaella Bianucci
    • , Elisa Pompianu
    • , Clizia Murgia
    • , Michele Guirguis
    • , Rosana Pla Orquin
    • , Noreen Tuross
    • , Peter van Dommelen
    • , Wolfgang Haak
    • , David Reich
    • , David Schlessinger
    • , Francesco Cucca
    • , Johannes Krause
    •  & John Novembre
  • Article
    | Open Access

    Although there is extensive theory predicting the effects of population bottlenecks on mutation load, there is little empirical evidence from recent bottlenecks. Here, Grossen et al. compare the consequences of population bottlenecks in six ibex species for genome-wide variation and mutation load.

    • Christine Grossen
    • , Frédéric Guillaume
    • , Lukas F. Keller
    •  & Daniel Croll
  • Article
    | Open Access

    Understanding tumour development at a granular level is a challenge in solid tumours. Here, the authors provide a cell atlas across tumour development in a genetic model of salivary gland squamous cell carcinoma using single-cell transcriptome and epitope profiling.

    • Samantha D. Praktiknjo
    • , Benedikt Obermayer
    • , Qionghua Zhu
    • , Liang Fang
    • , Haiyue Liu
    • , Hazel Quinn
    • , Marlon Stoeckius
    • , Christine Kocks
    • , Walter Birchmeier
    •  & Nikolaus Rajewsky
  • Article
    | Open Access

    Despite tremendous genomic resources in the Arabidopsis community, only a few whole genome de novo assemblies are available. Here, the authors report chromosome-level reference-quality assemblies of seven A. thaliana accessions and reveal hotspots of rearrangements with altered evolutionary dynamics.

    • Wen-Biao Jiao
    •  & Korbinian Schneeberger
  • Article
    | Open Access

    Teff is an indigenous cereal critical to food security in the Horn of Africa. Here, the authors report an improved genome assembly and observe the surprisingly low levels of large-scale structural rearrangement, homoeologous exchanges, or bias gene loss after the formation of this tetraploid species.

    • Robert VanBuren
    • , Ching Man Wai
    • , Xuewen Wang
    • , Jeremy Pardo
    • , Alan E. Yocca
    • , Hao Wang
    • , Srinivasa R. Chaluvadi
    • , Guomin Han
    • , Douglas Bryant
    • , Patrick P. Edger
    • , Joachim Messing
    • , Mark E. Sorrells
    • , Todd C. Mockler
    • , Jeffrey L. Bennetzen
    •  & Todd P. Michael
  • Article
    | Open Access

    Most currently available statistical tools for the analysis of ATAC-seq data were repurposed from tools developed for other functional genomics data (e.g. ChIP-seq). Here, Gabitto et al develop ChromA, a Bayesian statistical approach for the analysis of both bulk and single-cell ATAC-seq data.

    • Mariano I. Gabitto
    • , Anders Rasmussen
    • , Orly Wapinski
    • , Kathryn Allaway
    • , Nicholas Carriero
    • , Gordon J. Fishell
    •  & Richard Bonneau
  • Article
    | Open Access

    Whether the immune system aging differs between men and women is barely known. Here the authors characterize gene expression, chromatin state and immune subset composition in the blood of healthy humans 22 to 93 years of age, uncovering shared as well as sex-unique alterations, and create a web resource to interactively explore the data.

    • Eladio J. Márquez
    • , Cheng-han Chung
    • , Radu Marches
    • , Robert J. Rossi
    • , Djamel Nehar-Belaid
    • , Alper Eroglu
    • , David J. Mellert
    • , George A. Kuchel
    • , Jacques Banchereau
    •  & Duygu Ucar
  • Article
    | Open Access

    Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

    • Shimin Shuai
    • , Federico Abascal
    • , Samirkumar B. Amin
    • , Gary D. Bader
    • , Pratiti Bandopadhayay
    • , Jonathan Barenboim
    • , Rameen Beroukhim
    • , Johanna Bertl
    • , Keith A. Boroevich
    • , Søren Brunak
    • , Peter J. Campbell
    • , Joana Carlevaro-Fita
    • , Dimple Chakravarty
    • , Calvin Wing Yiu Chan
    • , Ken Chen
    • , Jung Kyoon Choi
    • , Jordi Deu-Pons
    • , Priyanka Dhingra
    • , Klev Diamanti
    • , Lars Feuerbach
    • , J. Lynn Fink
    • , Nuno A. Fonseca
    • , Joan Frigola
    • , Carlo Gambacorti-Passerini
    • , Dale W. Garsed
    • , Mark Gerstein
    • , Gad Getz
    • , Qianyun Guo
    • , Ivo G. Gut
    • , David Haan
    • , Mark P. Hamilton
    • , Nicholas J. Haradhvala
    • , Arif O. Harmanci
    • , Mohamed Helmy
    • , Carl Herrmann
    • , Julian M. Hess
    • , Asger Hobolth
    • , Ermin Hodzic
    • , Chen Hong
    • , Henrik Hornshøj
    • , Keren Isaev
    • , Jose M. G. Izarzugaza
    • , Rory Johnson
    • , Todd A. Johnson
    • , Malene Juul
    • , Randi Istrup Juul
    • , Andre Kahles
    • , Abdullah Kahraman
    • , Manolis Kellis
    • , Ekta Khurana
    • , Jaegil Kim
    • , Jong K. Kim
    • , Youngwook Kim
    • , Jan Komorowski
    • , Jan O. Korbel
    • , Sushant Kumar
    • , Andrés Lanzós
    • , Erik Larsson
    • , Michael S. Lawrence
    • , Donghoon Lee
    • , Kjong-Van Lehmann
    • , Shantao Li
    • , Xiaotong Li
    • , Ziao Lin
    • , Eric Minwei Liu
    • , Lucas Lochovsky
    • , Shaoke Lou
    • , Tobias Madsen
    • , Kathleen Marchal
    • , Iñigo Martincorena
    • , Alexander Martinez-Fundichely
    • , Yosef E. Maruvka
    • , Patrick D. McGillivray
    • , William Meyerson
    • , Ferran Muiños
    • , Loris Mularoni
    • , Hidewaki Nakagawa
    • , Morten Muhlig Nielsen
    • , Marta Paczkowska
    • , Keunchil Park
    • , Kiejung Park
    • , Jakob Skou Pedersen
    • , Tirso Pons
    • , Sergio Pulido-Tamayo
    • , Benjamin J. Raphael
    • , Jüri Reimand
    • , Iker Reyes-Salazar
    • , Matthew A. Reyna
    • , Esther Rheinbay
    • , Mark A. Rubin
    • , Carlota Rubio-Perez
    • , S. Cenk Sahinalp
    • , Gordon Saksena
    • , Leonidas Salichos
    • , Chris Sander
    • , Steven E. Schumacher
    • , Mark Shackleton
    • , Ofer Shapira
    • , Ciyue Shen
    • , Raunak Shrestha
    • , Shimin Shuai
    • , Nikos Sidiropoulos
    • , Lina Sieverling
    • , Nasa Sinnott-Armstrong
    • , Lincoln D. Stein
    • , Joshua M. Stuart
    • , David Tamborero
    • , Grace Tiao
    • , Tatsuhiko Tsunoda
    • , Husen M. Umer
    • , Liis Uusküla-Reimand
    • , Alfonso Valencia
    • , Miguel Vazquez
    • , Lieven P. C. Verbeke
    • , Claes Wadelius
    • , Lina Wadi
    • , Jiayin Wang
    • , Jonathan Warrell
    • , Sebastian M. Waszak
    • , Joachim Weischenfeldt
    • , David A. Wheeler
    • , Guanming Wu
    • , Jun Yu
    • , Jing Zhang
    • , Xuanping Zhang
    • , Yan Zhang
    • , Zhongming Zhao
    • , Lihua Zou
    • , Christian von Mering
    • , Steven Gallinger
    •  & Lincoln Stein
  • Article
    | Open Access

    Dingoes evolved in isolation from both their domesticated and wild ancestors. Here, the authors investigate the genomic basis of the feralization of dingoes and trace their origin to domestic dogs that migrated to Australia approximately 8300 years ago.

    • Shao-jie Zhang
    • , Guo-Dong Wang
    • , Pengcheng Ma
    • , Liang-liang Zhang
    • , Ting-Ting Yin
    • , Yan-hu Liu
    • , Newton O. Otecko
    • , Meng Wang
    • , Ya-ping Ma
    • , Lu Wang
    • , Bingyu Mao
    • , Peter Savolainen
    •  & Ya-ping Zhang
  • Article
    | Open Access

    Despite widespread transcription of LncRNA in mammalian systems, their contribution to metabolic homeostasis at the cellular and tissue level remains elusive. Here Pradas-Juni et al. describe a transcription factor–LncRNA pathway that couples hepatocyte nutrient sensing to regulation of glucose metabolism in mice.

    • Marta Pradas-Juni
    • , Nils R. Hansmeier
    • , Jenny C. Link
    • , Elena Schmidt
    • , Bjørk Ditlev Larsen
    • , Paul Klemm
    • , Nicola Meola
    • , Hande Topel
    • , Rute Loureiro
    • , Ines Dhaouadi
    • , Christoph A. Kiefer
    • , Robin Schwarzer
    • , Sajjad Khani
    • , Matteo Oliverio
    • , Motoharu Awazawa
    • , Peter Frommolt
    • , Joerg Heeren
    • , Ludger Scheja
    • , Markus Heine
    • , Christoph Dieterich
    • , Hildegard Büning
    • , Ling Yang
    • , Haiming Cao
    • , Dario F. De Jesus
    • , Rohit N. Kulkarni
    • , Branko Zevnik
    • , Simon E. Tröder
    • , Uwe Knippschild
    • , Peter A. Edwards
    • , Richard G. Lee
    • , Masayuki Yamamoto
    • , Igor Ulitsky
    • , Eduardo Fernandez-Rebollo
    • , Thomas Q. de Aguiar Vallim
    •  & Jan-Wilhelm Kornfeld
  • Article
    | Open Access

    Ibrutinib, a Bruton tyrosine kinase inhibitor, provides effective treatment for chronic lymphocytic leukemia (CLL). Here, the authors describe time-dependent molecular changes to malignant cells and to the immune system in patients undergoing ibrutinib therapy, with can be used for therapy monitoring.

    • André F. Rendeiro
    • , Thomas Krausgruber
    • , Nikolaus Fortelny
    • , Fangwen Zhao
    • , Thomas Penz
    • , Matthias Farlik
    • , Linda C. Schuster
    • , Amelie Nemc
    • , Szabolcs Tasnády
    • , Marienn Réti
    • , Zoltán Mátrai
    • , Donát Alpár
    • , Csaba Bödör
    • , Christian Schmidl
    •  & Christoph Bock
  • Article
    | Open Access

    The endothelial to haematopoietic transition (EHT) is the process where haemogenic endothelium differentiates into haematopoietic stem and progenitor cells (HSPCs). Here the authors use single cell transcriptomics and antibody screening to identify CD44 as a marker of EHT that is required for EHT and HSPC development.

    • Morgan Oatley
    • , Özge Vargel Bölükbası
    • , Valentine Svensson
    • , Maya Shvartsman
    • , Kerstin Ganter
    • , Katharina Zirngibl
    • , Polina V. Pavlovich
    • , Vladislava Milchevskaya
    • , Vladimira Foteva
    • , Kedar N. Natarajan
    • , Bianka Baying
    • , Vladimir Benes
    • , Kiran R. Patil
    • , Sarah A. Teichmann
    •  & Christophe Lancrin
  • Article
    | Open Access

    Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.

    • Mark Pinese
    • , Paul Lacaze
    • , Emma M. Rath
    • , Andrew Stone
    • , Marie-Jo Brion
    • , Adam Ameur
    • , Sini Nagpal
    • , Clare Puttick
    • , Shane Husson
    • , Dmitry Degrave
    • , Tina Navin Cristina
    • , Vivian F. S. Kahl
    • , Aaron L. Statham
    • , Robyn L. Woods
    • , John J. McNeil
    • , Moeen Riaz
    • , Margo Barr
    • , Mark R. Nelson
    • , Christopher M. Reid
    • , Anne M. Murray
    • , Raj C. Shah
    • , Rory Wolfe
    • , Joshua R. Atkins
    • , Chantel Fitzsimmons
    • , Heath M. Cairns
    • , Melissa J. Green
    • , Vaughan J. Carr
    • , Mark J. Cowley
    • , Hilda A. Pickett
    • , Paul A. James
    • , Joseph E. Powell
    • , Warren Kaplan
    • , Greg Gibson
    • , Ulf Gyllensten
    • , Murray J. Cairns
    • , Martin McNamara
    • , Marcel E. Dinger
    •  & David M. Thomas
  • Article
    | Open Access

    Mikania micrantha is an extremely fast-growing invasive plant species that can cause serious damage to natural ecosystems. Here, the authors assemble its chromosome-scale reference genome and explore possible mechanisms that contribute to its rapid growth.

    • Bo Liu
    • , Jian Yan
    • , Weihua Li
    • , Lijuan Yin
    • , Ping Li
    • , Hanxia Yu
    • , Longsheng Xing
    • , Minling Cai
    • , Hengchao Wang
    • , Mengxin Zhao
    • , Jin Zheng
    • , Feng Sun
    • , Zhenzhen Wang
    • , Zhaoyang Jiang
    • , Qiaojing Ou
    • , Shubin Li
    • , Lu Qu
    • , Qilei Zhang
    • , Yaping Zheng
    • , Xi Qiao
    • , Yu Xi
    • , Yan Zhang
    • , Fan Jiang
    • , Cong Huang
    • , Conghui Liu
    • , Yuwei Ren
    • , Sen Wang
    • , Hangwei Liu
    • , Jianyang Guo
    • , Haihong Wang
    • , Hui Dong
    • , Changlian Peng
    • , Wanqiang Qian
    • , Wei Fan
    •  & Fanghao Wan
  • Article
    | Open Access

    The South African quality protein maize (QPM) cultivars have the desired high lysine content and kernel hardness due to o2 mutation and the introgression of modifiers of o2 (Mo2) QTLs, respectively. Here, the authors assemble the genome of a QPM line and identify candidate genes underlying Mo2 QTLs.

    • Changsheng Li
    • , Xiaoli Xiang
    • , Yongcai Huang
    • , Yong Zhou
    • , Dong An
    • , Jiaqiang Dong
    • , Chenxi Zhao
    • , Hongjun Liu
    • , Yubin Li
    • , Qiong Wang
    • , Chunguang Du
    • , Joachim Messing
    • , Brian A. Larkins
    • , Yongrui Wu
    •  & Wenqin Wang
  • Article
    | Open Access

    DNA methylation is associated with complex traits and the expression of genes and proteins. Here, Zaghlool et al. perform epigenome-wide association studies for 1,123 plasma proteins, replicate obtained protein (p)QTMs in an independent cohort and find overlap of pQTMs with expression QTMs and previously reported disease associations.

    • Shaza B. Zaghlool
    • , Brigitte Kühnel
    • , Mohamed A. Elhadad
    • , Sara Kader
    • , Anna Halama
    • , Gaurav Thareja
    • , Rudolf Engelke
    • , Hina Sarwath
    • , Eman K. Al-Dous
    • , Yasmin A. Mohamoud
    • , Thomas Meitinger
    • , Rory Wilson
    • , Konstantin Strauch
    • , Annette Peters
    • , Dennis O. Mook-Kanamori
    • , Johannes Graumann
    • , Joel A. Malek
    • , Christian Gieger
    • , Melanie Waldenberger
    •  & Karsten Suhre
  • Article
    | Open Access

    Single strand breaks represent the most common form of DNA damage yet no methods to map them in a genome-wide fashion at single nucleotide resolution exist. Here the authors develop such a method and apply to uncover patterns of single-strand DNA “breakome” in different biological conditions.

    • Huifen Cao
    • , Lorena Salazar-García
    • , Fan Gao
    • , Thor Wahlestedt
    • , Chun-Lin Wu
    • , Xueer Han
    • , Ye Cai
    • , Dongyang Xu
    • , Fang Wang
    • , Lu Tang
    • , Natalie Ricciardi
    • , DingDing Cai
    • , Huifang Wang
    • , Mario P. S. Chin
    • , James A. Timmons
    • , Claes Wahlestedt
    •  & Philipp Kapranov
  • Article
    | Open Access

    Stroke risk is influenced by genetic and lifestyle factors and previously a genomic risk score (GRS) for stroke was proposed, albeit with limited predictive power. Here, Abraham et al. develop a metaGRS that is composed of several stroke-related GRSs and demonstrate improved predictive power compared with individual GRS or classic risk factors.

    • Gad Abraham
    • , Rainer Malik
    • , Ekaterina Yonova-Doing
    • , Agus Salim
    • , Tingting Wang
    • , John Danesh
    • , Adam S. Butterworth
    • , Joanna M. M. Howson
    • , Michael Inouye
    •  & Martin Dichgans
  • Article
    | Open Access

    Newly acquired plasmids are frequently lost due to fitness costs. Here, Zhang et al. show that the evolution of satellite plasmids with gene deletions can reduce fitness costs by driving down the copy number of full plasmids and thus favor maintenance of the full plasmid and its novel accessory genes.

    • Xue Zhang
    • , Daniel E. Deatherage
    • , Hao Zheng
    • , Stratton J. Georgoulis
    •  & Jeffrey E. Barrick
  • Article
    | Open Access

    Why transposable elements (TEs) accumulate in polyploids and the evolutionary implications remain unclear. Here, the authors show that following whole genome duplication, relaxed purifying selection is the main driver of TE over-accumulation, which provides variants for rapid local adaptation.

    • Pierre Baduel
    • , Leandro Quadrana
    • , Ben Hunter
    • , Kirsten Bomblies
    •  & Vincent Colot
  • Article
    | Open Access

    The edematous form of severe acute childhood malnutrition (ESAM) presents with more severe multi-organ dysfunction than non-edematous SAM (NESAM). Here the authors assess genome-wide DNA methylation in buccal cells of SAM children and find that ESAM is characterized by hypomethylation at genes associated with disorders of nutrition and metabolism, including fatty liver and diabetes.

    • Katharina V. Schulze
    • , Shanker Swaminathan
    • , Sharon Howell
    • , Aarti Jajoo
    • , Natasha C. Lie
    • , Orgen Brown
    • , Roa Sadat
    • , Nancy Hall
    • , Liang Zhao
    • , Kwesi Marshall
    • , Thaddaeus May
    • , Marvin E. Reid
    • , Carolyn Taylor-Bryan
    • , Xueqing Wang
    • , John W. Belmont
    • , Yongtao Guan
    • , Mark J. Manary
    • , Indi Trehan
    • , Colin A. McKenzie
    •  & Neil A. Hanchard
  • Article
    | Open Access

    Uterine adenomyosis often co-occurs with endometriosis or leiomyoma, but little is known about its molecular underpinnings. Here, the authors show that KRAS mutations are frequent in this disease, which might reduce sensitivity to progestin treatment via epigenetic silencing of the progesterone receptor.

    • Satoshi Inoue
    • , Yasushi Hirota
    • , Toshihide Ueno
    • , Yamato Fukui
    • , Emiko Yoshida
    • , Takuo Hayashi
    • , Shinya Kojima
    • , Reina Takeyama
    • , Taiki Hashimoto
    • , Tohru Kiyono
    • , Masako Ikemura
    • , Ayumi Taguchi
    • , Tomoki Tanaka
    • , Yosuke Tanaka
    • , Seiji Sakata
    • , Kengo Takeuchi
    • , Ayako Muraoka
    • , Satoko Osuka
    • , Tsuyoshi Saito
    • , Katsutoshi Oda
    • , Yutaka Osuga
    • , Yasuhisa Terao
    • , Masahito Kawazu
    •  & Hiroyuki Mano
  • Article
    | Open Access

    Birch pitch is thought to have been used in prehistoric times as hafting material or antiseptic and tooth imprints suggest that it was chewed. Here, the authors report a 5,700 year-old piece of chewed birch pitch from Denmark from which they successfully recovered a complete ancient human genome and oral microbiome DNA.

    • Theis Z. T. Jensen
    • , Jonas Niemann
    • , Katrine Højholt Iversen
    • , Anna K. Fotakis
    • , Shyam Gopalakrishnan
    • , Åshild J. Vågene
    • , Mikkel Winther Pedersen
    • , Mikkel-Holger S. Sinding
    • , Martin R. Ellegaard
    • , Morten E. Allentoft
    • , Liam T. Lanigan
    • , Alberto J. Taurozzi
    • , Sofie Holtsmark Nielsen
    • , Michael W. Dee
    • , Martin N. Mortensen
    • , Mads C. Christensen
    • , Søren A. Sørensen
    • , Matthew J. Collins
    • , M. Thomas P. Gilbert
    • , Martin Sikora
    • , Simon Rasmussen
    •  & Hannes Schroeder
  • Article
    | Open Access

    Four genome-wide associated loci are currently known for malaria susceptibility. Here, the authors expand on earlier work by combining data from 11 malaria-endemic countries and additional population sequencing informing an African-enriched imputation reference panel, with findings including a previously unreported association on chromosome 6.

    • Gavin Band
    • , Quang Si Le
    • , Geraldine M. Clarke
    • , Katja Kivinen
    • , Christina Hubbart
    • , Anna E. Jeffreys
    • , Kate Rowlands
    • , Ellen M. Leffler
    • , Muminatou Jallow
    • , David J. Conway
    • , Fatoumatta Sisay-Joof
    • , Giorgio Sirugo
    • , Umberto d’Alessandro
    • , Ousmane B. Toure
    • , Mahamadou A. Thera
    • , Salimata Konate
    • , Sibiri Sissoko
    • , Valentina D. Mangano
    • , Edith C. Bougouma
    • , Sodiomon B. Sirima
    • , Lucas N. Amenga-Etego
    • , Anita K. Ghansah
    • , Abraham V. O. Hodgson
    • , Michael D. Wilson
    • , Anthony Enimil
    • , Daniel Ansong
    • , Jennifer Evans
    • , Subulade A. Ademola
    • , Tobias O. Apinjoh
    • , Carolyne M. Ndila
    • , Alphaxard Manjurano
    • , Chris Drakeley
    • , Hugh Reyburn
    • , Nguyen Hoan Phu
    • , Nguyen Thi Ngoc Quyen
    • , Cao Quang Thai
    • , Tran Tinh Hien
    • , Yik Ying Teo
    • , Laurens Manning
    • , Moses Laman
    • , Pascal Michon
    • , Harin Karunajeewa
    • , Peter Siba
    • , Steve Allen
    • , Angela Allen
    • , Melanie Bahlo
    • , Timothy M. E. Davis
    • , Victoria Simpson
    • , Jennifer Shelton
    • , Chris C. A. Spencer
    • , George B. J. Busby
    • , Angeliki Kerasidou
    • , Eleanor Drury
    • , Jim Stalker
    • , Alexander Dilthey
    • , Alexander J. Mentzer
    • , Gil McVean
    • , Kalifa A. Bojang
    • , Ogobara Doumbo
    • , David Modiano
    • , Kwadwo A. Koram
    • , Tsiri Agbenyega
    • , Olukemi K. Amodu
    • , Eric Achidi
    • , Thomas N. Williams
    • , Kevin Marsh
    • , Eleanor M. Riley
    • , Malcolm Molyneux
    • , Terrie Taylor
    • , Sarah J. Dunstan
    • , Jeremy Farrar
    • , Ivo Mueller
    • , Kirk A. Rockett
    •  & Dominic P. Kwiatkowski
  • Article
    | Open Access

    The kidney is vascularized with highly specialized and zonated endothelial cells that are essential for its filtration function. Here, Barry et al. provide a single-cell RNA sequencing analysis of the kidney vasculature that highlights its transcriptional heterogeneity and uncovers pathways important for its development and function.

    • David M. Barry
    • , Elizabeth A. McMillan
    • , Balvir Kunar
    • , Raphael Lis
    • , Tuo Zhang
    • , Tyler Lu
    • , Edward Daniel
    • , Masataka Yokoyama
    • , Jesus M. Gomez-Salinero
    • , Angara Sureshbabu
    • , Ondine Cleaver
    • , Annarita Di Lorenzo
    • , Mary E. Choi
    • , Jenny Xiang
    • , David Redmond
    • , Sina Y. Rabbany
    • , Thangamani Muthukumar
    •  & Shahin Rafii
  • Article
    | Open Access

    Cell senescence involves stable arrest of cell proliferation and changes in gene expression and 3D genome reorganization. Here, the authors show that human condensin II complex participates in reorganization of the chromatin compartments, primarily through switching from heterochromatic B to euchromatic A compartments.

    • Osamu Iwasaki
    • , Hideki Tanizawa
    • , Kyoung-Dong Kim
    • , Andrew Kossenkov
    • , Timothy Nacarelli
    • , Sanki Tashiro
    • , Sonali Majumdar
    • , Louise C. Showe
    • , Rugang Zhang
    •  & Ken-ichi Noma
  • Article
    | Open Access

    N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are eukaryotic mRNA modifications. Here the authors develop m6A-Crosslinking-Exonuclease-sequencing to map quantitative methylome changes at single-base-resolution after individually knocking out each known methyltransferase or demethylase.

    • Casslynn W. Q. Koh
    • , Yeek Teck Goh
    •  & W. S. Sho Goh
  • Article
    | Open Access

    Although most are silenced, certain transposable elements (TEs) have been co-opted by the host. Here, the authors quantify the epigenomic status of TEs using data from the Roadmap Epigenomics Project, provide a systematic profile of TE activity across normal human tissues and development, finding that TEs encompass a quarter of the human regulatory epigenome, with 47% of TEs in regulatory states.

    • Erica C. Pehrsson
    • , Mayank N. K. Choudhary
    • , Vasavi Sundaram
    •  & Ting Wang
  • Article
    | Open Access

    The basis of sexual dimorphism in non-model species may be elusive, in part due to a lack of genomic and molecular resources. Here, Li et al. report a high-quality anuran genome and reveal candidate genes and pathways associated with shaping sexually dimorphic nuptial spines in a moustache toad.

    • Jun Li
    • , Haiyan Yu
    • , Wenxia Wang
    • , Chao Fu
    • , Wei Zhang
    • , Fengming Han
    •  & Hua Wu
  • Article
    | Open Access

    Urinary tract infections (UTIs) are associated with changes in the gut microbiome. Here, the authors evaluate the relationship between the gut microbiome and development of UTI in kidney transplant patients and show that uropathogenic gut abundance might represent a risk factor for development of bacteriuria and UTI.

    • Matthew Magruder
    • , Adam N. Sholi
    • , Catherine Gong
    • , Lisa Zhang
    • , Emmanuel Edusei
    • , Jennifer Huang
    • , Shady Albakry
    • , Michael J. Satlin
    • , Lars F. Westblade
    • , Carl Crawford
    • , Darshana M. Dadhania
    • , Michelle Lubetzky
    • , Ying Taur
    • , Eric Littman
    • , Lilan Ling
    • , Philip Burnham
    • , Iwijn De Vlaminck
    • , Eric Pamer
    • , Manikkam Suthanthiran
    •  & John Richard Lee
  • Article
    | Open Access

    The off-target effects and on-target mutations of CRISPR editing in higher non-human primates are complex. Here the authors perform whole genome trio sequencing of rhesus monkeys and see no unexpected mutations.

    • Xin Luo
    • , Yaoxi He
    • , Chao Zhang
    • , Xiechao He
    • , Lanzhen Yan
    • , Min Li
    • , Ting Hu
    • , Yan Hu
    • , Jin Jiang
    • , Xiaoyu Meng
    • , Weizhi Ji
    • , Xudong Zhao
    • , Ping Zheng
    • , Shuhua Xu
    •  & Bing Su
  • Article
    | Open Access

    Thymic epithelial cells (TEC) are essential for the maturation of functional T cells, while thymus size is proportional to the overall output efficiency. Here the authors show, using transcriptome analyses, that mouse fetal TEC maintain a Myc-dependent genetic program to ensure a rapid increase in thymus size, and thereby expedited T cell generation.

    • Jennifer E. Cowan
    • , Justin Malin
    • , Yongge Zhao
    • , Mina O. Seedhom
    • , Christelle Harly
    • , Izumi Ohigashi
    • , Michael Kelly
    • , Yousuke Takahama
    • , Jonathan W. Yewdell
    • , Maggie Cam
    •  & Avinash Bhandoola
  • Article
    | Open Access

    Songbirds have extensive germline–soma genome differences due to developmental elimination of a germline-specific chromosome (GRC). Here, the authors show that the GRC contains dozens of expressed developmental genes, some of which have been on the GRC since the ancestor of all songbirds.

    • Cormac M. Kinsella
    • , Francisco J. Ruiz-Ruano
    • , Anne-Marie Dion-Côté
    • , Alexander J. Charles
    • , Toni I. Gossmann
    • , Josefa Cabrero
    • , Dennis Kappei
    • , Nicola Hemmings
    • , Mirre J. P. Simons
    • , Juan Pedro M. Camacho
    • , Wolfgang Forstmeier
    •  & Alexander Suh
  • Article
    | Open Access

    The neural tissues of coleoids have a greater fraction of nonsynonymous sites than synonymous sites subject to high levels of A-to-I RNA editing, a pattern thought to indicate widespread adaptive editing. Here the authors propose and provide evidence for an alternative, nonadaptive explanation.

    • Daohan Jiang
    •  & Jianzhi Zhang
  • Article
    | Open Access

    A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.

    • Jaime Iranzo
    • , Yuri I. Wolf
    • , Eugene V. Koonin
    •  & Itamar Sela
  • Article
    | Open Access

    The nematode Halicephalobus mephisto has been found more than 1 km underground and can tolerate high heat and low oxygen. Here Weinstein et al. report the genome and transcriptome of H. mephisto and identify genomic innovations that likely are responsible for its tolerance to heat.

    • Deborah J. Weinstein
    • , Sarah E. Allen
    • , Maggie C. Y. Lau
    • , Mariana Erasmus
    • , Kathryn C. Asalone
    • , Kathryn Walters-Conte
    • , Gintaras Deikus
    • , Robert Sebra
    • , Gaetan Borgonie
    • , Esta van Heerden
    • , Tullis C. Onstott
    •  & John R. Bracht
  • Article
    | Open Access

    Whole genome sequencing (WGS) holds promise to solve a subset of Mendelian disease cases for which exome sequencing did not provide a genetic diagnosis. Here, Wells et al. report a supervised machine learning model trained on functional, mutational and structural features for rank-scoring and interpreting variants in non-coding regions from WGS.

    • Alex Wells
    • , David Heckerman
    • , Ali Torkamani
    • , Li Yin
    • , Jonathan Sebat
    • , Bing Ren
    • , Amalio Telenti
    •  & Julia di Iulio
  • Article
    | Open Access

    Parkinson’s disease (PD) is characterized by neurodegeneration associated with loss of dopaminergic (DA) neurons and deposition of Lewy bodies. Here, Wang et al. use co-expression network analysis to pinpoint disease pathways and propose reduced expression of STMN2 as a cause of presynaptic function loss in PD.

    • Qian Wang
    • , Yuanxi Zhang
    • , Minghui Wang
    • , Won-Min Song
    • , Qi Shen
    • , Andrew McKenzie
    • , Insup Choi
    • , Xianxiao Zhou
    • , Ping-Yue Pan
    • , Zhenyu Yue
    •  & Bin Zhang
  • Article
    | Open Access

    Exceptional alpine plant diversity exists in the Hengduan Mountains. Here, through genome assembly and population genomics studies, the authors find notable intraspecific divergence among Cushion willow populations isolated by the sky island-like habitats and consider it contributes to speciation and biodiversity.

    • Jia-hui Chen
    • , Yuan Huang
    • , Benjamin Brachi
    • , Quan-zheng Yun
    • , Wei Zhang
    • , Wei Lu
    • , Hong-na Li
    • , Wen-qing Li
    • , Xu-dong Sun
    • , Guang-yan Wang
    • , Jun He
    • , Zhuo Zhou
    • , Kai-yun Chen
    • , Yun-heng Ji
    • , Ming-ming Shi
    • , Wen-guang Sun
    • , Yong-ping Yang
    • , Ren-gang Zhang
    • , Richard J. Abbott
    •  & Hang Sun
  • Article
    | Open Access

    Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.

    • Dasen Xie
    • , Yuanchao Xu
    • , Jinpeng Wang
    • , Wenrui Liu
    • , Qian Zhou
    • , Shaobo Luo
    • , Wu Huang
    • , Xiaoming He
    • , Qing Li
    • , Qingwu Peng
    • , Xueyong Yang
    • , Jiaqing Yuan
    • , Jigao Yu
    • , Xiyin Wang
    • , William J. Lucas
    • , Sanwen Huang
    • , Biao Jiang
    •  & Zhonghua Zhang
  • Article
    | Open Access

    The ‘parliament of genes’ hypothesis suggests that selfish genetic elements will be counteracted by suppressors that maintain equal transmission of the rest of the genome. Here, the authors find support for this hypothesis using mathematical models to explore a range of different scenarios.

    • Thomas W. Scott
    •  & Stuart A. West
  • Article
    | Open Access

    Strain Ug99 of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici, is a major threat to global food security. Here, the authors present genomic analyses supporting that Ug99 arose as a result of non-sexual genetic exchange between dikaryotic ancestors.

    • Feng Li
    • , Narayana M. Upadhyaya
    • , Jana Sperschneider
    • , Oadi Matny
    • , Hoa Nguyen-Phuc
    • , Rohit Mago
    • , Castle Raley
    • , Marisa E. Miller
    • , Kevin A. T. Silverstein
    • , Eva Henningsen
    • , Cory D. Hirsch
    • , Botma Visser
    • , Zacharias A. Pretorius
    • , Brian J. Steffenson
    • , Benjamin Schwessinger
    • , Peter N. Dodds
    •  & Melania Figueroa
  • Article
    | Open Access

    It is challenging to characterize diverse transcript isoforms by short-read sequencing. Here the authors report full-length transcriptomes in rat hippocampus by hybrid-sequencing, predict isoform-specific translational status, and reconstruct open reading frames validated by mass spectrometry.

    • Xi Wang
    • , Xintian You
    • , Julian D. Langer
    • , Jingyi Hou
    • , Fiona Rupprecht
    • , Irena Vlatkovic
    • , Claudia Quedenau
    • , Georgi Tushev
    • , Irina Epstein
    • , Bernhard Schaefke
    • , Wei Sun
    • , Liang Fang
    • , Guipeng Li
    • , Yuhui Hu
    • , Erin M. Schuman
    •  & Wei Chen
  • Article
    | Open Access

    Here, the authors report transcriptomes and proteomes of oocyst sporozoite and salivary gland sporozoite stages in rodent-infectious Plasmodium yoelii parasites and human infectious Plasmodium falciparum parasites and define two waves of translational repression during sporozoite maturation.

    • Scott E. Lindner
    • , Kristian E. Swearingen
    • , Melanie J. Shears
    • , Michael P. Walker
    • , Erin N. Vrana
    • , Kevin J. Hart
    • , Allen M. Minns
    • , Photini Sinnis
    • , Robert L. Moritz
    •  & Stefan H. I. Kappe
  • Article
    | Open Access

    Herpes simplex virus 1 (HSV-1) induces major reprogramming of the host cell environment. Here, the authors profile the transcriptomes of individual HSV-1-infected human fibroblasts and provide evidence of an antiviral program mediated by the activation of the host transcription factor NRF2.

    • Emanuel Wyler
    • , Vedran Franke
    • , Jennifer Menegatti
    • , Christine Kocks
    • , Anastasiya Boltengagen
    • , Samantha Praktiknjo
    • , Barbara Walch-Rückheim
    • , Jens Bosse
    • , Nikolaus Rajewsky
    • , Friedrich Grässer
    • , Altuna Akalin
    •  & Markus Landthaler