Epigenomics

Epigenomics is the systematic analysis of the global state of gene expression not attributable to mutational changes in the underlying DNA genome. An organism has multiple, cell type-specific, epigenomes comprising epigenetic marks such as DNA methylation, histone modification and specifically positioned nucleosomes.

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Latest Research and Reviews

  • Research |

    In this study, the authors use ATAC-seq and promoter capture Hi-C data from human adipocytes treated with fatty acids to identify gene–environment (G×E) interactions that influence body-mass index in humans. They report 154 genes that respond to saturated fat and discover 38 new G×E variants for body-mass index in data from the UK Biobank.

    • Kristina M. Garske
    • , David Z. Pan
    • , Zong Miao
    • , Yash V. Bhagat
    • , Caroline Comenho
    • , Christopher R. Robles
    • , Jihane N. Benhammou
    • , Marcus Alvarez
    • , Arthur Ko
    • , Chun Jimmie Ye
    • , Joseph R. Pisegna
    • , Karen L. Mohlke
    • , Janet S. Sinsheimer
    • , Markku Laakso
    •  & Päivi Pajukanta
    Nature Metabolism 1, 630-642
  • Research | | open

    Spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, the authors construct maize chromatin interaction maps using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and show their associations with gene expression and agronomic traits.

    • Yong Peng
    • , Dan Xiong
    • , Lun Zhao
    • , Weizhi Ouyang
    • , Shuangqi Wang
    • , Jun Sun
    • , Qing Zhang
    • , Pengpeng Guan
    • , Liang Xie
    • , Wenqiang Li
    • , Guoliang Li
    • , Jianbing Yan
    •  & Xingwang Li
  • Research | | open

    Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can discover specific protein-centered chromatin interactions in high resolution. Here, the authors use ChIA-PET to reveal the complex and dynamic interactions between proximal and distal regulatory regions of genes in maize.

    • En Li
    • , Han Liu
    • , Liangliang Huang
    • , Xiangbo Zhang
    • , Xiaomei Dong
    • , Weibin Song
    • , Haiming Zhao
    •  & Jinsheng Lai
  • Research | | open

    Our understanding of the functional link between differential DNA methylation and type 2 diabetes and obesity remains limited. Here the authors present a blood-based EWAS of fasting glucose and insulin among 4808 non-diabetic Europeans and identify nine CpGs not previously implicated in glucose, insulin homeostasis and diabetes.

    • Jun Liu
    • , Elena Carnero-Montoro
    • , Jenny van Dongen
    • , Samantha Lent
    • , Ivana Nedeljkovic
    • , Symen Ligthart
    • , Pei-Chien Tsai
    • , Tiphaine C. Martin
    • , Pooja R. Mandaviya
    • , Rick Jansen
    • , Marjolein J. Peters
    • , Liesbeth Duijts
    • , Vincent W. V. Jaddoe
    • , Henning Tiemeier
    • , Janine F. Felix
    • , Gonneke Willemsen
    • , Eco J. C. de Geus
    • , Audrey Y. Chu
    • , Daniel Levy
    • , Shih-Jen Hwang
    • , Jan Bressler
    • , Rahul Gondalia
    • , Elias L. Salfati
    • , Christian Herder
    • , Bertha A. Hidalgo
    • , Toshiko Tanaka
    • , Ann Zenobia Moore
    • , Rozenn N. Lemaitre
    • , Min A Jhun
    • , Jennifer A. Smith
    • , Nona Sotoodehnia
    • , Stefania Bandinelli
    • , Luigi Ferrucci
    • , Donna K. Arnett
    • , Harald Grallert
    • , Themistocles L. Assimes
    • , Lifang Hou
    • , Andrea Baccarelli
    • , Eric A. Whitsel
    • , Ko Willems van Dijk
    • , Najaf Amin
    • , André G. Uitterlinden
    • , Eric J. G. Sijbrands
    • , Oscar H. Franco
    • , Abbas Dehghan
    • , Tim D. Spector
    • , Josée Dupuis
    • , Marie-France Hivert
    • , Jerome I. Rotter
    • , James B. Meigs
    • , James S. Pankow
    • , Joyce B. J. van Meurs
    • , Aaron Isaacs
    • , Dorret I. Boomsma
    • , Jordana T. Bell
    • , Ayşe Demirkan
    •  & Cornelia M. van Duijn
  • Research | | open

    Environmental influences during prenatal development may have implications for health and disease later in life. Here, Czamara et al. assess DNA methylation in cord blood from new-born under various models including environmental and genetic effects individually and their additive or interaction effects.

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

    DNA modification generates unique electric signals in Oxford Nanopore sequencing data but the signals can be complicated to decipher. Here, the authors develop a deep learning framework, DeepMod, to detect DNA base modifications including 5mC and 6mA using Nanopore sequencing data

    • Qian Liu
    • , Li Fang
    • , Guoliang Yu
    • , Depeng Wang
    • , Chuan-Le Xiao
    •  & Kai Wang

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