Volume 29, Issue 4 | April 2019

Research
- - Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans
    Maria Zhivagui
    Alvin W.T. Ng
    Maude Ardin
    Mona I. Churchwell
    Manuraj Pandey
    Claire Renard Stephanie Villar Vincent Cahais Alexis Robitaille Liacine Bouaoun Adriana Heguy Kathryn Z. Guyton Martha R. Stampfer James McKay Monica Hollstein Magali Olivier
    ...[+11 authors]...,
    Steven G. Rozen
    Frederick A. Beland
    Michael Korenjak
    Jiri Zavadil
    First Published March 7, 2019
  - Coexpression patterns define epigenetic regulators associated with neurological dysfunction
    Leandros Boukas
    James M. Havrilla
    Peter F. Hickey
    Aaron R. Quinlan
    Hans T. Bjornsson
    First Published March 11, 2019
  - New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation
    Le Li
    Yuwei Gao
    Qiong Wu
    Alfred S.L. Cheng
    Kevin Y. Yip
    First Published February 19, 2019
  - CG dinucleotides enhance promoter activity independent of DNA methylation
    Dominik Hartl
    Arnaud R. Krebs
    Ralph S. Grand
    Tuncay Baubec
    Luke Isbel
    First Published February 1, 2019
  - TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
    Kasper D. Rasmussen
    Ivan Berest
    Sandra Keβler
    Koutarou Nishimura
    Lucía Simón-Carrasco
    George S. Vassiliou
    ...[+1 authors]...,
    Marianne T. Pedersen
    Jesper Christensen
    Judith B. Zaugg
    Kristian Helin
    First Published February 22, 2019
  - Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
    Marta Farré
    Jaebum Kim
    Anastasia A. Proskuryakova
    Yang Zhang
    Anastasia I. Kulemzina
    Qiye Li Yang Zhou Yingqi Xiong Jennifer L. Johnson Polina L. Perelman Warren E. Johnson Wesley C. Warren Anna V. Kukekova Guojie Zhang Stephen J. O'Brien Oliver A. Ryder
    ...[+11 authors]...,
    Alexander S. Graphodatsky
    Jian Ma
    Harris A. Lewin
    Denis M. Larkin
    First Published February 13, 2019
  - The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
    Drew R. Schield
    Daren C. Card
    Nicole R. Hales
    Blair W. Perry
    Giulia M. Pasquesi
    Heath Blackmon Richard H. Adams Andrew B. Corbin Cara F. Smith Balan Ramesh Jeffery P. Demuth Esther Betrán
    ...[+7 authors]...,
    Marc Tollis
    Jesse M. Meik
    Stephen P. Mackessy
    Todd A. Castoe
    First Published March 21, 2019
  - Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila
    Michelle Pherson
    Ziva Misulovin
    Maria Gause
    Dale Dorsett
    First Published February 22, 2019
  - Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome
    Keerthi T. Chathoth
    Nicolae Radu Zabet
    First Published February 1, 2019
  - Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment
    Theodore Gouliouris
    Kathy E. Raven
    Danesh Moradigaravand
    Catherine Ludden
    Francesc Coll
    Beth Blane Plamena Naydenova Carolyne Horner Nicholas M. Brown
    ...[+4 authors]...,
    Jukka Corander
    Direk Limmathurotsakul
    Julian Parkhill
    Sharon J. Peacock
    First Published March 21, 2019
Methods
- - Resolving the full spectrum of human genome variation using Linked-Reads
    Patrick Marks
    Sarah Garcia
    Alvaro Martinez Barrio
    Kamila Belhocine
    Jorge Bernate
    Rajiv Bharadwaj Keith Bjornson Claudia Catalanotti Josh Delaney Adrian Fehr Ian T. Fiddes Brendan Galvin Haynes Heaton Jill Herschleb Christopher Hindson Esty Holt Cassandra B. Jabara Susanna Jett Nikka Keivanfar Sofia Kyriazopoulou-Panagiotopoulou Monkol Lek Bill Lin Adam Lowe Shazia Mahamdallie Shamoni Maheshwari Tony Makarewicz Jamie Marshall Francesca Meschi Christopher J. O'Keefe Heather Ordonez Pranav Patel Andrew Price Ariel Royall Elise Ruark Sheila Seal Michael Schnall-Levin Preyas Shah David Stafford Stephen Williams Indira Wu
    ...[+35 authors]...,
    Andrew Wei Xu
    Nazneen Rahman
    Daniel MacArthur
    Deanna M. Church
    First Published March 20, 2019
  - Long-read single-molecule maps of the functional methylome
    Hila Sharim
    Assaf Grunwald
    Tslil Gabrieli
    Yael Michaeli
    Sapir Margalit
    Dmitry Torchinsky Rani Arielly Gil Nifker Matyas Juhasz Felix Gularek Miguel Almalvez Brandon Dufault Sreetama Sen Chandra Alexander Liu Surajit Bhattacharya Yi-Wen Chen Eric Vilain Kathryn R. Wagner Jonathan Pevsner Jeff Reifenberger Ernest T. Lam Alex R. Hastie
    ...[+17 authors]...,
    Han Cao
    Hayk Barseghyan
    Elmar Weinhold
    Yuval Ebenstein
    First Published March 7, 2019
  - Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression
    Di Huang
    Hanna M. Petrykowska
    Brendan F. Miller
    Laura Elnitski
    Ivan Ovcharenko
    First Published March 18, 2019
  - Improved discovery of genetic interactions using CRISPRiSeq across multiple environments
    Mia Jaffe
    Adam Dziulko
    Justin D. Smith
    Robert P. St.Onge
    Sasha F. Levy
    First Published February 19, 2019
Resources
- - GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
    Yi Shao
    Chunyan Chen
    Hao Shen
    Bin Z. He
    Daqi Yu
    Shuai Jiang Shilei Zhao Zhiqiang Gao Zhenglin Zhu Xi Chen Yan Fu
    ...[+6 authors]...,
    Hua Chen
    Ge Gao
    Manyuan Long
    Yong E. Zhang
    First Published March 12, 2019
  - Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses
    Bérénice A. Benayoun
    Elizabeth A. Pollina
    Param Priya Singh
    Salah Mahmoudi
    Itamar Harel
    First Published March 11, 2019
Corrigenda
- - Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution
    Amit Blumberg
    Edward J. Rice
    Anshul Kundaje
    Charles G. Danko
    Dan Mishmar
    First Published April 1, 2019
  - Corrigendum: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
    Agustín F. Fernández
    Gustavo F. Bayón
    Rocío G. Urdinguio
    Estela G. Toraño
    María G. García
    Antonella Carella Sandra Petrus-Reurer Cecilia Ferrero Pablo Martinez-Camblor Isabel Cubillo Javier García-Castro Jesús Delgado-Calle Flor M. Pérez-Campo José A. Riancho Clara Bueno Pablo Menéndez Anouk Mentink Katia Mareschi Fabian Claire Corrado Fagnani Emanuela Medda Virgilia Toccaceli Sonia Brescianini Sebastián Moran Manel Esteller Alexandra Stolzing
    ...[+21 authors]...,
    Jan de Boer
    Lorenza Nisticò
    Maria A. Stazi
    Mario F. Fraga
    First Published April 1, 2019

Table of Contents

Volume 29, Issue 4 | April 2019

Research

Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans

Coexpression patterns define epigenetic regulators associated with neurological dysfunction

New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation

CG dinucleotides enhance promoter activity independent of DNA methylation

TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells

Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila

Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

Methods

Resolving the full spectrum of human genome variation using Linked-Reads

Long-read single-molecule maps of the functional methylome

Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression

Improved discovery of genetic interactions using CRISPRiSeq across multiple environments

Resources

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

Corrigenda

Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution

Corrigendum: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells

Table of Contents

Volume 29, Issue 4 | April 2019

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Research

Methods

Resources

Corrigenda