Articles

Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements

The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation ...

Authors: Cristina Vicente-García, Barbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter W. J. Rigby, Damien P. Devos, Jose L. Gómez-Skarmeta and Jaime J. Carvajal

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversificat...

Authors: Fiona M. Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R. Hvidsten, Anthony K. Redmond, Sigbjørn Lien, Samuel A. M. Martin, Peter W. H. Holland, Simen R. Sandve and Daniel J. Macqueen

“Like sugar in milk”: reconstructing the genetic history of the Parsi population

The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations...

Authors: Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G. Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi…

CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion

CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exo...

Authors: Haiwei Mou, Jordan L. Smith, Lingtao Peng, Hao Yin, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Qiongqiong Wu, Deniz M. Ozata, Yingxiang Li, Daniel G. Anderson, Charles P. Emerson, Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng…

Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost

Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that hav...

Authors: Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Ken Pendavis, Shane C. Burgess, Manfred Grabherr, Miriam Friedman-Einat and Leif Andersson

Unexpected consequences: exon skipping caused by CRISPR-generated mutations

A new study finds that splicing disruption is a frequent consequence of mutations generated by CRISPR/Cas9 gene-editing technology, and alleles designed to be null can express aberrant proteins. This new infor...

Authors: Joshua J. Sharpe and Thomas A. Cooper

Epigenetic aging clocks in mice and men

Epigenetic clocks provide powerful tools to evaluate nutritional, hormonal, and genetic effects on aging. What can we learn from differences between species in how these clocks tick?

Authors: Wolfgang Wagner

Correspondence on Lovell et al.: response to Bornelöv et al.

While the analysis of Bornelöv et al. is informative, they provide evidence for the existence of only 3% of the reported avian missing genes set, and thus do not significantly challenge our main findings that ...

Authors: Peter V. Lovell and Claudio V. Mello

Multiple gene movements into and out of haploid sex chromosomes

Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out f...

Authors: Agnieszka P. Lipinska, Nicholas R. T. Toda, Svenja Heesch, Akira F. Peters, J. Mark Cock and Susana M. Coelho

Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants

Global warming severely affects flowering time and reproductive success of plants. Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses...

Authors: A. Pajoro, E. Severing, G. C. Angenent and R. G. H. Immink

The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and...

Authors: Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He and Heng Zhang

Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons

Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produc...

Authors: Qingxin Song, Tianzhen Zhang, David M. Stelly and Z. Jeffrey Chen

Optimizing complex phenotypes through model-guided multiplex genome engineering

We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide m...

Authors: Gleb Kuznetsov, Daniel B. Goodman, Gabriel T. Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J. Lajoie and George M. Church

Millstone: software for multiplex microbial genome analysis and engineering

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a...

Authors: Daniel B. Goodman, Gleb Kuznetsov, Marc J. Lajoie, Brian W. Ahern, Michael G. Napolitano, Kevin Y. Chen, Changping Chen and George M. Church

N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration

Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that ...

Authors: Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G. Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M. Clark, Hui Ling, Masayoshi Shimizu…

Emerging roles of chromatin in the maintenance of genome organization and function in plants

Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the...

Authors: Zaida Vergara and Crisanto Gutierrez

Unreeling the chromatin thread: a genomic perspective on organization around the periphery of the Arabidopsis nucleus

The first genome-wide examination of the chromatin landscape at the periphery of the plant cell nucleus reveals substantial enrichment of heterochromatin and Polycomb-based repressive chromatin.

Authors: Fredy Barneche and Celia Baroux

Going beyond genetics to discover cancer targets

Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer.

Authors: Gabriel J. Sandoval and William C. Hahn

The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana

Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enri...

Authors: Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E. Jacobsen and Frédéric Berger

A comparative evaluation of genome assembly reconciliation tools

The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or par...

Authors: Hind Alhakami, Hamid Mirebrahim and Stefano Lonardi

Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins

Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Condit...

Authors: Rolen M. Quadros, Hiromi Miura, Donald W. Harms, Hisako Akatsuka, Takehito Sato, Tomomi Aida, Ronald Redder, Guy P. Richardson, Yutaka Inagaki, Daisuke Sakai, Shannon M. Buckley, Parthasarathy Seshacharyulu, Surinder K. Batra, Mark A. Behlke, Sarah A. Zeiner, Ashley M. Jacobi…

Quantifying the mapping precision of genome-wide association studies using whole-genome sequencing data

Understanding the mapping precision of genome-wide association studies (GWAS), that is the physical distances between the top associated single-nucleotide polymorphisms (SNPs) and the causal variants, is essen...

Authors: Yang Wu, Zhili Zheng, Peter M. Visscher and Jian Yang

EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels

The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recentl...

Authors: Josquin Daron and R. Keith Slotkin

Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

Authors: Christof Angermueller, Heather J. Lee, Wolf Reik and Oliver Stegle

Missing heritability and where to find it

A report on the 11th Genomics of Rare Disease meeting held at the Wellcome Genome Campus, Hinxton, Cambridge, UK, 5–7 April, 2017.

Authors: Santhosh Girirajan

Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants

Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new orga...

Authors: Jun Xiao, Run Jin and Doris Wagner

An evolutionary case for functional gene body methylation in plants and animals

Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation.

Authors: Daniel Zilberman

Challenges and emerging directions in single-cell analysis

Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enable...

Authors: Guo-Cheng Yuan, Long Cai, Michael Elowitz, Tariq Enver, Guoping Fan, Guoji Guo, Rafael Irizarry, Peter Kharchenko, Junhyong Kim, Stuart Orkin, John Quackenbush, Assieh Saadatpour, Timm Schroeder, Ramesh Shivdasani and Itay Tirosh

Horizontal gene transfer is not a hallmark of the human genome

Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been...

Authors: Steven L. Salzberg

Multi-omics approaches to disease

High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which ...

Authors: Yehudit Hasin, Marcus Seldin and Aldons Lusis

Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

The structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constrai...

Authors: Jean-Michel Arbona, Sébastien Herbert, Emmanuelle Fabre and Christophe Zimmer

PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice

Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression b...

Authors: Emily Maclary, Michael Hinten, Clair Harris, Shriya Sethuraman, Srimonta Gayen and Sundeep Kalantry

Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana

Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arab...

Authors: Fernando A. Rabanal, Terezie Mandáková, Luz M. Soto-Jiménez, Robert Greenhalgh, David L. Parrott, Stefan Lutzmayer, Joshua G. Steffen, Viktoria Nizhynska, Richard Mott, Martin A. Lysak, Richard M. Clark and Magnus Nordborg

Erratum to: Unraveling the clonal hierarchy of somatic genomic aberrations

Authors: Davide Prandi, Sylvan C. Baca, Alessandro Romanel, Christopher E. Barbieri, Juan-Miguel Mosquera, Jacqueline Fontugne, Himisha Beltran, Andrea Sboner, Levi A. Garraway, Mark A. Rubin and Francesca Demichelis

The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants

The evolution of gene body methylation (gbM), its origins, and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridipl...

Authors: Adam J. Bewick, Chad E. Niederhuth, Lexiang Ji, Nicholas A. Rohr, Patrick T. Griffin, Jim Leebens-Mack and Robert J. Schmitz

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance

Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutatio...

Authors: Gustavo C. Cerqueira, Ian H. Cheeseman, Steve F. Schaffner, Shalini Nair, Marina McDew-White, Aung Pyae Phyo, Elizabeth A. Ashley, Alexandre Melnikov, Peter Rogov, Bruce W. Birren, François Nosten, Timothy J. C. Anderson and Daniel E. Neafsey

Longitudinal study of Plasmodium pathogens identifies new loci associated with artemisinin resistance

A longitudinal analysis of malaria parasite genomes has revealed new markers that can be used in public health efforts to limit the spread of multidrug-resistant malaria.

Authors: Elizabeth A. Winzeler

The impact of rare and low-frequency genetic variants in common disease

Despite thousands of genetic loci identified to date, a large proportion of genetic variation predisposing to complex disease and traits remains unaccounted for. Advances in sequencing technology enable focuse...

Authors: Lorenzo Bomba, Klaudia Walter and Nicole Soranzo

The MHC locus and genetic susceptibility to autoimmune and infectious diseases

In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advanc...

Authors: Vasiliki Matzaraki, Vinod Kumar, Cisca Wijmenga and Alexandra Zhernakova

SCALE: modeling allele-specific gene expression by single-cell RNA sequencing

Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between t...

Authors: Yuchao Jiang, Nancy R. Zhang and Mingyao Li

Proximal methylation features associated with nonrandom changes in gene body methylation

Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the ...

Authors: Colette L. Picard and Mary Gehring

The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy

Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates ...

Authors: Andrej Trauner, Qingyun Liu, Laura E. Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England…

Heroes of peer review: Robert Lowe

In the second of our series of articles celebrating peer reviewers, we talk to Robert Lowe, who is a Lecturer in computational biology at Queen Mary University of London, UK, and a valued reviewer for Genome Biol...

Authors: Robert Lowe

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort

The gut microbiome is a complex and metabolically active community that directly influences host phenotypes. In this study, we profile gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finni...

Authors: Elin Org, Yuna Blum, Silva Kasela, Margarete Mehrabian, Johanna Kuusisto, Antti J. Kangas, Pasi Soininen, Zeneng Wang, Mika Ala-Korpela, Stanley L. Hazen, Markku Laakso and Aldons J. Lusis

H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity

Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recrui...

Authors: Yue Zhou, Francisco J. Romero-Campero, Ángeles Gómez-Zambrano, Franziska Turck and Myriam Calonje

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

Recent technological advances have enabled DNA methylation to be assayed at single-cell resolution. However, current protocols are limited by incomplete CpG coverage and hence methods to predict missing methyl...

Authors: Christof Angermueller, Heather J. Lee, Wolf Reik and Oliver Stegle

Multi-tissue DNA methylation age predictor in mouse

DNA methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an un...

Authors: Thomas M. Stubbs, Marc Jan Bonder, Anne-Katrien Stark, Felix Krueger, Ferdinand von Meyenn, Oliver Stegle and Wolf Reik

SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling

Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues...

Authors: Grace O. Silva, Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou and Mengjie Chen

Structuring supplemental materials in support of reproducibility

Supplements are increasingly important to the scientific record, particularly in genomics. However, they are often underutilized. Optimally, supplements should make results findable, accessible, interoperable,...

Authors: Dov Greenbaum, Joel Rozowsky, Victoria Stodden and Mark Gerstein

Coming out: the experience of LGBT+ people in STEM

Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three openly LGBT+ researchers on their experiences in biology.

Authors: Ben Barres, Beth Montague-Hellen and Jeremy Yoder