Articles

Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity

Although the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly...

Authors: Benjamin Planterose Jiménez, Fan Liu, Amke Caliebe, Diego Montiel González, Jordana T. Bell, Manfred Kayser and Athina Vidaki

Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes

Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular l...

Authors: Xiaoyu Yang, Chenjiang You, Xufeng Wang, Lei Gao, Beixin Mo, Lin Liu and Xuemei Chen

Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.

Authors: Jiantao Guan, Yaoguang Xu, Yang Yu, Jun Fu, Fei Ren, Jiying Guo, Jianbo Zhao, Quan Jiang, Jianhua Wei and Hua Xie

Histone modifications during the life cycle of the brown alga Ectocarpus

Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of development...

Authors: Simon Bourdareau, Leila Tirichine, Bérangère Lombard, Damarys Loew, Delphine Scornet, Yue Wu, Susana M. Coelho and J. Mark Cock

In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants

mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence cont...

Authors: Zhenshan Liu, Qi Liu, Xiaofei Yang, Yueying Zhang, Matthew Norris, Xiaoxi Chen, Jitender Cheema, Huakun Zhang and Yiliang Ding

scMC learns biological variation through the alignment of multiple single-cell genomics datasets

Distinguishing biological from technical variation is crucial when integrating and comparing single-cell genomics datasets across different experiments. Existing methods lack the capability in explicitly disti...

Authors: Lihua Zhang and Qing Nie

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer

Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recogniz...

Authors: Miho Oka, Liu Xu, Toshihiro Suzuki, Toshiaki Yoshikawa, Hiromi Sakamoto, Hayato Uemura, Akiyasu C. Yoshizawa, Yutaka Suzuki, Tetsuya Nakatsura, Yasushi Ishihama, Ayako Suzuki and Masahide Seki

Reference flow: reducing reference bias using multiple population genomes

Most sequencing data analyses start by aligning sequencing reads to a linear reference genome, but failure to account for genetic variation leads to reference bias and confounding of results downstream. Other ...

Authors: Nae-Chyun Chen, Brad Solomon, Taher Mun, Sheila Iyer and Ben Langmead

Comprehensive integrative profiling of upper tract urothelial carcinomas

Crosstalk between genetic, epigenetic, and immune alterations in upper tract urothelial carcinomas and their role in shaping muscle invasiveness and patient outcome are poorly understood.

Authors: Xiaoping Su, Xiaofan Lu, Sehrish Khan Bazai, Eva Compérat, Roger Mouawad, Hui Yao, Morgan Rouprêt, Jean-Philippe Spano, David Khayat, Irwin Davidson, Nizar N. Tannir, Fangrong Yan and Gabriel G. Malouf

SpRY greatly expands the genome editing scope in rice with highly flexible PAM recognition

Plant genome engineering mediated by various CRISPR-based tools requires specific protospacer adjacent motifs (PAMs), such as the well-performed NGG, NG, and NNG, to initiate target recognition, which notably ...

Authors: Ziyan Xu, Yongjie Kuang, Bin Ren, Daqi Yan, Fang Yan, Carl Spetz, Wenxian Sun, Guirong Wang, Xueping Zhou and Huanbin Zhou

Compacting a synthetic yeast chromosome arm

Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel ...

Authors: Zhouqing Luo, Kang Yu, Shangqian Xie, Marco Monti, Daniel Schindler, Yuan Fang, Shijun Zhao, Zhenzhen Liang, Shuangying Jiang, Meiwei Luan, Chuanle Xiao, Yizhi Cai and Junbiao Dai

Integrated genomic and transcriptomic analysis reveals unique characteristics of hepatic metastases and pro-metastatic role of complement C1q in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers due to its high metastasis rate in the liver. However, little is known about the molecular features of hepatic metastases due to diffic...

Authors: Jianyu Yang, Ping Lin, Minwei Yang, Wei Liu, Xueliang Fu, Dejun Liu, Lingye Tao, Yanmiao Huo, Junfeng Zhang, Rong Hua, Zhigang Zhang, Yixue Li, Liwei Wang, Jing Xue, Hong Li and Yongwei Sun

How the pan-genome is changing crop genomics and improvement

Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to ...

Authors: Rafael Della Coletta, Yinjie Qiu, Shujun Ou, Matthew B. Hufford and Candice N. Hirsch

Mentorship is not co-authorship: a revisit to mentorship

Authors: Lana X. Garmire

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual

Bone accrual impacts lifelong skeletal health, but genetic discovery has been primarily limited to cross-sectional study designs and hampered by uncertainty about target effector genes. Here, we capture this d...

Authors: Diana L. Cousminer, Yadav Wagley, James A. Pippin, Ahmed Elhakeem, Gregory P. Way, Matthew C. Pahl, Shana E. McCormack, Alessandra Chesi, Jonathan A. Mitchell, Joseph M. Kindler, Denis Baird, April Hartley, Laura Howe, Heidi J. Kalkwarf, Joan M. Lappe, Sumei Lu…

Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes...

Authors: José A. Campoy, Hequan Sun, Manish Goel, Wen-Biao Jiao, Kat Folz-Donahue, Nan Wang, Manuel Rubio, Chang Liu, Christian Kukat, David Ruiz, Bruno Huettel and Korbinian Schneeberger

Author Correction: Stairway Plot 2: demographic history inference with folded SNP frequency spectra

An amendment to this paper has been published and can be accessed via the original article.

Authors: Xiaoming Liu and Yun-Xin Fu

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available s...

Authors: Michael R. Garvin, Erica T. Prates, Mirko Pavicic, Piet Jones, B. Kirtley Amos, Armin Geiger, Manesh B. Shah, Jared Streich, Joao Gabriel Felipe Machado Gazolla, David Kainer, Ashley Cliff, Jonathon Romero, Nathan Keith, James B. Brown and Daniel Jacobson

FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibi...

Authors: Kai Kruse, Clemens B. Hug and Juan M. Vaquerizas

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diver...

Authors: Daniel R. Utter, Gary G. Borisy, A. Murat Eren, Colleen M. Cavanaugh and Jessica L. Mark Welch

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitati...

Authors: Alon Shaiber, Amy D. Willis, Tom O. Delmont, Simon Roux, Lin-Xing Chen, Abigail C. Schmid, Mahmoud Yousef, Andrea R. Watson, Karen Lolans, Özcan C. Esen, Sonny T. M. Lee, Nora Downey, Hilary G. Morrison, Floyd E. Dewhirst, Jessica L. Mark Welch and A. Murat Eren

Convergent network effects along the axis of gene expression during prostate cancer progression

Tumor-specific genomic aberrations are routinely determined by high-throughput genomic measurements. It remains unclear how complex genome alterations affect molecular networks through changing protein levels ...

Authors: Konstantina Charmpi, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C. Toussaint, Christine E. Fritz, Chunhui Yuan, Hao Chen, Niels J. Rupp, Ailsa Christiansen, Dorothea Rutishauser, Jan H. Rüschoff, Christian Fankhauser, Karim Saba, Cedric Poyet…

Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome

Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically...

Authors: Emma K. Accorsi, Eric A. Franzosa, Tiffany Hsu, Regina Joice Cordy, Ayala Maayan-Metzger, Hanaa Jaber, Aylana Reiss-Mandel, Madeleine Kline, Casey DuLong, Marc Lipsitch, Gili Regev-Yochay and Curtis Huttenhower

GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data

Most methods for inferring gene-gene interactions from expression data focus on intracellular interactions. The availability of high-throughput spatial expression data opens the door to methods that can infer ...

Authors: Ye Yuan and Ziv Bar-Joseph

Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing

The presence of nuclear mitochondrial DNA (numtDNA) has been reported within several nuclear genomes. Next to mitochondrial protein-coding genes, numtDNA sequences also encode for mitochondrial tRNA genes. How...

Authors: Simon M. Hoser, Anne Hoffmann, Andreas Meindl, Maximilian Gamper, Jörg Fallmann, Stephan H. Bernhart, Lisa Müller, Melanie Ploner, Matthias Misslinger, Leopold Kremser, Herbert Lindner, Stephan Geley, Heiner Schaal, Peter F. Stadler and Alexander Huettenhofer

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is...

Authors: Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall, Jing Zhang, Jason Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P. White and Mark Gerstein

Response to “A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication”

Authors: Gökçe Aköz and Magnus Nordborg

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription

Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higher-order organization and transcriptional activity in living cell...

Authors: Ying Feng, Yao Wang, Xiangnan Wang, Xiaohui He, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie and Hanhui Ma

A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication

The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-spec...

Authors: Tao Shi and Jinming Chen

Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs

As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and ...

Authors: Shuai He, Lin-He Wang, Yang Liu, Yi-Qi Li, Hai-Tian Chen, Jing-Hong Xu, Wan Peng, Guo-Wang Lin, Pan-Pan Wei, Bo Li, Xiaojun Xia, Dan Wang, Jin-Xin Bei, Xiaoshun He and Zhiyong Guo

Response to Brinkmann et al. “Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States”

We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with an...

Authors: Ana T. Duggan, Edward C. Holmes and Hendrik N. Poinar

Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the USA

According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends o...

Authors: Annika Brinkmann, Aline R. V. Souza, José Esparza, Andreas Nitsche and Clarissa R. Damaso

The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements

Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and res...

Authors: Ping-Li Liu, Xi Zhang, Jian-Feng Mao, Yan-Ming Hong, Ren-Gang Zhang, Yilan E, Shuai Nie, Kaihua Jia, Chen-Kun Jiang, Jian He, Weiwei Shen, Qizouhong He, Wenqing Zheng, Samar Abbas, Pawan Kumar Jewaria, Xuechan Tian…

Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

One ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging....

Authors: Ida Höijer, Josefin Johansson, Sanna Gudmundsson, Chen-Shan Chin, Ignas Bunikis, Susana Häggqvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel den Hoed, Marie-Louise Bondeson, Lars Feuk, Ulf Gyllensten and Adam Ameur

Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants

To meet increasing global food demand, breeders and scientists aim to improve the yield and quality of major food crops. Plant diseases threaten food security and are expected to increase because of climate ch...

Authors: Syed Shan-e-Ali Zaidi, Ahmed Mahas, Hervé Vanderschuren and Magdy M. Mahfouz

Human A-to-I RNA editing SNP loci are enriched in GWAS signals for autoimmune diseases and under balancing selection

Adenosine-to-inosine (A-to-I) RNA editing plays important roles in diversifying the transcriptome and preventing MDA5 sensing of endogenous dsRNA as nonself. To date, few studies have investigated the populati...

Authors: Hui Zhang, Qiang Fu, Xinrui Shi, Ziqing Pan, Wenbing Yang, Zichao Huang, Tian Tang, Xionglei He and Rui Zhang

DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis

Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more pron...

Authors: Pierre Bourguet, Leticia López-González, Ángeles Gómez-Zambrano, Thierry Pélissier, Amy Hesketh, Magdalena E. Potok, Marie-Noëlle Pouch-Pélissier, Magali Perez, Olivier Da Ines, David Latrasse, Charles I. White, Steven E. Jacobsen, Moussa Benhamed and Olivier Mathieu

From FAANG to fork: application of highly annotated genomes to improve farmed animal production

Authors: Emily L. Clark, Alan L. Archibald, Hans D. Daetwyler, Martien A. M. Groenen, Peter W. Harrison, Ross D. Houston, Christa Kühn, Sigbjørn Lien, Daniel J. Macqueen, James M. Reecy, Diego Robledo, Mick Watson, Christopher K. Tuggle and Elisabetta Giuffra

The evolution of relapse of adult T cell acute lymphoblastic leukemia

Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent...

Authors: Inés Sentís, Santiago Gonzalez, Eulalia Genescà, Violeta García-Hernández, Ferran Muiños, Celia Gonzalez, Erika López-Arribillaga, Jessica Gonzalez, Lierni Fernandez-Ibarrondo, Loris Mularoni, Lluís Espinosa, Beatriz Bellosillo, Josep-Maria Ribera, Anna Bigas, Abel Gonzalez-Perez and Nuria Lopez-Bigas

A pitfall for machine learning methods aiming to predict across cell types

Machine learning models that predict genomic activity are most useful when they make accurate predictions across cell types. Here, we show that when the training and test sets contain the same genomic loci, th...

Authors: Jacob Schreiber, Ritambhara Singh, Jeffrey Bilmes and William Stafford Noble

Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a clinically heterogeneous autoimmune disease characterized by the development of anti-nuclear antibodies. Susceptibility to SLE is multifactorial, with a combination of g...

Authors: Prithvi Raj, Ran Song, Honglin Zhu, Linley Riediger, Dong-Jae Jun, Chaoying Liang, Carlos Arana, Bo Zhang, Yajing Gao, Benjamin E. Wakeland, Igor Dozmorov, Jinchun Zhou, Jennifer A. Kelly, Bernard R. Lauwerys, Joel M. Guthridge, Nancy J. Olsen…

Stairway Plot 2: demographic history inference with folded SNP frequency spectra

Inferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using S...

Authors: Xiaoming Liu and Yun-Xin Fu

A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila

Advances in CRISPR technology have immensely improved our ability to manipulate nucleic acids, and the recent discovery of the RNA-targeting endonuclease Cas13 adds even further functionality. Here, we show th...

Authors: Nhan Huynh, Noah Depner, Raegan Larson and Kirst King-Jones

Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription

The eukaryotic genome is hierarchically structured yet highly dynamic. Regulating transcription in this environment demands a high level of coordination to permit many proteins to interact with chromatin fiber...

Authors: Haitham A. Shaban, Roman Barth and Kerstin Bystricky

A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos

During mammalian early embryogenesis, expression and epigenetic heterogeneity emerge before the first cell fate determination, but the programs causing such determinate heterogeneity are largely unexplored.

Authors: Chengchen Zhao, Naiqian Zhang, Yalin Zhang, Nuermaimaiti Tuersunjiang, Shaorong Gao, Wenqiang Liu and Yong Zhang

Do malignant cells sleep at night?

Biological rhythms regulate the biology of most, if not all living creatures, from whole organisms to their constitutive cells, their microbiota, and also parasites. Here, we present the hypothesis that intern...

Authors: Luis Enrique Cortés-Hernández, Zahra Eslami-S, Antoine M. Dujon, Mathieu Giraudeau, Beata Ujvari, Frédéric Thomas and Catherine Alix-Panabières

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive morta...

Authors: Marco Gerdol, Rebeca Moreira, Fernando Cruz, Jessica Gómez-Garrido, Anna Vlasova, Umberto Rosani, Paola Venier, Miguel A. Naranjo-Ortiz, Maria Murgarella, Samuele Greco, Pablo Balseiro, André Corvelo, Leonor Frias, Marta Gut, Toni Gabaldón, Alberto Pallavicini…

SVFX: a machine learning framework to quantify the pathogenicity of structural variants

There is a lack of approaches for identifying pathogenic genomic structural variants (SVs) although they play a crucial role in many diseases. We present a mechanism-agnostic machine learning-based workflow, c...

Authors: Sushant Kumar, Arif Harmanci, Jagath Vytheeswaran and Mark B. Gerstein

Pathway information extracted from 25 years of pathway figures

Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual cu...

Authors: Kristina Hanspers, Anders Riutta, Martina Summer-Kutmon and Alexander R. Pico

Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage

Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chrom...

Authors: Yasutaka Kakui, Christopher Barrington, David J. Barry, Tereza Gerguri, Xiao Fu, Paul A. Bates, Bhavin S. Khatri and Frank Uhlmann