Genomic analysis articles within Nature Communications

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  • Article
    | Open Access

    Droplet-based high throughput single cell sequencing techniques can often lose information on transcript splicing and heterogenity. Here the authors introduce ScNaUmi-seq, which uses Oxford Nanopore sequencing and barcoding to generate high accuracy full length sequences.

    • Kevin Lebrigand
    • , Virginie Magnone
    •  & Rainer Waldmann

  • Article
    | Open Access

    Early life exposure to environmental stressors, including endocrine disrupting chemicals (EDCs), can impact health later in life. Here, the authors show that neonatal EDC exposure in rats causes epigenetic reprogramming in the liver, which is transcriptionally silent until animals are placed on a Western-style diet.

    • Lindsey S. Treviño
    • , Jianrong Dong
    •  & Cheryl Lyn Walker

  • Article
    | Open Access

    The initial mutational processes and how these lead to progression in multiple myeloma (MM) are unclear. Here, the authors identify mutational signatures that occur over time in a large cohort of MM patients and suggest features that may help in early diagnosis.

    • Even H. Rustad
    • , Venkata Yellapantula
    •  & Francesco Maura

  • Article
    | Open Access

    Prior to genome assembly, the raw sequencing reads must be analyzed for assessment of major genome characteristics such as genome size, heterozygosity, and repetitiveness. For this purpose, the authors introduce GenomeScope 2.0, an extension of GenomeScope for polyploid genomes, and Smudgeplot, which can estimate a genome’s ploidy.

    • T. Rhyker Ranallo-Benavidez
    • , Kamil S. Jaron
    •  & Michael C. Schatz

  • Article
    | Open Access

    Epstein-Barr virus (EBV) episomes tether to the host chromosome via EBNA1. Here, using circular chromosome conformation capture (4C), Kim et al. identify attachment sites and show that EBV episomes preferentially associate with transcriptionally silenced genes in Burkitt lymphoma cells.

    • Kyoung-Dong Kim
    • , Hideki Tanizawa
    •  & Paul M. Lieberman

  • 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
    •  & Philipp Kapranov

  • Article
    | Open Access

    Meiotic crossovers (COs) generate genetic variation and ensure proper chromosome segregation. Here, the authors develop a method for identifying COs at kilobase resolution in pooled recombinants using linked-read sequencing data, and apply it to investigate genome-wide CO landscapes of Arabidopsis thaliana.

    • Hequan Sun
    • , Beth A. Rowan
    •  & Korbinian Schneeberger

  • Article
    | Open Access

    Meiotic DSB formation, repair and recombination occur in a continuum of substages termed leptonema, zygonema, pachynema, and diplonema. Here, authors develop a method for isolating pure sub-populations of nuclei that allows for detailed study of meiotic substages.

    • Kwan-Wood Gabriel Lam
    • , Kevin Brick
    •  & R. Daniel Camerini-Otero

  • Article
    | Open Access

    Squamous cell lung cancer has dismal prognosis due to the dearth of effective treatments. Here, the authors perform an integrated proteogenomic analysis of the disease, revealing three proteomics-based subtypes and suggesting potential therapeutic opportunities.

    • Paul A. Stewart
    • , Eric A. Welsh
    •  & Eric B. Haura

  • Article
    | Open Access

    Sequencing of newly synthesised RNA can reveal the transcriptional dynamics in a population of cells. Here the authors develop NASC-seq to bring this sensitivity and temporal resolution to single-cell analysis.

    • Gert-Jan Hendriks
    • , Lisa A. Jung
    •  & Rickard Sandberg

  • Article
    | Open Access

    Meiotic crossover (CO) landscape differs inter- and intra-species, as well as between sexes. Here, the authors show that male meiosis produces more COs than female in maize and detect CO maturation inefficiency in some genetic backgrounds, which may help to improve breeding efficiency.

    • Cheng Luo
    • , Xiang Li
    •  & Jianbing Yan

  • Article
    | Open Access

    Due to various structural and sequence complexities, the human Y chromosome is challenging to sequence and characterize. Here, the authors develop a strategy to sequence native, unamplified flow sorted Y chromosomes with a nanopore sequencing platform, and report the first assembly of a human Y chromosome of African origin.

    • Lukas F. K. Kuderna
    • , Esther Lizano
    •  & Tomas Marques-Bonet

  • Article
    | Open Access

    Natural hair colour in Europeans is a complex genetic trait. Here, the authors carry out a genome-wide association study using UK BioBank data, suggesting that in combination with pigmentation genes, variants with roles in hair texture and growth can affect hair colouration or our perception of it.

    • Michael D. Morgan
    • , Erola Pairo-Castineira
    •  & Ian J. Jackson

  • Article
    | Open Access

    In vivo existence of guanine-rich four-stranded RNA structures (G4-RNAs) has been a matter of debate. Here the authors developed a protocol, G4RP-seq, to capture and identify transcriptome-wide G4-RNA, providing insights into the formation of transient G4-RNA in live human cells.

    • Sunny Y. Yang
    • , Pauline Lejault
    •  & David Monchaud

  • Article
    | Open Access

    Algorithms designed to find rare cells in single cell RNA-seq data sets cannot cope with data sets containing tens of thousands of cells. Here the authors present Finder of Rare Entities (FiRE), an algorithm that uses the Sketching technique to assign a rareness score to every expression profile in large RNA-seq data sets.

    • Aashi Jindal
    • , Prashant Gupta
    •  & Debarka Sengupta

  • Article
    | Open Access

    Termination of RNA polymerase II (RNAPII) transcription is an essential step of gene expression. Here the authors provide evidence that in fission yeast termination of ncRNA genes occurs by a cleavage-dependent mechanism involving recruitment of mRNA 3′ end processing factors and requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases.

    • Marc Larochelle
    • , Marc-Antoine Robert
    •  & François Bachand

  • Article
    | Open Access

    In Drosophila the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. Here the authors provide evidence that MSL2 also targets autosomal genes required for proper development and that MSL2 binds and similarly regulates mouse orthologues.

    • Claudia Isabelle Keller Valsecchi
    • , M. Felicia Basilicata
    •  & Asifa Akhtar

  • Article
    | Open Access

    Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.

    • Citao Liu
    • , Shujun Ou
    •  & Chengcai Chu

  • Article
    | Open Access

    Single-cell RNA-barcoding and sequencing is an efficient, genome-wide method to characterize cellular identities. Here the authors systematically evaluate the protocol and develop molecular crowding SCRB-seq with improved sensitivity and cost-efficiency.

    • Johannes W. Bagnoli
    • , Christoph Ziegenhain
    •  & Wolfgang Enard

  • Article
    | Open Access

    The UK Biobank provides data for three depression-related phenotypes. Here, Howard et al. perform a genome-association study for broad depression, probable major depressive disorder (MDD) and hospital record-coded MDD in up to 322,580 UK Biobank participants which highlights excitatory synaptic pathways.

    • David M. Howard
    • , Mark J. Adams
    •  & Andrew M. McIntosh

  • Article
    | Open Access

    Physical mapping of DNA can be used to detect structural variants and for whole-genome haplotype assembly. Here, the authors use CRISPR-Cas9 and high-speed atomic force microscopy to ‘nanomap’ single molecules of DNA.

    • Andrey Mikheikin
    • , Anita Olsen
    •  & Jason Reed

  • Article
    | Open Access

    Single-cell genomics can be used to study uncultured microorganisms. Here, Stepanauskas et al. present a method combining improved multiple displacement amplification and FACS, to obtain genomic sequences and cell size information from uncultivated microbial cells and viral particles in environmental samples.

    • Ramunas Stepanauskas
    • , Elizabeth A. Fergusson
    •  & Arvydas Lubys

  • Article
    | Open Access

    Viruses play an important role in microbial communities but, due to limitations of available techniques, our understanding of viral diversity is limited. Here, the authors use SVGs and identify highly abundant viruses in marine communities that have been previously overlooked.

    • Francisco Martinez-Hernandez
    • , Oscar Fornas
    •  & Manuel Martinez-Garcia

  • Article
    | Open Access

    Chromatin architecture is a key regulator of transcriptional processes, however current methods to investigate it have technical limitations. Here, the authors describe a novel chromatin capture technique, CATCH, which can be used to identify and characterize complex genomic interaction networks.

    • Ryan J. Bourgo
    • , Hari Singhal
    •  & Geoffrey L. Greene

  • Article
    | Open Access

    Laser capture microscopy (LCM) coupled with global transcriptome profiling requires relatively large numbers of cells. Here, the authors show that LCM coupled with full-length mRNA-sequencing (LCM-seq) can sequence single cells, and that LCM-seq can provide biological insight on highly similar neuronal populations.

    • Susanne Nichterwitz
    • , Geng Chen
    •  & Eva Hedlund

  • Article
    | Open Access

    Increasing progranulin (PGRN) levels is a promising approach for treating frontotemporal dementia and other neurodegenerative diseases. Here Nicholson et al.show that the prosaposin (PSAP) locus is associated with plasma PGRN levels and demonstrate that PSAP can alter PGRN levels and its oligomerization.

    • Alexandra M. Nicholson
    • , NiCole A. Finch
    •  & Rosa Rademakers

  • Article
    | Open Access

    Deficit in transcription factor Tbx1 causes heart defects in humans and mice. Here the authors show that Tbx1 regulates gene expression by recruiting histone methyltransferases that affect chromatin marks, and that a drug inhibiting histone demethylation ameliorates the cardiovascular phenotype in Tbx1 haploinsufficient or hypomorphic mice.

    • Filomena Gabriella Fulcoli
    • , Monica Franzese
    •  & Antonio Baldini

  • Article
    | Open Access

    This study examines ancient genomes of individuals from the late Iron Age to the middle Anglo-Saxon period in the East of England. Using a newly devised analytic algorithm, the author also estimate the relative ancestry of East English genome derived from Anglo-Saxon migrations and to the rest of Europe.

    • Stephan Schiffels
    • , Wolfgang Haak
    •  & Richard Durbin

  • Article
    | Open Access

    SARD1 and CBP60g are two plant transcription factors that regulate salicylic acid biosynthesis in response to pathogens. Here, Sun et al.show that they bind a wide array of loci related to multiple defence signalling pathways suggesting a broader role as regulators of the plant immune response.

    • Tongjun Sun
    • , Yaxi Zhang
    •  & Yuelin Zhang

  • Article
    | Open Access

    Availability of computing power can limit computational analysis of large genetic and genomic datasets. Here, Canela-Xandri, et al. describe a software called DISSECT that is capable of analyzing large-scale genetic data by distributing the work across thousands of networked computers.

    • Oriol Canela-Xandri
    • , Andy Law
    •  & Albert Tenesa

  • Article
    | Open Access

    The importance of the tumour microenvironment has now been realised, however the presence of non-tumour cells in cancer samples can complicate genomic analyses. Here, the authors estimate tumour purity in 10,000 samples from the TCGA dataset and can detect a signature of T cell activation.

    • Dvir Aran
    • , Marina Sirota
    •  & Atul J. Butte

  • Article
    | Open Access

    Neutrophils are abundant immune cells important for antimicrobial defence and in autoimmunity. Here, by mapping expression quantitative trait loci (eQTL) in neutrophils of Chinese ethnicity from Singapore, Andiappan et al.provide a resource for understanding immune-related trait associated genetic variants.

    • Anand Kumar Andiappan
    • , Rossella Melchiotti
    •  & Olaf Rotzschke

  • Article
    | Open Access

    The shape of the pinna varies widely in the general human population but the genetic basis of this variation is unknown. Here Adhikari et al. conduct a genome-wide association study in Latin Americans and discover seven gene regions influencing pinna morphology, including EDAR and TBX15.

    • Kaustubh Adhikari
    • , Guillermo Reales
    •  & Andrés Ruiz-Linares

  • Article
    | Open Access

    Bacterial DNA methylation is involved in many processes, from host defense to antibiotic resistance, however current methods for examining methylated genomes lack single-cell resolution. Here Beaulaurier et al. present Single Molecule Modification Analysis of Long Reads, a new tool for de novodetection of epigenetic heterogeneity.

    • John Beaulaurier
    • , Xue-Song Zhang
    •  & Gang Fang

  • Article
    | Open Access

    The protein factors that bind to regulatory regions in the genome have not been systematically mapped. Here the authors performed chromatin immunoprecipitations for histone modifications associated with promoters, enhancers or heterochromatin in mouse embryonic stem cells and assigned a genome location to many factors important for pluripotency.

    • Erik Engelen
    • , Johannes H. Brandsma
    •  & Raymond A. Poot

  • Article
    | Open Access

    Microsporidia are intracellular parasitic fungi that infect diverse animal hosts including humans. Here, Desjardins et al.present genomic and transcriptomic data for two microsporidia that infect disease-transmitting mosquitoes, highlighting differences in potential host interplay mechanisms.

    • Christopher A. Desjardins
    • , Neil D. Sanscrainte
    •  & Christina A Cuomo

  • Article |

    Compromised function of regulatory T cells can lead to autoimmunity. Here the authors show that miR-125a stabilizes regulatory T-cell function and is downregulated in lupus and Crohn’s disease, as well as autoimmune mouse models, and that a chemical miR-125a analogue reverts established disease in a mouse model of multiple sclerosis.

    • Wen Pan
    • , Shu Zhu
    •  & Nan Shen

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