Sequencing articles within Nature Communications

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  • Article
    | Open Access

    Gene flow is classically thought to impede local adaptation via parallel evolution. However, a genomic study on Hawaiian crickets from different island populations finds evidence of parallel adaptation to the same lethal parasitoid in spite of strong ongoing gene flow.

    • Xiao Zhang
    • , Jack G. Rayner
    •  & Nathan W. Bailey

  • Article
    | Open Access

    The human proteome represents a crucial link between complex disease and genetic/environmental factors. Here, the authors investigate 257 cardiometabolic-relevant protein biomarkers in whole genome sequencing data from 1328 individuals, revealing the genetic architecture underlying biomarker variation.

    • Arthur Gilly
    • , Young-Chan Park
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Nanopore sequencing (ONT) has been used in SARS-CoV-2 studies, however adoption of ONT for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. Here, the authors perform a comprehensive evaluation of ONT analytical performance on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls.

    • Rowena A. Bull
    • , Thiruni N. Adikari
    •  & Ira W. Deveson

  • Article
    | Open Access

    Chromatin structure and topology play important roles in the regulation of gene expression. Here the authors study the spatio-temporal re-organization of promoter-enhancer interactions in pluripotent ES and skeletal muscle stem cells and the corresponding impact on gene expression as a consequence of myogenic commitment and differentiation.

    • Nan Zhang
    • , Julen Mendieta-Esteban
    •  & Brian David Dynlacht

  • Article
    | Open Access

    The success of protein evolution is dependent on the sequence context mutations are introduced into. Here the authors present UMIC-seq that allows consensus generation for closely related genes by using unique molecular identifiers linked to gene variants.

    • Paul Jannis Zurek
    • , Philipp Knyphausen
    •  & Florian Hollfelder

  • Article
    | Open Access

    Identifying chemical-genetic interactions in mammalian cells is limited to low-throughput or computational methods. Here, the authors present QMAP-Seq, a broadly accessible and scalable approach that uses NGS for pooled high-throughput chemical-genetic profiling in mammalian cells.

    • Sonia Brockway
    • , Geng Wang
    •  & Marc L. Mendillo

  • Article
    | Open Access

    Cell types in the adult Drosophila ovary vary during homeostasis and differing environmental conditions. Here, the authors use single-cell RNA-sequencing to identify 26 ovarian cell populations and show cellular plasticity in which escort cells can convert to follicle stem cells upon starvation.

    • Katja Rust
    • , Lauren E. Byrnes
    •  & Todd G. Nystul

  • Article
    | Open Access

    The origin and nature of rebound HIV-1 virus following antiretroviral therapy (ART) discontinuation still remains unclear. Here, Liu et al. suggest that intact proviral DNA in peripheral blood and lymph node mononuclear cells during ART suppression likely is the source of viral rebound following ART discontinuation.

    • Po-Ting Liu
    • , Brandon F. Keele
    •  & Dan H. Barouch

  • Article
    | Open Access

    The immunopathological features of SARS-CoV-2 infection in the lungs remain unclear. Here, the authors provide a comprehensive characterization of post mortem lung tissues of COVID-19 patients and find two distinct patterns characterized by differential expression of interferon stimulated genes (ISGs), which correlate to viral loads, cytokines, lung damage and time of hospitalization, suggesting ISG profiles to mark disease progression

    • Ronny Nienhold
    • , Yari Ciani
    •  & Kirsten D. Mertz

  • Article
    | Open Access

    The pathophysiology of epilepsy is unclear. Here, the authors present single-nuclei transcriptomic profiling of human temporal lobe epilepsy from patients. They identified epilepsy-associated neuronal subtypes, and a panel of dysregulated genes, predicting neuronal circuits contributing to epilepsy.

    • Ulrich Pfisterer
    • , Viktor Petukhov
    •  & Konstantin Khodosevich

  • Article
    | Open Access

    Working with cancer genomes from multiple projects can increase investigative power, but quality of sequences can vary. Here, the authors present a framework for comparing whole genome sequencing quality to help researchers guide downstream analyses and exclude poor quality samples.

    • Justin P. Whalley
    • , Ivo Buchhalter
    •  & Ivo G. Gut

  • Article
    | Open Access

    For many neurodevelopmental disorder (NDD) risk genes, the significance for mutational burden is unestablished. Here, the authors sequence 125 candidate NDD genes in over 16,000 NDD cases; case-control mutational burden analysis identifies 48 genes with a significant burden of severe ultra-rare mutations.

    • Tianyun Wang
    • , Kendra Hoekzema
    •  & Evan E. Eichler

  • Article
    | Open Access

    Mandibuloacral dysplasias (MADs) are rare progeroid syndromes characterized by nuclear morphological and functional abnormalities. Here the authors report that loss of mitochondrial membrane protein MTX2 causes a progeroid MAD sharing clinical features with lamin-associated progeroid syndromes.

    • Sahar Elouej
    • , Karim Harhouri
    •  & Annachiara De Sandre-Giovannoli

  • Article
    | Open Access

    The mechanisms regulating stem cells to give rise to human interfollicular epidermis are unclear. Here, the authors use single cell RNA sequencing to identify heterogeneity within the human neonatal interfollicular epidermis and distinct spatial positioning of at least four basal stem cell populations.

    • Shuxiong Wang
    • , Michael L. Drummond
    •  & Scott X. Atwood

  • Article
    | Open Access

    The relative abundance of specific tRNA can impact protein production rate, folding, and messenger RNA stability. Here the authors describe QuantM-tRNA seq — a method to monitor tRNA abundance and sequence variants — and uncover distinctions in isodecoder expression between tissues that are independent of the anticodon pool of each tRNA family.

    • Otis Pinkard
    • , Sean McFarland
    •  & Jeff Coller

  • Article
    | Open Access

    The molecular basis of the clinically important MAM blood group antigen present in most humans is unknown. We identify EMP3 as its encoding gene, establishing MAM as a new blood group system, and demonstrate the role of EMP3 in erythropoiesis through its interaction with the signalling molecule CD44.

    • Nicole Thornton
    • , Vanja Karamatic Crew
    •  & David J. Anstee

  • Article
    | Open Access

    Studying emerging pathogens is often challenging due to the lack of information. Here the authors show that dual RNA-seq, profiling the host and pathogen transcriptome simultaneously, helps uncovering the biology of Orientia tsutsugamushi, a major cause of febrile illness in South-East Asia, and its interaction with the host.

    • Bozena Mika-Gospodorz
    • , Suparat Giengkam
    •  & Jeanne Salje

  • Article
    | Open Access

    DNA is an attractive digital data storing medium due to high information density and longevity. Here the authors use millions of sequences to investigate inherent biases in DNA synthesis and PCR amplification.

    • Yuan-Jyue Chen
    • , Christopher N. Takahashi
    •  & Karin Strauss

  • Article
    | Open Access

    Single cell RNA-seq is a powerful method to assign cell identity, but the purity of cell clusters arising from this data is not clear. Here the authors present an entropy-based statistic called ROGUE to quantify the purity of cell clusters, and identify subtypes within clusters.

    • Baolin Liu
    • , Chenwei Li
    •  & Zemin Zhang

  • Article
    | Open Access

    Structural variants (SVs) contribute to the genetic architecture of many brain-related disorders. Here, the authors integrate SV calls from genome sequencing (n = 755) with RNA-seq data (n = 629) from post-mortem dorsal lateral prefrontal cortex to annotate the gene regulatory effects of SVs in the human brain and their potential to contribute to disease.

    • Lide Han
    • , Xuefang Zhao
    •  & Douglas M. Ruderfer

  • Article
    | Open Access

    The complexity of structural variation (SV) and short tandem repeats (STRs) makes it necessary to apply different calling and filtering strategies to sequencing datasets. Here, Jakubosky et al. report a comprehensive SV and STR callset from whole-genome sequencing of 477 individuals from iPSCORE and HipSci using five algorithms.

    • David Jakubosky
    • , Erin N. Smith
    •  & Kelly A. Frazer

  • Article
    | Open Access

    The impact of late Pleistocene climate change on ecosystems has been hard to assess. Here, the authors sequence ancient DNA from Hall’s Cave, Texas and find that both plant and vertebrate diversity decreased with cooling, and though plant diversity recovered with rewarming, megafauna went extinct.

    • Frederik V. Seersholm
    • , Daniel J. Werndly
    •  & Michael Bunce

  • Article
    | Open Access

    Sample index hopping results in various artefacts in multiplexed scRNA-seq experiments. Here, the authors introduce a statistical model to estimate sample index hopping rate in droplet-based scRNA-seq data and show that artifacts can be corrected by purging phantom molecules from the data.

    • Rick Farouni
    • , Haig Djambazian
    •  & Hamed S. Najafabadi

  • Article
    | Open Access

    Memory B cells are important for protecting the host from pathogen rechallenge, but their properties and locations remain ill-defined. Here the authors show, using single-cell transcriptomics and repertoire analyses, that mouse spleen and bone marrow host distinct populations of isotype-switched memory B cells to potentially optimize for rapid recall responses.

    • René Riedel
    • , Richard Addo
    •  & Andreas Radbruch

  • Article
    | Open Access

    Most human protein-coding genes are expressed as multiple isoforms. Here the authors present ORF Capture-seq that uses cloned ORFs as probes to capture and sequence full length transcript sequences. This enables highly sensitive characterization of eukaryotic transcriptomes.

    • Gloria M. Sheynkman
    • , Katharine S. Tuttle
    •  & Marc Vidal

  • Article
    | Open Access

    Regulating polyadenylation is important for mRNA stability, which can in turn affect B cell maturation and humoral immune responses. Here the authors use Nanopore poly(A) sequencing to explore the importance of the cytoplasmic poly(A) polymerase TENT5C, particularly in the production of immunoglobulins.

    • Aleksandra Bilska
    • , Monika Kusio-Kobiałka
    •  & Seweryn Mroczek

  • Article
    | Open Access

    Nitrogen-starved fission yeast cells survive for weeks without dividing. Here, the authors show that some of these surviving cells accumulate mutations in the stress- and mitogen-activated protein kinase pathways and outcompete their parental cells, which provide nutrients for the mutant cells.

    • Rostyslav Makarenko
    • , Claire Denis
    •  & Benoît Arcangioli

  • Article
    | Open Access

    Traditional methods for determining cell type composition lack scalability, while single-cell technologies remain costly and noisy compared to bulk RNA-seq. Here, the authors present a highly efficient tool to measure cellular heterogeneity in bulk expression through robust integration of single-cell information.

    • Brandon Jew
    • , Marcus Alvarez
    •  & Eran Halperin

  • Article
    | Open Access

    Sample contamination has been reported in high throughput RNA sequencing. Here the authors analyze the RNA sequencing data from the Genotype-Tissue Expression project and describe how highly expressed, tissue specific genes contaminate across samples, which is corroborated in other data sets.

    • Tim O. Nieuwenhuis
    • , Stephanie Y. Yang
    •  & Marc K. Halushka

  • Article
    | Open Access

    The mechanisms of action of proteasome inhibitors (PI) in multiple myeloma (MM) treatment are not fully elucidated. Here, the authors use unbiased phosphoproteomics in PI-treated MM and show increased phosphorylation of splicing-associated proteins, ultimately revealing splicing interference as a mode of PI action as well as demonstrating the spliceosome as a specific therapeutic vulnerability in this disease.

    • Hector H. Huang
    • , Ian D. Ferguson
    •  & Arun P. Wiita

  • Article
    | Open Access

    Collagen production by lung cells is critical to maintain organ architecture but can also drive pathological scarring. Here the authors perform single cell RNA sequencing of collagen-producing lung cells identifying a subset of pathologic fibroblasts characterized by Cthrc1 expression which are concentrated within fibroblastic foci in fibrotic lungs and show a pro-fibrotic phenotype.

    • Tatsuya Tsukui
    • , Kai-Hui Sun
    •  & Dean Sheppard

  • Article
    | Open Access

    Common variants identified by large-scale genomewide association studies cannot account fully account for the heritability of schizophrenia (SCZ). Here, the authors report high-coverage whole-genome sequencing of 1162 SCZ cases and 936 controls and explore the contribution of different types of variants to SCZ.

    • Matthew Halvorsen
    • , Ruth Huh
    •  & Jin P. Szatkiewicz

  • Article
    | Open Access

    Differential expression (DE) and gene set enrichment (GSE) analysis tend to be carried out separately. Here, the authors present iDEA (integrative Differential expression and gene set Enrichment Analysis) for the analysis of scRNAseq data which uses a Baysian approach to jointly model DE and GSE for improved power in both tasks.

    • Ying Ma
    • , Shiquan Sun
    •  & Xiang Zhou

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