Sequencing articles within Nature Communications

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  • Article
    | Open Access

    3D brain organoids have been used to investigate human brain development and pathology. Here the authors establish human ventral midbrain organoids coupled with single cell sequencing to study developing and mature dopamine neurons and use silk scaffolding to generate bioengineered brain organoids

    • Alessandro Fiorenzano
    • , Edoardo Sozzi
    •  & Malin Parmar

  • Article
    | Open Access

    Developmental genes are frequently controlled by multiple enhancers sharing similar specificities, so deletions of such regulatory elements often fail to reveal their full function. Here the authors use the Pitx1 testbed locus to characterize the regulatory and cellular identity alterations following the deletion in vivo of one of its enhancers.

    • Raquel Rouco
    • , Olimpia Bompadre
    •  & Guillaume Andrey

  • Article
    | Open Access

    Nanopore direct RNA Sequencing data contain information about the presence of RNA modifications, but their detection poses substantial challenges. Here the authors introduce Nanocompore, a new methodology for modification detection from Nanopore data.

    • Adrien Leger
    • , Paulo P. Amaral
    •  & Tony Kouzarides

  • Article
    | Open Access

    Craniofacial development depends on formation and maintenance of sutures between bones of the skull. Here the authors identify enriched expression of the hedgehog inhibitor Hhip, specifically in the mesenchyme of the murine coronal suture, and show sutural dysgenesis in Hhip−/− mutants.

    • Greg Holmes
    • , Ana S. Gonzalez-Reiche
    •  & Ethylin Wang Jabs

  • Article
    | Open Access

    Global transcriptional differences across lobular units in the liver remain unknown. Here the authors perform spatial transcriptomics of liver tissue to delineate transcriptional differences in physical space, confirm lobular zonation along transcriptional gradients and suggest the presence of previously uncharacterized structures within liver tissue.

    • Franziska Hildebrandt
    • , Alma Andersson
    •  & Johan Ankarklev

  • Article
    | Open Access

    The molecular mechanisms that drive hematopoietic stem cell functional decline under conditions of telomere shortening are not completely understood. Here the authors demonstrate that hematopoietic stem cells with short telomeres induced by mutations affecting telomerase complex genes undergo differentiation towards megakaryopoiesis through the activation of the IFI16-mediated interferon response.

    • Natthakan Thongon
    • , Feiyang Ma
    •  & Simona Colla

  • Article
    | Open Access

    Obtaining accurate variant calls from multiple displacement amplified single cell DNA sequencing data needs dedicated models that account for amplification bias and copy errors. Here, the authors describe ProSolo, a model for calling single nucleotide variants with control over the false discovery rate.

    • David Lähnemann
    • , Johannes Köster
    •  & Alexander Schönhuth

  • Article
    | Open Access

    Perturbations of the cardiopharyngeal mesoderm can lead to congenital defects in individuals with 22q11.2 deletion syndrome. Here the authors use single cell RNA-sequencing to identify a multilineage primed population within the mesoderm, marked by Tbx1, which has bipotent properties to form cardiac and branchiomeric muscle cells.

    • Hiroko Nomaru
    • , Yang Liu
    •  & Bernice E. Morrow

  • Article
    | Open Access

    The role of the transcriptional effector SMAD4 in vertebrate embryo development remains unresolved. Here the authors show that in the absence of Smad4, dorsal/ventral embryo patterning is disrupted due to the loss of BMP signaling, while Nodal signaling is maintained, but insufficient for optimal endoderm specification.

    • Luca Guglielmi
    • , Claire Heliot
    •  & Caroline S. Hill

  • Article
    | Open Access

    Chronic desynchronization between physiological and behavioral rhythms has been linked to the onset of metabolic diseases. Here the authors control the cyclic metabolic signals in a microfluidic device to study the effects of the timing, period and frequency of glucose and insulin on the transcriptome of cultured fibroblasts.

    • Onelia Gagliano
    • , Camilla Luni
    •  & Nicola Elvassore

  • Article
    | Open Access

    Quantification of rare somatic mutations is essential for basic research and translational applications. Here the authors present Quantitative Blocker Displacement Amplification allowing for accurate detection of mutations below 0.01% VAF.

    • Peng Dai
    • , Lucia Ruojia Wu
    •  & David Yu Zhang

  • Article
    | Open Access

    Ribosome can mediate piRNA biogenesis from long non-coding RNAs following translation of the short open reading frames. Here the authors show that 80S ribosome also guides piRNA production from 3’ UTR of protein-coding genes after translation of long open reading frames, indicating a general piRNA biogenesis mechanism regardless of their precursor ORF length.

    • Yu H. Sun
    • , Ruoqiao Huiyi Wang
    •  & Xin Zhiguo Li

  • Article
    | Open Access

    The Lake Malawi cichlid fishes are an example of extreme vertebrate radiation; however, there is very little sequence divergence among the species. Here the authors present a comparative genome-wide methylome study to suggest DNA methylation played a major role in the extensive phenotypic diversity amongst these fishes.

    • Grégoire Vernaz
    • , Milan Malinsky
    •  & Eric A. Miska

  • Article
    | Open Access

    Transcription in archaea is known to be regulated through the recruitment of RNA polymerase to promoters. Here, the authors show that the archaeon Saccharolobus solfataricus regulates transcription globally through a rate-limiting promoter-proximal elongation step.

    • Fabian Blombach
    • , Thomas Fouqueau
    •  & Finn Werner

  • Article
    | Open Access

    Intricate color patterns are a defining aspect of morphological diversity in the Felidae. Here the authors apply morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established.

    • Christopher B. Kaelin
    • , Kelly A. McGowan
    •  & Gregory S. Barsh

  • Article
    | Open Access

    Shwachman-Diamond syndrome (SDS) is a leukemia predisposition disorder that is caused by defective release of eIF6 during ribosome assembly. Here the authors show that acquired somatic EIF6 mutations are frequent in the hematopoietic cells from individuals with SDS and provide a selective advantage over non-modified cells.

    • Shengjiang Tan
    • , Laëtitia Kermasson
    •  & Patrick Revy

  • Article
    | Open Access

    Tendon self-renewal occurs rarely and reconstructive surgery comes with significant limitations. Here the authors present an induced pluripotent stem cell-based method to generate tenocytes, analyze their developmental trajectory using scRNA-seq, and demonstrate their contribution to motor function recovery after Achilles tendon injury via engraftment and paracrine effects.

    • Taiki Nakajima
    • , Akihiro Nakahata
    •  & Makoto Ikeya

  • Article
    | Open Access

    Mesomelic dysplasia, a severe shortening and bending of the limb, has been linked to rearrangements in the HoxD cluster in humans and mice. Here the authors engineer a 1 Mb inversion including the HoxD gene cluster and use this model to provide a mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.

    • Christopher Chase Bolt
    • , Lucille Lopez-Delisle
    •  & Denis Duboule

  • Article
    | Open Access

    Osteoporosis and bone fractures affect millions of patients worldwide and are often due to increased bone resorption. Here the authors identify the cytoplasmic protein ELMO1 as an important ‘signaling node’ promoting the bone resorption function of osteoclasts.

    • Sanja Arandjelovic
    • , Justin S. A. Perry
    •  & Kodi S. Ravichandran

  • Article
    | Open Access

    The development of the coronal suture remains incompletely understood. Here the authors perform scRNA-seq and expression validation to uncover the cellular diversity within the murine embryonic coronal suture, thus revealing possible mechanisms for its loss in craniosynostosis.

    • D’Juan T. Farmer
    • , Hana Mlcochova
    •  & Stephen R. F. Twigg

  • Article
    | Open Access

    Despite being a common congenital facial anomaly, the genetic etiology of craniofacial microsomia (CFM) is not well understood. Here, the authors use exome and genome sequencing of 146 individuals with CFM to identify haploinsufficient variants in SF3B2 as a prevalent underlying cause.

    • Andrew T. Timberlake
    • , Casey Griffin
    •  & Daniela V. Luquetti

  • Article
    | Open Access

    Metastatic and locally-advanced neuroendocrine neoplasms (aNEN) display heterogeneous clinical and genetic characteristics. Here, the authors investigate the mutational landscape of 85 aNEN by whole genome sequencing and identify distinct subpopulations, tumour mutational burden patterns, drivers and actionable somatic alterations.

    • Job van Riet
    • , Harmen J. G. van de Werken
    •  & Bianca Mostert

  • Article
    | Open Access

    DNA probes used in next generation sequencing (NGS) have variable hybridisation kinetics, resulting in non-uniform coverage. Here, the authors develop a deep learning model to predict NGS depth using DNA probe sequences and apply to human and non-human sequencing panels.

    • Jinny X. Zhang
    • , Boyan Yordanov
    •  & David Yu Zhang

  • Article
    | Open Access

    Single-cell RNA-seq reveals the cellular heterogeneity in development and disease. Here the authors present a single-nucleus RNA-seq2 that allows deep characterization of nuclei isolated from frozen archived tissues, apply it for transcriptional profiling of individual hepatocytes, and determine a functional crosstalk between liver zonation and ploidy.

    • M. L. Richter
    • , I. K. Deligiannis
    •  & C. P. Martinez-Jimenez

  • Article
    | Open Access

    The transcriptional regulators underlying the induction and differentiation of dense connective tissues remain largely unknown. Here the authors generate tendon and fibrocartilage cells from mouse embryonic stem cells and apply scRNA-seq to identify molecular regulation of the cell fate switch between these lineages.

    • Deepak A. Kaji
    • , Angela M. Montero
    •  & Alice H. Huang

  • Article
    | Open Access

    Secondary structures and long-range RNA interactions of the SARS-CoV-2 genome have been investigated by various sequencing methods. Here the authors use an RNA-RNA hybrid sequencing method to predict the secondary and tertiary structure of the SRAS-CoV-2 RNA genome in the virion.

    • Changchang Cao
    • , Zhaokui Cai
    •  & Yuanchao Xue

  • Article
    | Open Access

    Human Treg cells are central to immune tolerance, yet their heterogeneity and differentiation remain incompletely understood. Here the authors perform single-cell RNA and T cell receptor sequencing to resolve Treg cells from healthy individuals and patients with or without acute graft-versus-host disease revealing Treg complexity in health and disease.

    • Yuechen Luo
    • , Changlu Xu
    •  & Xiaoming Feng

  • Article
    | Open Access

    The gene regulatory network controlling the bifurcation of common progenitors into the neural retina and retinal-pigmented epithelium programs remains poorly understood. Here the authors study transcriptome dynamics and chromatin accessibility during this process in zebrafish, revealing network redundancy, as well as context-dependent and sequential transcription factor activity.

    • Lorena Buono
    • , Jorge Corbacho
    •  & Juan-Ramón Martínez-Morales

  • Article
    | Open Access

    Whether the adult testis harbours a somatic progenitor population is unknown. Here, the authors provide evidence that the testis interstitial cells expressing the transcription factor Tcf21 maintain adult testis homeostasis during aging, and act as potential reserve somatic progenitors following injury.

    • Yu-chi Shen
    • , Adrienne Niederriter Shami
    •  & Saher Sue Hammoud

  • Article
    | Open Access

    Mobile element insertions (MEIs) are a source of repetitive genetic variation and can lead to genetic disorders. Here the authors use Cas9-targeted nanopore sequencing to efficiently saturate enrichment for known and non-reference MEIs.

    • Torrin L. McDonald
    • , Weichen Zhou
    •  & Alan P. Boyle

  • Article
    | Open Access

    Several existing algorithms predict the methylation of DNA using Nanopore sequencing signals, but it is unclear how they compare in performance. Here, the authors benchmark the performance of several such tools, and propose METEORE, a consensus tool that improves prediction accuracy.

    • Zaka Wing-Sze Yuen
    • , Akanksha Srivastava
    •  & Eduardo Eyras

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