Transcriptomics articles within Nature Communications

Featured

  • Article
    | Open Access

    A feature of cohesin mutations in patients with Cornelia de Lange Syndrome (CdLS) is intellectual disability, but the underlying mechanisms have remained obscure. Here the authors show gene expression is deregulated in CdLS neurons and is recapitulated in a mouse model with cohesin depletion, which can be restored by re-expression of cohesin.

    • Felix D. Weiss
    • , Lesly Calderon
    •  & Matthias Merkenschlager

  • Article
    | Open Access

    Identifying enriched gene sets in transcriptomic data is routine analysis. Here, the authors show that conventional gene category enrichment analysis (GCEA) applied to brain-wide atlas data yields biased results and develop a flexible ensemble-based null model framework to enable appropriate inference in GCEA.

    • Ben D. Fulcher
    • , Aurina Arnatkeviciute
    •  & Alex Fornito

  • Article
    | Open Access

    After injury to the nervous system, many neurons fail to initiate transcriptional programs needed for axon growth. Here the authors examine co-operative binding of factors to regulatory DNA to predict combinations that improve axon growth when ectopically co-expressed.

    • Ishwariya Venkatesh
    • , Vatsal Mehra
    •  & Murray G. Blackmore

  • Article
    | Open Access

    The full heterogeneity and different functional roles of cholinergic neurons in the adult spinal cord remain to be defined. Here the authors develop a targeted single nuclear RNA sequencing approach and use it to identify an array of cholinergic interneurons, as well as visceral and skeletal motor neurons.

    • Mor R. Alkaslasi
    • , Zoe E. Piccus
    •  & Claire E. Le Pichon

  • Article
    | Open Access

    As human skeletal muscle ages, gene expression programs change and reflect damage accumulation and homeostatic resilience mechanisms. Here, the authors present a detailed framework of the global transcriptome that characterizes skeletal muscle during aging in healthy individuals.

    • Robert A. Tumasian III
    • , Abhinav Harish
    •  & Luigi Ferrucci

  • Article
    | Open Access

    Short read RNA sequencing and DNA sequence contain useful information for profiling polyadenylation sites, but each also possesses inherent limitations when examined independently. Aptardi combines these data and significantly improves annotation of polyadenylation sites in the expressed transcriptome.

    • Ryan Lusk
    • , Evan Stene
    •  & Laura M. Saba

  • Article
    | Open Access

    Image features from histological slides can be used as informative endophenotypes in association studies for tissue-localized pathologies. Here, the authors develop ImageCCA, a framework for joint analysis of paired gene expression and histology data derived from automatically extracted image features.

    • Jordan T. Ash
    • , Gregory Darnell
    •  & Barbara E. Engelhardt

  • Article
    | Open Access

    It is unclear how changes in gene expression are induced by changes in oxygen levels during late lung development. Here, the authors provide data from MULTI-seq scRNAseq in mice showing exposure to higher oxygen levels affects cell fates, especially for alveolarisation, and define gene/cell signatures of impaired lung development under hyperoxia.

    • Maria Hurskainen
    • , Ivana Mižíková
    •  & Bernard Thébaud

  • Article
    | Open Access

    Malignant rhabdoid tumours (MRT) have been suggested to originate in the ectoderm-derived neural crest. Here, the authors analyse MRTs using phylogenetics, scRNA-seq, and patient-derived organoids; they find evidence for an MRT origin in the neural crest lineage and suggest differentiation treatment with HDAC/mTOR inhibitors.

    • Lars Custers
    • , Eleonora Khabirova
    •  & Jarno Drost

  • Article
    | Open Access

    The response to hypoxia can significantly impact oncogenic processes. Here, the authors define the early transcriptional response to acute hypoxia and identify HIF1A target genes as part of this acute response, providing a resource for investigating context-dependent roles of HIF1A in the biology of cancer.

    • Zdenek Andrysik
    • , Heather Bender
    •  & Joaquin M. Espinosa

  • Article
    | Open Access

    Leukaemic stem cells drive acute myeloid leukaemia (AML) progression and relapse but they are incompletely characterized. Here, the authors combine single-cell transcriptomics and clonal tracking using nuclear and mitochondrial somatic variants to distinguish healthy, pre-leukaemic and leukaemic stem cells in AML.

    • Lars Velten
    • , Benjamin A. Story
    •  & Lars M. Steinmetz

  • Article
    | Open Access

    Understanding the molecular effects of disease variants in relevant tissues is essential to understanding and treating disease. Here, the authors discover expression and protein quantitative trait loci in cartilage and synovium from 115 osteoarthritis patients to pinpoint genes of action and potential drug treatments.

    • Julia Steinberg
    • , Lorraine Southam
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Carbon dots have attracted much attention for biomedical applications but potential degradation and associated toxicity are still poorly understood. Here, the authors report on a study into the photo-degradation of carbon dots, the products produced and associated cytotoxicity.

    • Yue-Yue Liu
    • , Nan-Yang Yu
    •  & Ai-Jun Miao

  • Article
    | Open Access

    Single cell genomics uses cells from the same individual, or pseudoreplicates, that can introduce biases and inflate type I error rates. Here the authors apply generalized linear mixed models with a random effect for individual, to properly account for both zero inflation and the correlation structure among cells within an individual.

    • Kip D. Zimmerman
    • , Mark A. Espeland
    •  & Carl D. Langefeld

  • Article
    | Open Access

    Genome-wide studies of de novo genes have tended to focus on genomic open reading frames (ORFs). Here, Blevins et al. use deep transcriptomics and synteny information to identify de novo transcripts in the yeast Saccharomyces cerevisiae, many of which are expressed from the alternative DNA strand.

    • William R. Blevins
    • , Jorge Ruiz-Orera
    •  & M. Mar Albà

  • Article
    | Open Access

    Corneal epithelium shares similar molecular signatures to other stratified epithelia. Here, the authors map super-enhancers and accessible chromatin in corneal epithelium, identifying a transcription regulatory circuit, including RUNX1, PAX6, and SMAD3, required for corneal epithelial identity and homeostasis.

    • Mingsen Li
    • , Huaxing Huang
    •  & Hong Ouyang

  • Article
    | Open Access

    Circular RNAs have been identified using short-read RNA sequencing. Here, the authors report isoCirc, a long-read sequencing method to characterize full-length circRNA isoforms and generate a catalogue of full-length circRNA isoforms in 12 human tissues and one human cell line.

    • Ruijiao Xin
    • , Yan Gao
    •  & Yi Xing

  • Article
    | Open Access

    Anterior vaginal prolapse (AVP), the most common form of pelvic organ prolapse, has deleterious effects on women’s health. Here the authors employ single-cell RNA-seq to construct a transcriptomic atlas of vaginal wall cells from AVP patients, and find that extracellular matrix dysregulation and immune reaction are associated with AVP.

    • Yaqian Li
    • , Qing-Yang Zhang
    •  & Lan Zhu

  • Article
    | Open Access

    Hepatocyte 12-hour rhythms have a role in cellular stress and metabolic functions. Here, the authors demonstrate disrupting the 12-hour clock through deletion of XBP1 is associated with the development of NAFLD as well as disruption of phospholipid composition and the maintenance of lipid homeostasis.

    • Huan Meng
    • , Naomi M. Gonzales
    •  & Bert W. O’Malley

  • Article
    | Open Access

    Single-cell transcriptomics enhanced our ability to profile heterogeneous cell populations. It is not known which statistical frameworks are performant to detect subpopulation-level responses. Here, the authors developed a simulation framework to evaluate various methods across a range of scenarios.

    • Helena L. Crowell
    • , Charlotte Soneson
    •  & Mark D. Robinson

  • Article
    | Open Access

    The liver possesses the ability to regenerate following sudden injury. Here, the authors use single-cell RNA-sequencing and in situ transcriptional analyses to identify a new phase of liver regeneration in mice aimed at maintaining essential functions throughout the regenerative process.

    • Chad M. Walesky
    • , Kellie E. Kolb
    •  & Wolfram Goessling

  • Article
    | Open Access

    Multi-Omic approaches are a powerful way for obtaining in-depth understanding of a cell’s state. Here the authors present DISCO, combining digital microfluidics, laser cell lysis, and artificial intelligence-driven image processing to analyze single-cell genomes, transcriptomes and proteomes in a mixed population.

    • Julian Lamanna
    • , Erica Y. Scott
    •  & Aaron R. Wheeler

  • Article
    | Open Access

    Inferring cell type proportions from transcriptomics data is affected by data transformation, normalization, choice of method and the markers used. Here, the authors use single-cell RNAseq datasets to evaluate the impact of these factors and propose guidelines to maximise deconvolution performance.

    • Francisco Avila Cobos
    • , José Alquicira-Hernandez
    •  & Katleen De Preter

  • Article
    | Open Access

    Dissecting the cellular heterogeneity embedded in single-cell transcriptomic data is challenging. Here, the authors introduce the concept of multiresolution cell-state decomposition as a practical approach to simultaneously capture both fine- and coarse-grain patterns of variability.

    • Shahin Mohammadi
    • , Jose Davila-Velderrain
    •  & Manolis Kellis

  • Article
    | Open Access

    Mutations in TREM2 alter risk for Alzheimer’s disease, though the mechanisms underlying risk in human cells are unclear. Here, the authors use iPS-microglia and chimeric mice to highlight altered survival, phagocytosis, migration, and transcriptional programs in microglia lacking TREM2.

    • Amanda McQuade
    • , You Jung Kang
    •  & Mathew Blurton-Jones

  • Article
    | Open Access

    This study presents and validates a novel approach to reliably identify structural variations (SVs) in non-model genomes using whole genome sequencing, which was used to detect 15,483 SVs in 492 Atlantic salmon, shedding light on their roles in genome evolution and the genetic architecture of domestication.

    • Alicia C. Bertolotti
    • , Ryan M. Layer
    •  & Daniel J. Macqueen

  • Article
    | Open Access

    ACE2 and TMPRSS2 have received recent attention as entry factors for SARS-CoV-2. Here the authors analyze nasal airway transcriptome data from 695 children determining ACE2 and TMPRSS2 expression is induced by viral and type2 inflammation, respectively, and both exhibit eQTLs that vary across world populations.

    • Satria P. Sajuthi
    • , Peter DeFord
    •  & Max A. Seibold

  • Article
    | Open Access

    Transcriptional factors (TFs) bind in a combinatorial fashion to specify the on-and-off states of genes in a complex and redundant regulatory network. Here, the authors construct the transcription regulatory network in maize leaf using 104 TFs ChIP-seq data and train machine learning models to predict TF binding and colocalization.

    • Xiaoyu Tu
    • , María Katherine Mejía-Guerra
    •  & Silin Zhong

  • Article
    | Open Access

    The pathophysiological role of dopamine D1 receptor (D1R) in chronic heart failure remains elusive. Here the authors show that D1R-expressing cardiomyocytes appear in chronic heart failure and play a pivotal role in triggering lethal ventricular arrhythmias.

    • Toshihiro Yamaguchi
    • , Tomokazu S. Sumida
    •  & Issei Komuro

  • Article
    | Open Access

    The development of activated B cells into antibody-secreting cells (ASC) is a critical step for humoral immunity. Here the authors show, using adoptive transfers and single cell RNA sequencing, that commitment to ASC occurs soon following B cell activation, and is coordinated by specific transcriptome programs and proliferation kinetics.

    • Christopher D. Scharer
    • , Dillon G. Patterson
    •  & Jeremy M. Boss

  • Article
    | Open Access

    To define and distinguish fibroblasts from vascular mural cells have remained challenging. Here, using single-cell RNA sequencing and tissue imaging, the authors provide a molecular basis for cell type classification and reveal inter- and intra-organ diversity of these cell types.

    • Lars Muhl
    • , Guillem Genové
    •  & Christer Betsholtz

  • Article
    | Open Access

    Common fragile sites are regions susceptible to replication stress and are prone to chromosomal instability. Here, the authors, by analyzing the contribution of 3D chromatin organization, identify and characterize a fragility signature and precisely map these fragility regions.

    • Dan Sarni
    • , Takayo Sasaki
    •  & Batsheva Kerem

  • Article
    | Open Access

    The transcriptional regulator PRDM15 is expressed at low levels in normal tissues but overexpressed in B-cell lymphomas. Here, the authors show that PRDM15 depletion does not affect adult somatic cell homeostasis but leads to a metabolic crisis which impairs B-cell lymphomagenesis.

    • Slim Mzoughi
    • , Jia Yi Fong
    •  & Ernesto Guccione

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