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| Open AccessA concerted neuron–astrocyte program declines in ageing and schizophrenia
A synaptic neuron and astrocyte program (SNAP) varies among healthy humans, may shape interindividual differences in synapses and plasticity, and is undermined in schizophrenia and with advancing age.
- Emi Ling
- , James Nemesh
- & Steven A. McCarroll
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Article
| Open AccessIncomplete transcripts dominate the Mycobacterium tuberculosis transcriptome
A study reveals that most transcripts in Mycobacterium tuberculosis are incomplete, likely because of the tendency of the transcription machinery in this species to pause on genomic DNA.
- Xiangwu Ju
- , Shuqi Li
- & Shixin Liu
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Article
| Open AccessSpatial transcriptomics reveal neuron–astrocyte synergy in long-term memory
Spatial and single-cell transcriptomic analyses of the mouse basolateral amygdala reveal transcriptomic signatures, spatial resolution and interactions of cells that constitute the memory engram, including crucial neuron–astrocyte interactions.
- Wenfei Sun
- , Zhihui Liu
- & Stephen R. Quake
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News & Views |
Gene expression of single cells mapped in tissue sections
A tool that tags individual cells in a tissue with a unique barcode means that the gene-expression profile of each cell can be plotted in its original location. This allows spatial information to be captured at single-cell resolution.
- Patrik L. Ståhl
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News & Views Forum |
Cellular atlases of the entire mouse brain
In a huge collaborative effort, millions of cells in the mouse brain have been mapped in detail. Two scientists examine the resulting wealth of insights into gene regulation in brain cells, neuronal connections and how our own brains evolved.
- Maria Antonietta Tosches
- & Heather J. Lee
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Article
| Open AccessThe molecular cytoarchitecture of the adult mouse brain
To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq, a recently developed spatial transcriptomics method with near-cellular resolution, across the entire mouse brain.
- Jonah Langlieb
- , Nina S. Sachdev
- & Evan Z. Macosko
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Article
| Open AccessA human embryonic limb cell atlas resolved in space and time
Using single-cell and spatial transcriptomics, human embryonic limb development across space and time and the diversification and cross-species conservation of cells are demonstrated.
- Bao Zhang
- , Peng He
- & Sarah A. Teichmann
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Article
| Open AccessEmbryo-scale reverse genetics at single-cell resolution
We present the ‘zebrafish single-cell atlas of perturbed embryos’, single-cell trancriptomic data of developing zebrafish embryos across various timepoints and with genetic perturbations.
- Lauren M. Saunders
- , Sanjay R. Srivatsan
- & Cole Trapnell
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Career Column |
Methods section too short? Use online protocols to make complex techniques understandable
New wet-lab methods can be hard to share owing to their complexity, but with a little extra effort, you can give users a leg-up in getting started.
- Lars Borm
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Career Column |
Embracing the command line: my unexpected career in computational biology
A crash course in bioinformatics put Ming Tommy Tang on a different path.
- Ming Tommy Tang
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Article
| Open AccessSpatial atlas of the mouse central nervous system at molecular resolution
In situ spatial transcriptomic analysis of more than 1 million cells are used to create a 200-nm-resolution spatial molecular atlas of the adult mouse central nervous system and identify previously unknown tissue architectures.
- Hailing Shi
- , Yichun He
- & Xiao Wang
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Article
| Open AccessTranscriptional linkage analysis with in vivo AAV-Perturb-seq
An in vivo single-cell CRISPR screening method identifies transcriptional phenotypes of 22q11.2 deletion syndrome associated with a broad dysregulation of a class of disease susceptibility genes that are important for RNA processing and synaptic function.
- Antonio J. Santinha
- , Esther Klingler
- & Randall J. Platt
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Technology Feature |
The quest to map the mouse brain
By combining single-cell sequencing with methods to map the spatial location of gene expression, scientists are unravelling the extraordinary cellular diversity of the brain.
- Diana Kwon
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Article
| Open AccessEndothelial sensing of AHR ligands regulates intestinal homeostasis
Single-cell transcriptomics and in vivo challenge models establish a key role for the aryl hydrocarbon receptor in regulating the function of enteric endothelial cells in response to environmental cues.
- Benjamin G. Wiggins
- , Yi-Fang Wang
- & Chris Schiering
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News & Views |
Cell-level reference maps for the human body take shape
The HuBMAP consortium has generated spatially resolved cell atlases for the human intestine, kidney and placenta, which enable analysis of tissue organization in unprecedented detail.
- Roser Vento-Tormo
- & Roser Vilarrasa-Blasi
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Article
| Open AccessSpatially resolved multiomics of human cardiac niches
Single-cell and spatial transcriptomic analysis of eight human heart tissues reveals the cellular profiles and tissue architecture of niches including the cardiac conduction system, and a new tool, drug2cell, identifies drug target expression.
- Kazumasa Kanemaru
- , James Cranley
- & Sarah A. Teichmann
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News & Views |
Patterns of tumour transcriptional variability
The compilation and analysis of a compendium of single-cell RNA-sequencing studies across various cancers reveals recurring gene-expression programs that underpin tumour heterogeneity.
- Raymond W. S. Ng
- & Sydney M. Shaffer
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Career Column |
Why it’s worth making computational methods easy to use
Jean Fan and her team launched a digital campaign using YouTube, GitHub and blogs to make a computational-biology tool accessible to all. Here’s what they learnt.
- Jean Fan
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News |
Ageing studies in five animals suggest how to reverse decline
Smoothing the speed bumps in an important cellular pathway seems to be implicated in ageing.
- Gemma Conroy
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Article
| Open AccessGenomic–transcriptomic evolution in lung cancer and metastasis
Computational and machine-learning approaches that integrate genomic and transcriptomic variation from paired primary and metastatic non-small cell lung cancer samples from the TRACERx cohort reveal the role of transcriptional events in tumour evolution.
- Carlos Martínez-Ruiz
- , James R. M. Black
- & Nicholas McGranahan
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News |
Did flu come from fish? Genetics points to influenza’s aquatic origin
Corals, sturgeon and other aquatic creatures harbour signs of infection by influenza and its distant relatives.
- Ewen Callaway
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Technology Feature |
Innovative technologies crowd the short-read sequencing market
With a dizzying range of strategies available, laboratories must weigh up their options to find the best fit for their projects
- Michael Eisenstein
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Technology Feature |
Which single-cell analysis tool is best? Scientists offer advice
In the fast-paced field of single-cell biology, studies that compare methods can help scientists to pick the right technique for their research.
- Amber Dance
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Article |
Microbial predators form a new supergroup of eukaryotes
Provora is an ancient supergroup of microbial predators that are genetically, morphologically and behaviourally distinct from other eukaryotes, and comprise two divergent clades of predators—Nebulidia and Nibbleridia—that differ fundamentally in ultrastructure, behaviour and gene content.
- Denis V. Tikhonenkov
- , Kirill V. Mikhailov
- & Patrick J. Keeling
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Article
| Open AccessBroad transcriptomic dysregulation occurs across the cerebral cortex in ASD
RNA sequencing reveals widespread transcriptomic changes across the cerebral cortex in autism spectrum disorder, including primary sensory regions, in addition to association regions, as well as an attenuation of regional identity.
- Michael J. Gandal
- , Jillian R. Haney
- & Daniel H. Geschwind
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Article
| Open AccessLive-seq enables temporal transcriptomic recording of single cells
Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy, can address a range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.
- Wanze Chen
- , Orane Guillaume-Gentil
- & Bart Deplancke
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Article |
Spatial multi-omic map of human myocardial infarction
A time-resolved high-resolution map of human cardiac remodelling after myocardial infarction, integrating single-cell transcriptomic, chromatin accessibility and spatial transcriptomic data, provides a valuable resource for the field.
- Christoph Kuppe
- , Ricardo O. Ramirez Flores
- & Rafael Kramann
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Article |
RNA editing underlies genetic risk of common inflammatory diseases
cis-RNA editing quantitative trait loci, which are associated with immunogenic double-stranded RNAs, underlie genome-wide association study variants in common autoimmune and inflammatory diseases.
- Qin Li
- , Michael J. Gloudemans
- & Jin Billy Li
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News & Views |
A gene-expression axis defines neuron behaviour
A combination of functional imaging and gene-expression profiling in brain tissue has been used to unravel the properties of 35 subtypes of neuron in mice, revealing a gene-expression axis that governs each subtype’s activity.
- Hongkui Zeng
- & Saskia E. J. de Vries
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Technology Feature |
How to make spatial maps of gene activity — down to the cellular level
Computational and experimental methods are bringing researchers closer to their goal of revealing exactly where in a cell or tissue each gene is expressed.
- Michael Eisenstein
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Article |
Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy
- Mark Chaffin
- , Irinna Papangeli
- & Patrick T. Ellinor
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Article |
Differential cofactor dependencies define distinct types of human enhancers
The systematic categorization of human enhancers by their cofactor dependencies provides a conceptual framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes.
- Christoph Neumayr
- , Vanja Haberle
- & Alexander Stark
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News & Views |
A cell atlas for migraine research
The trigeminal nerve has a key role in migraine. An atlas of cell types and gene-expression profiles for cells in this nerve in mice and humans promises to improve our understanding of head pain.
- Philip R. Holland
- & Peter J. Goadsby
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Article |
Single-cell eQTL models reveal dynamic T cell state dependence of disease loci
A single-cell Poisson model is used to analyse eQTLs in memory T cells across continuous, dynamic cell states, revealing that the cell context is critical to understanding variation in eQTLs and their association with disease.
- Aparna Nathan
- , Samira Asgari
- & Soumya Raychaudhuri
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Article
| Open AccessIntron-mediated induction of phenotypic heterogeneity
Experiments in yeast show that introns have a role in inducing phenotypic heterogeneity and that intron-mediated regulation of ribosomal proteins confers a fitness advantage by enabling yeast populations to diversify under nutrient-scarce conditions.
- Martin Lukačišin
- , Adriana Espinosa-Cantú
- & Tobias Bollenbach
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Article |
Molecular hallmarks of heterochronic parabiosis at single-cell resolution
A transcriptomics study demonstrates cell-type-specific responses to differentially aged blood and shows young blood to have restorative and rejuvenating effects that may be invoked through enhanced mitochondrial function.
- Róbert Pálovics
- , Andreas Keller
- & Tony Wyss-Coray
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Article
| Open AccessTDP-43 represses cryptic exon inclusion in the FTD–ALS gene UNC13A
TDP-43 controls an exon splicing event in UNC13A that results in the inclusion of a cryptic exon associated with frontotemporal dementia and amyotrophic lateral sclerosis.
- X. Rosa Ma
- , Mercedes Prudencio
- & Aaron D. Gitler
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Technology Feature |
Revealing chromosome contours, one dot at a time
Methods that meld imaging with sequencing are uncovering the organizational principles of the genome — and how it influences cell fates.
- Amber Dance
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Article |
A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk
A method called vessel isolation and nuclei extraction for sequencing (VINE-seq) produces a molecular map of vascular and perivascular cell types in the human brain and reveals their contributions to Alzheimer’s disease risk.
- Andrew C. Yang
- , Ryan T. Vest
- & Tony Wyss-Coray
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Article |
Single-cell dissection of the human brain vasculature
A study describes single-cell characterization of the human cerebrovasculature, revealing human-specific transcriptomic signatures and providing insights into transcriptional changes associated with Huntington’s disease.
- Francisco J. Garcia
- , Na Sun
- & Myriam Heiman
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News & Views |
A blood test to predict complications of pregnancy
Cell-free RNA transcripts in maternal blood can be analysed to monitor the progression of pregnancy and to predict a potentially harmful pregnancy-specific condition called pre‑eclampsia.
- Lydia L. Shook
- & Andrea G. Edlow
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Article
| Open AccessLocal and systemic responses to SARS-CoV-2 infection in children and adults
Mechanisms explaining the milder clinical syndrome that is observed in children with SARS-CoV-2 infection.
- Masahiro Yoshida
- , Kaylee B. Worlock
- & Kerstin B. Meyer
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Article |
Non-genetic determinants of malignant clonal fitness at single-cell resolution
Non-genetic malignant clonal dominance is a cell-intrinsic and heritable property that underpins clonal output and response to therapy in cancer.
- Katie A. Fennell
- , Dane Vassiliadis
- & Mark A. Dawson
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News & Views Forum |
A census of cell types in the brain’s motor cortex
An atlas of the cell types found in the motor cortex of the brain has been built using various types of data. Two neuroscientists explain the technological feats involved in the project, as well as the utility of the resource for future research.
- Johan Winnubst
- & Silvia Arber
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Review Article |
Exploring tissue architecture using spatial transcriptomics
This review describes the state of spatial transcriptomics technologies and analysis tools that are being used to generate biological insights in diverse areas of biology.
- Anjali Rao
- , Dalia Barkley
- & Itai Yanai
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Article |
Molecular architecture of the developing mouse brain
A comprehensive single-cell transcriptomic atlas of the mouse brain between gastrulation and birth identifies hundreds of cellular states and reveals the spatiotemporal organization of brain development.
- Gioele La Manno
- , Kimberly Siletti
- & Sten Linnarsson
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Technology Feature |
Single-cell analysis enters the multiomics age
A rapidly growing collection of software tools is helping researchers to analyse multiple huge ‘-omics’ data sets.
- Jeffrey M. Perkel
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Article |
Dysregulation of brain and choroid plexus cell types in severe COVID-19
Single-nucleus transcriptomes of frontal cortex and choroid plexus samples from patients with COVID-19 reveal pathological cell states that are similar to those associated with human neurodegenerative diseases and chronic brain disorders.
- Andrew C. Yang
- , Fabian Kern
- & Tony Wyss-Coray
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Research Summary |
Protein architecture of the yeast genome
Use of chromatin immunoprecipitation with exonuclease treatment (ChIP–exo) determines the positional organization of hundreds of chromosomal proteins throughout the Saccharomyces cerevisiae genome. The resulting ultra-high-resolution map provides insight into the regulation of genes, enhancers, replication origins, centromeres, subtelomeres and transposons.
- B. Franklin Pugh