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Open AccessSystematic benchmarking of single-cell ATAC-sequencing protocols
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of syst...
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Publisher Correction: p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity
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Article
Open AccessCell-type-directed design of synthetic enhancers
Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes1. It has been a long-standing goal in the field to ...
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Article
Open AccessSingle-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is...
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Article
Open AccessSCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inferenc...
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Article
Open AccessCell type diversity in a develo** octopus brain
Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The brain cell types that control their sophisticated behavioral repe...
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Article
How regulatory sequences learn cell representations
New computational method uses convolutional neural networks for cis-regulatory sequence analysis to analyze and cluster scATAC-seq data.
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Article
Open AccessComparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq
Multiplexing of samples in single-cell RNA-seq studies allows a significant reduction of the experimental costs, straightforward identification of doublets, increased cell throughput, and reduction of sample-s...
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Article
Decoding gene regulation in the fly brain
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome analysis1–6, three-dimensional morphological classification7 and electron microscopy map** of the connectome8,9 have re...
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Article
Open AccessActuation enhances patterning in human neural tube organoids
Tissues achieve their complex spatial organization through an interplay between gene regulatory networks, cell-cell communication, and physical interactions mediated by mechanical forces. Current strategies to...
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Article
Open AccessPublisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03287-8.
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Chromatin accessibility profiling methods
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied characteristic of the eukaryotic genome. As active regulatory DNA elements are generally ‘accessible’, the genome-wide ...
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Article
LifeTime and improving European healthcare through cell-based interceptive medicine
Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell re...
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Article
Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma
Melanoma cells can switch between a melanocytic and a mesenchymal-like state. Scattered evidence indicates that additional intermediate state(s) may exist. Here, to search for such states and decipher their un...
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A scalable SCENIC workflow for single-cell gene regulatory network analysis
This protocol explains how to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data using software containers and Nextflow pipelines. SCENIC reconstructs reg...
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Open AccessGenomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings
The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this di...
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cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data
We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/c...
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Open AccessEstablishment of the mayfly Cloeon dipterum as a new model system to investigate insect evolution
The great capability of insects to adapt to new environments promoted their extraordinary diversification, resulting in the group of Metazoa with the largest number of species distributed worldwide. To underst...
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Article
Phenotype molding of stromal cells in the lung tumor microenvironment
Cancer cells are embedded in the tumor microenvironment (TME), a complex ecosystem of stromal cells. Here, we present a 52,698-cell catalog of the TME transcriptome in human lung tumors at single-cell resoluti...
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Article
The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes
Transcriptional enhancers function as docking platforms for combinations of transcription factors (TFs) to control gene expression. How enhancer sequences determine nucleosome occupancy, TF recruitment and tra...
