Chromatin Accessibility
Methods and Protocols
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William J. Greenleaf
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Article
Publisher Correction: PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape
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Article
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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Article
The killifish germline regulates longevity and somatic repair in a sex-specific manner
Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in sha** vertebrate aging remains largely unknown. In this study, ...
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Article
Open AccessGenome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome
In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystall...
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Article
PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape
Adaptive immunity relies on specialized effector functions elicited by lymphocytes, yet how antigen recognition activates appropriate effector responses through nonspecific signaling intermediates is unclear. ...
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Article
Open AccessMulticenter integrated analysis of noncoding CRISPRi screens
The ENCODE Consortium’s efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to ...
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Article
Open AccessThe chromatin landscape of the euryarchaeon Haloferax volcanii
Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations fir...
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Article
Open AccessGlobal map** of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions
Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs a...
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Article
Open AccessIntegration of spatial and single-cell data across modalities with weakly linked features
Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integra...
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Article
Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases
Genome-wide association studies have identified many loci associated with hair and skin disease, but identification of causal variants requires deciphering of gene-regulatory networks in relevant cell types. W...
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Article
Open AccessOrganization of the human intestine at single-cell resolution
The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health1. The intes...
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Article
High-throughput biochemistry in RNA sequence space: predicting structure and function
RNAs are central to fundamental biological processes in all known organisms. The set of possible intramolecular interactions of RNA nucleotides defines the range of alternative structural conformations of a sp...
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Article
Single-cell transcriptomic landscape of the develo** human spinal cord
Understanding spinal cord assembly is essential to elucidate how motor behavior is controlled and how disorders arise. The human spinal cord is exquisitely organized, and this complex organization contributes ...
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Article
Open AccessCasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA map**
Detecting and mitigating off-target activity is critical to the practical application of CRISPR-mediated genome and epigenome editing. While numerous methods have been developed to map Cas9 binding specificity...
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Protocol
Genome-Wide Map** of Active Regulatory Elements Using ATAC-seq
Active cis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property has turned out to be immensely useful for identifying cREs geno...
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Protocol
Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq
The ability to analyze the transcriptomic and epigenomic states of individual single cells has in recent years transformed our ability to measure and understand biological processes. Recent advancements have f...
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Article
Current and future perspectives of single-cell multi-omics technologies in cardiovascular research
Single-cell technology has become an indispensable tool in cardiovascular research since its first introduction in 2009. Here, we highlight the recent remarkable progress in using single-cell technology to stu...
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Book
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Article
Aging-associated HELIOS deficiency in naive CD4+ T cells alters chromatin remodeling and promotes effector cell responses
Immune aging combines cellular defects in adaptive immunity with the activation of pathways causing a low-inflammatory state. Here we examined the influence of age on the kinetic changes in the epigenomic and ...
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Protocol
Single-Molecule Map** of Chromatin Accessibility Using NOMe-seq/dSMF
The bulk of gene expression regulation in most organisms is accomplished through the action of transcription factors (TFs) on cis-regulatory elements (CREs). In eukaryotes, these CREs are generally characterized ...
