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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
Open AccessWhole genome deconvolution unveils Alzheimer’s resilient epigenetic signature
Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) accurately depicts the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However, bulk sequencing entangl...
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Article
Open AccessSingle-cell spatial proteomic imaging for human neuropathology
Neurodegenerative disorders are characterized by phenotypic changes and hallmark proteopathies. Quantifying these in archival human brain tissues remains indispensable for validating animal models and understa...
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Article
Chromatin accessibility profiling by ATAC-seq
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by p...
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Article
ecDNA hubs drive cooperative intermolecular oncogene expression
Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation1. Gene induction typically involves cis-regulatory eleme...
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Article
LKB1 inactivation modulates chromatin accessibility to drive metastatic progression
Metastasis is the leading cause of cancer-related deaths and enables cancer cells to compromise organ function by expanding in secondary sites. Since primary tumours and metastases often share the same constel...
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Article
Open AccessAuthor Correction: ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
A Correction to this paper has been published: https://doi.org/10.1038/s41588-021-00850-x.
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Article
Open AccessArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological mea...
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Article
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases
Genome-wide association studies of neurological diseases have identified thousands of variants associated with disease phenotypes. However, most of these variants do not alter coding sequences, making it diffi...
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Article
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia
Identifying the causes of human diseases requires deconvolution of abnormal molecular phenotypes spanning DNA accessibility, gene expression and protein abundance1–3. We present a single-cell framework that integ...
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Article
Circular ecDNA promotes accessible chromatin and high oncogene expression
Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultra...
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Article
Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion
Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for map** transposa...
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Article
HiChIRP reveals RNA-associated chromosome conformation
Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and o...
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Article
Transcript-indexed ATAC-seq for precision immune profiling
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide–major histocompatibility complex (MHC) ligands. He...
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Article
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
High-resolution contact maps of active enhancers and target genes generated by H3K27ac HiChIP in primary human cells provide rational guides to link noncoding disease-associated risk variants to candidate caus...
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Article
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
The Omni-ATAC protocol improves the signal-to-background ratio in chromatin accessibility profiles and is suitable for a range of cell lines and primary cell types, as well as frozen tissue.
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Article
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
Howard Chang, Ravindra Majeti and colleagues define the chromatin accessibility and transcriptional landscapes in 13 human primary blood cell types and in acute myeloid leukemia cells. They identify potential ...
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Article
A humanized bone marrow ossicle xenotransplantation model enables improved engraftment of healthy and leukemic human hematopoietic cells
Mice bearing ossicles containing human bone marrow stromal cells enable improved leukemia engraftment and detection of high frequencies of human leukemia-initiating cells.
