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Article
Open AccessKLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress
Physiologic laminar shear stress (LSS) induces an endothelial gene expression profile that is vasculo-protective. In this report, we delineate how LSS mediates changes in the epigenetic landscape to promote th...
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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
A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells
Genetic variations underlying susceptibility to complex autoimmune and allergic diseases are concentrated within noncoding regulatory elements termed enhancers1. The functions of a large majority of disease-assoc...
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Article
Open AccessGWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways
Systemic sclerosis (SSc) is an autoimmune disease that shows one of the highest mortality rates among rheumatic diseases. We perform a large genome-wide association study (GWAS), and meta-analysis with previou...
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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
Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment
Human embryonic stem cell (hESC) differentiation promises advances in regenerative medicine1–3, yet conversion of hESCs into transplantable cells or tissues remains poorly understood. Using our keratinocyte diffe...
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Article
Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation
In this Letter, analysis of steady-state regulatory T (Treg) cell percentages from Il2ra enhancer deletion (EDEL) and wild-type (WT) mice revealed no differences between them (Extended Data Fig. 9d). This anal...
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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
Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation
Adam Rubin, Brook Barajas, Mayra Furlan-Magaril and colleagues studied dynamic chromatin across the genome of differentiating human skin keratinocytes, identifying both stable and reorganizing classes of trans...
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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
Discovery of stimulation-responsive immune enhancers with CRISPR activation
The authors use tiled CRISPR activation for functional enhancer discovery across two autoimmunity risk loci, CD69 and IL2RA, and identify elements with features of stimulus-responsive enhancers, including an IL2R...
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Article
HiChIP: efficient and sensitive analysis of protein-directed genome architecture
HiChIP combines chromosome conformation capture with immunoprecipitation- and tagmentation-based library preparation to uncover the 3D chromatin architecture focused around a protein of interest.
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Article
Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE
icSHAPE allows transcriptome-wide RNA structure profiling in living cells. It uses a clickable SHAPE reagent to enable biotin-based enrichment of SHAPE-modified RNA, reducing the necessary sequencing depth.
