Understanding the mechanisms that regulate cell type-specific transcriptional programs
requires developing a lexicon of their genomic regulatory elements. We developed a …

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage
by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting …

Localized accessibility of critical DNA sequences to the regulatory machinery is a key
requirement for regulation of human genes. Here we describe a high-resolution, genome …

A large number of putative cis-regulatory sequences have been annotated in the human
genome, but the genes they control remain poorly defined. To bridge this gap, we generate …

DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA and harbor
disease-and phenotypic trait-associated genetic variation. We established high-precision …

Discriminating the gene target of a distal regulatory element from other nearby transcribed
genes is a challenging problem with the potential to illuminate the causal underpinnings of …

Understanding how eukaryotic enhancers are bound and regulated by specific
combinations of transcription factors is still a major challenge. To better map transcription …

In contrast to single-cell approaches for measuring gene expression and DNA accessibility,
single-cell methods for analyzing histone modifications are limited by low sensitivity and …

Cells use protein-DNA and protein-protein interactions to regulate transcription. A
biophysical understanding of this process has, however, been limited by the lack of methods …

Studies of genome regulation routinely use high-throughput DNA sequencing approaches to
determine where specific proteins interact with DNA, and they rely on DNA amplification and …