The laboratory mouse shares the majority of its protein-coding genes with humans, making
it the premier model organism in biomedical research, yet the two mammals differ in …

Genome-wide association studies have identified many noncoding variants associated with
common diseases and traits. We show that these variants are concentrated in regulatory …

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned
the discovery of all classes of cis-regulatory elements including enhancers, promoters, …

Genomes contain both a genetic code specifying amino acids and a regulatory code specifying
transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I …

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-scale …

Although DNA methylation is commonly invoked as a mechanism for transcriptional repression,
the extent to which it actively silences transcription factor (TF) occupancy sites in vivo is …

The function of human regulatory regions depends exquisitely on their local genomic
environment and on cellular context, complicating experimental analysis of common disease- and …

DNA binding proteins find their cognate sequences within genomic DNA through
recognition of specific chemical and structural features. Here we demonstrate that high-resolution …

We developed a quantitative methodology, digital analysis of chromatin structure (DACS),
for high-throughput, automated mapping of DNase I-hypersensitive sites and associated cis-…

Identification of functional, noncoding elements that regulate transcription in the context of
complex genomes is a major goal of modern biology. Localization of functionality to specific …