Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …

A class of cis-regulatory elements, called enhancers, play a central role in orchestrating
spatiotemporally precise gene-expression programs during development. Consequently …

Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter
gene expression, yet how they regulate transcription remains unknown. We found that STRs …

Genome-wide association studies have identified loci underlying human diseases, but the
causal nucleotide changes and mechanisms remain largely unknown. Here we developed a …

Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …

Designing promoters with desirable properties is essential in synthetic biology. Human
experts are skilled at identifying strong explicit patterns in small samples, while deep …

Understanding the mechanisms of protein-DNA binding is critical in comprehending gene
regulation. Three-dimensional DNA structure, also described as DNA shape, plays a key …

Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-
binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF …

Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …

Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …