Silencers and enhancers targeted by a common transcription factor in photoreceptors are distinguished by the number and diversity of binding transcription factor binding sites they contain.

The independent effects of transcription factor binding sites are large regardless of sequence context, but the interactions between sites are context dependent.

The transcriptional control system of a sea urchin gene reveals the deep evolutionary conservation of a gene regulatory network underlying morphogenesis.

A computer model built on insights gained from comprehensive experimental analysis reveals mechanisms of blood stem cell regulation.

While photoreceptor and bipolar cells exhibit very similar cis-regulatory grammars, subtle differences in homeodomain motif enrichment represent a key distinction driving the divergence in their transcriptomes.

Combinatorial transcription factor binding shared by multiple species enriches for essential biological pathways and coincides with disease-causing regulatory DNA mutations.

Genome sequencing of mice selected for longer limbs reveals that rapid selection response is due to both discrete loci and polygenic adaptation.

Yeast promoters can harbor multiple natural DNA variants that influence gene expression, interact genetically, evolve under negative selection, alter transcription factor motifs, and remain challenging to predict.

The timing and outcome of mammalian cell lineage decisions can be controlled by slow, stochastic events on individual regulatory gene loci.

A novel strategy is presented for quantitatively measuring protein-DNA and protein-protein interactions that regulate transcription in living cells.