Shadow enhancers are seemingly redundant transcriptional cis-regulatory elements that
regulate the same gene and drive overlapping expression patterns. Recent studies have …

Gap genes are involved in segment determination during the early development of the fruit
fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize …

The prevailing view of metazoan gene regulation is that individual genes are independently
regulated by their own dedicated sets of transcriptional enhancers. Past studies have …

Recent advances in technology have led to a dramatic increase in the number of available
transcription factor ChIP-seq and ChIP-chip data sets. Understanding the motif content of …

MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary
sites in the 3′ untranslated regions of target genes in animals and, by unknown …

Chromatin modifications are associated with many aspects of gene expression, yet their role
in cellular transitions during development remains elusive. Here, we use a new approach to …

We describe the comprehensive characterization of homeodomain DNA-binding specificities
from a metazoan genome. The analysis of all 84 independent homeodomains from D …

Identifying the genomic regions bound by sequence-specific regulatory factors is central
both to deciphering the complex DNA cis-regulatory code that controls transcription in …

Sequencing of multiple related species followed by comparative genomics analysis
constitutes a powerful approach for the systematic understanding of any genome. Here, we …

Cooperative binding of transcription factors (TFs) to promoters and other regulatory regions
is essential for precise gene expression. The classical model of cooperativity requires direct …