Genomic approaches towards finding cis-regulatory modules in animals

Abstract

Differential gene expression is the fundamental mechanism underlying animal development and cell differentiation. However, it is a challenge to identify comprehensively and accurately the DNA sequences that are required to regulate gene expression: namely, cis-regulatory modules (CRMs). Three major features, either singly or in combination, are used to predict CRMs: clusters of transcription factor binding site motifs, non-coding DNA that is under evolutionary constraint and biochemical marks associated with CRMs, such as histone modifications and protein occupancy. The validation rates for predictions indicate that identifying diagnostic biochemical marks is the most reliable method, and understanding is enhanced by the analysis of motifs and conservation patterns within those predicted CRMs.

Figure 1. Rationales for three approaches to CRM prediction

(a) Individual instances of TFBS motifs are expected to cluster in CRMs. The instances for each TFBS motif in a sequence (colored circle) are shown on separate gray lines. (b) Evolutionary constraint is expected to preserve clusters of TFBS motif instances in multiple species. All motif instances are shown on a single line for each species. A multispecies sequence alignment shows an example of phylogenetic footprints in a known erythroid enhancer; in the lower panel, nucleotides that differ from the reference sequence (mouse) are colored blue and phylogenetic footprints are indicated by boxes labeled by transcription factors that are known or predicted to bind to them. (c) ChIP-seq assays should show peaks in CRMs. A subset of TF-bound DNA segments will not have a motif instance, which can result from interactions with another bound site.