cdBEST

cdBEST identifies chromatin domain boundary elements in 12 Drosophila species by detecting protein recognition sequences and motif clusters to map boundaries that restrict inappropriate enhancer-promoter interactions.

Key Features:

• Recognition Sequences: Utilizes known recognition sequences of proteins that interact with boundary elements to locate candidate sites.
• Motif Clusters: Searches for clusters of motifs under specific constraints to predict boundary element sequences.
• Comparative Analysis: Performs comparative analysis across multiple Drosophila species to assess conservation and genomic context.
• Implementation: Implemented in Perl and applied to genomes from 12 Drosophila species.

Scientific Applications:

• Boundary Identification in D. melanogaster: Identified 4,576 boundary sequences in the Drosophila melanogaster genome.
• Transposable Element Associations: Found that more than 170 predicted boundary sequences are repetitive and show homology to transposable elements.
• Conservation of Repetitive Boundaries: Observed that repetitive sequences within boundaries are a common feature across drosophilid genomes.
• Experimental Validation: Enhancer-blocking assays confirmed that approximately 80% of predicted boundaries function as boundaries in vivo.

Methodology:

Implemented in Perl; utilizes known protein recognition sequences; searches for constrained clusters of motifs to predict boundary elements; and performs comparative analysis across 12 Drosophila species.