Ab initio identification of functionally interacting pairs of cis-regulatory elements

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Cis-regulatory elements are crucial for biological processes.
• Understanding how these elements cooperate is key to deciphering gene regulation.
• Previous methods often overlook compositional biases in sequence analysis.

Purpose of the Study:

• To develop a statistical method for detecting co-occurring cis-regulatory elements.
• To identify pairs of DNA motifs that show preferential co-occurrence and co-conservation.
• To investigate the functional role of these motif pairs in RNA splicing.

Main Methods:

• Developed compositionally orthogonalized co-occurrence analysis (coCOA) to detect motif pairs.
• Applied coCOA to human and mouse intron sequences.
• Introduced a novel co-conservation measure to assess motif pair conservation.
• Utilized a splicing reporter assay to test the functional impact of identified motif pairs.

Main Results:

• Identified three clusters of co-occurring oligonucleotide pairs in human and mouse introns.
• Discovered a significant cluster of GC-rich 5′ intron motifs co-occurring with AU-rich 3′ intron motifs.
• Demonstrated that these motif pairs are preferentially co-conserved, suggesting functional relevance.
• Found enrichment of these motif pairs in introns flanking alternative cassette exons.
• Showed that these motif pairs cooperatively silence splicing of intervening exons in a reporter assay.

Conclusions:

• The coCOA method effectively identifies co-occurring and co-conserved cis-regulatory elements.
• Specific motif pairs at intron ends play a cooperative role in regulating alternative splicing, likely through exon silencing.
• This approach has broad applicability for studying cooperative regulatory elements in various biological contexts.