Caenorhabditis elegans transposable elements harbor diverse transcription factor DNA-binding sites

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Transposable elements (TEs) are mobile DNA sequences that can alter genome structure and function.
• TEs can influence gene regulation by providing regulatory sequences, including transcription factor binding sites.
• The contribution of TEs to the repertoire of transcription factor binding motifs in Caenorhabditis elegans is not fully understood.

Purpose of the Study:

• To comprehensively investigate the extent to which transposable elements provide transcription factor binding motifs in the Caenorhabditis elegans genome.
• To identify transcription factor binding motifs that are significantly enriched within transposable elements.
• To assess the functional relevance of TE-derived transcription factor binding sites.

Main Methods:

• Genomic mapping of DNA-binding motifs for 201 transcription factors in C. elegans.
• Analysis of motif distribution within transposable elements versus the rest of the genome.
• Identification of transcription factor motifs significantly enriched in transposable elements.
• Assessment of chromatin accessibility and transcription factor binding at TE-resident motifs.

Main Results:

• Nearly all examined transcription factors have binding motifs located within transposable elements.
• All types of transposable elements contain at least one transcription factor motif.
• 45 transcription factor motifs were found to be >20-fold enriched in transposable elements.
• TE-derived motifs are located in accessible chromatin and bound by cognate transcription factors.
• TEs with bound motifs are located near the promoters of ~12% of protein-coding genes.

Conclusions:

• Transposable elements are a major source of transcription factor binding motifs in C. elegans.
• These TE-provided binding sites are functional and can influence gene expression.
• Transposable elements play a significant, previously underappreciated role in shaping transcriptional regulation and genome evolution in C. elegans.