Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer...

Area of Science:

• Developmental Biology
• Genomics
• Computational Biology

Background:

• Identifying transcription factor binding sites and target genes typically integrates gene expression data with cis-regulatory sequence analysis.
• Comparative genomics enhances the prediction of cis-regulatory elements, but gene expression data is often limited to a single species.

Purpose of the Study:

• To investigate tissue-specific, cross-species gene expression profiling combined with cross-species motif discovery.
• To identify conserved genes and transcription factor targets involved in retinal determination across different Drosophila species.

Main Methods:

• Compared expression level quantification and cross-species integration methods using Tag-seq data.
• Derived conserved genes during retinal determination across Drosophila melanogaster, Drosophila yakuba, and Drosophila virilis.
• Validated predicted transcription factor binding sites and enhancers using RNA-seq and in vivo reporter assays.

Main Results:

• Identified a set of conserved genes enriched for binding sites of eye-related transcription factors, including the zinc-finger Glass.
• Validated the majority of predicted Glass targets, showing they are expressed downstream from Glass.
• Identified eight of nine candidate enhancers driving GFP in eye discs, with seven colocalizing with Glass protein.

Conclusions:

• Demonstrated the combined use of cross-species expression profiling and motif discovery to define a core developmental program.
• Expanded the known Glass transcriptional targets from one gene to at least 62 conserved targets.