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Transcription start site evolution in Drosophila
Bradley J Main1, Andrew D Smith, Hyosik Jang
1Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, CA, USA.
Molecular Biology and Evolution
|May 8, 2013
Summary
We developed a new method to identify transcription start sites (TSS) across four Drosophila species. TSS location and promoter activity are largely conserved, but TSS peak shape often diverges, especially in ribosomal protein genes.
Area of Science:
- Evolutionary Genomics
- Molecular Biology
- Drosophila melanogaster Research
Background:
- Transcription start site (TSS) evolution is poorly understood in Drosophila due to limited genomic annotations in non-model species.
- Accurate identification of TSS is crucial for understanding gene regulation and evolutionary dynamics.
Purpose of the Study:
- To develop and apply a novel method for identifying transcription start sites (TSS) in four Drosophila species.
- To investigate the conservation and divergence of TSS location, promoter activity, and peak shape across related Drosophila species.
- To explore potential genomic factors influencing TSS evolution, such as mutation rates and gene function.
Main Methods:
- Developed a selective 5'-end mRNA sequencing method to identify TSS.
- Applied the method to Drosophila melanogaster, D. simulans, D. sechellia, and D. pseudoobscura.
- Verified D. melanogaster TSS against existing annotations and RNA-seq data.
- Used multiple sequence alignments to identify orthologous TSS across species.
- Estimated promoter-specific expression (PSE) and TSS peak shape from mapped sequencing reads.
Main Results:
- Successfully identified and paired orthologous TSS between D. melanogaster and other species, with high conservation rates (83-86% for D. simulans and D. sechellia, 55% for D. pseudoobscura).
- Found largely conserved TSS location and promoter activity among orthologous pairs.
- Observed frequent divergence in TSS peak shape, particularly for TSS that had shifted location.
- Noted a high proportion of unpaired TSS in D. pseudoobscura, potentially linked to increased upstream mutation rates.
- Identified an enrichment of ribosomal protein genes among diverged TSS, suggesting non-uniform evolutionary patterns.
Conclusions:
- The novel 5'-end sequencing method effectively identifies and compares TSS across Drosophila species.
- TSS evolution involves both conserved features (location, promoter activity) and dynamic changes (peak shape, especially in specific gene classes).
- TSS evolution is not uniform across the genome, with ribosomal protein genes showing distinct patterns of divergence.
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