Transcription start site evolution in Drosophila

Bradley Main, Andrew D. Smith, Hyosik Jang, Sergey V. Nuzhdin

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Transcription start site (TSS) evolution remains largely undescribed in Drosophila, likely due to limited annotations in non-melanogaster species. In this study, we introduce a concise new method that selectively sequences from the 5'-end of mRNA and used it to identify TSS in four Drosophila species, including Drosophila melanogaster, D. simulans, D. sechellia, and D. pseudoobscura. For verification, we compared our results in D. melanogaster with known annotations, published 5'-rapid amplification of cDNA ends data, and with RNAseq from the same mRNA pool. Then, we paired 2,849 D. melanogaster TSS with its closest equivalent TSS in each species (likely to be its true ortholog) using the available multiple sequence alignments. Most of the D. melanogaster TSSs were successfully paired with an ortholog in each species (83%, 86%, and 55% for D. simulans, D. sechellia, and D. pseudoobscura, respectively). On the basis of the number and distribution of reads mapped at each TSS, we also estimated promoter-specific expression (PSE) and TSS peak shape, respectively. Among paired TSS orthologs, the location and promoter activity were largely conserved. TSS location appears important as PSE, and TSS peak shape was more frequently divergent among TSS that had moved. Unpaired TSS were surprisingly common in D. pseudoobscura. An increased mutation rate upstream of TSS might explain this pattern. We found an enrichment of ribosomal protein genes among diverged TSS, suggesting that TSS evolution is not uniform across the genome.

Original languageEnglish (US)
Pages (from-to)1966-1974
Number of pages9
JournalMolecular Biology and Evolution
Volume30
Issue number8
DOIs
StatePublished - Jan 1 2013
Externally publishedYes

Fingerprint

Transcription Initiation Site
Drosophila
transcription (genetics)
Drosophila melanogaster
mutation
amplification
genome
promoter regions
protein
gene
Drosophila sechellia
Drosophila pseudoobscura
Drosophila simulans
Messenger RNA
rapid amplification of cDNA ends
Sequence Alignment
Ribosomal Proteins
ribosomal proteins
sequence alignment
Mutation Rate

Keywords

  • CAGE
  • Drosophila
  • Gene expression
  • Promoter
  • Transcription start site
  • TSS

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Transcription start site evolution in Drosophila. / Main, Bradley; Smith, Andrew D.; Jang, Hyosik; Nuzhdin, Sergey V.

In: Molecular Biology and Evolution, Vol. 30, No. 8, 01.01.2013, p. 1966-1974.

Research output: Contribution to journalArticle

Main, Bradley ; Smith, Andrew D. ; Jang, Hyosik ; Nuzhdin, Sergey V. / Transcription start site evolution in Drosophila. In: Molecular Biology and Evolution. 2013 ; Vol. 30, No. 8. pp. 1966-1974.
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