ArticleMolecular biology and evolution2013
Transcription start site evolution in Drosophila.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 36 citations in OpenAlex.
- Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors.BMC genomics · 2024Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Mutational scans reveal differential evolvability ofPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- Indel driven rapid evolution of core nuclear pore protein gene promoters.Scientific reports · 2023Article
- Extensive non-coding sequence divergence between the major human pathogenFrontiers in fungal biology · 2022Article
- Transcription initiation of distant core promoters in a large-sized genome of an insect.BMC biology · 2021Article
- Episodes of Rapid Recovery of the Functional Activity of theFrontiers in genetics · 2021Article
- PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes.Frontiers in genetics · 2021Article
- Pervasive and dynamic transcription initiation inGenome research · 2019Article
- Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans.PLoS genetics · 2019Article
- Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome.Genome research · 2018Article
- Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species.Genome biology · 2017Article
- The punctilious RNA polymerase II core promoter.Genes & development · 2017Review
- Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments.PLoS genetics · 2017Article
- Promoter shape varies across populations and affects promoter evolution and expression noise.Nature genetics · 2017Article
- Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila.Genome biology and evolution · 2015Article
- GBshape: a genome browser database for DNA shape annotations.Nucleic acids research · 2015Article
- Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.Genome research · 2014Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.