Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences
Open accessAbstract
Comparative genomic approaches to gene and cis -regulatory prediction are based on the principle that differential DNA sequence conservation reflects variation in functional constraint. Using this principle, we analyze noncoding sequence conservation in Drosophila for 40 loci with known or suspected cis -regulatory function encompassing >100 kb of DNA. We estimate the fraction of noncoding DNA conserved in both intergenic and intronic regions and describe the length distribution of ungapped conserved noncoding blocks. On average, 22%–26% of noncoding sequences surveyed are conserved in Drosophila , with median block length ∼19 bp. We show that point substitution in conserved noncoding blocks exhibits transition bias as well as lineage effects in base composition, and occurs more than an order of magnitude more frequently than insertion/deletion (indel) substitution. Overall, patterns of noncoding DNA structure and evolution differ remarkably little between intergenic and intronic conserved blocks, suggesting that the effects of transcription per se contribute minimally to the constraints operating on these sequences. The results of this study have implications for the development of alignment and prediction algorithms specific to noncoding DNA, as well as for models of cis -regulatory DNA sequence evolution.
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Insect estimates of conserved fractions for intronic and intergenic regions are roughly 1.5-2 times higher than estimates based on D. melanogaster/D. virilis comparisons.
“while in insects, our estimates of these fractions for intronic and intergenic regions are roughly 1-1/2-2 ן higher than estimates based on D. melanogaster/D.virilis comparisons (Bergman and Kreitman 2001).”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Bergman and Kreitman 2001
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- Authors
- Bergman, C. M., & Kreitman, M.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2001-08-01
- Volume
- 11
- Issue
- 8
- Pages
- 1335-1345
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W7098600529
- Cited by
- 165
- References
- 0
- Citations by year
- 2026: 2 · 2024: 1 · 2023: 1 · 2020: 2 · 2019: 3 · 2018: 1 · 2017: 2 · 2016: 1 · 2015: 3 · 2014: 6 · 2013: 3 · 2012: 5
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Funders
- National Science Foundation (9604477)
- University of Chicago
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- cis-regulatory elements, Drosophila, intergenic regions, introns, sequence conservation, transition bias, nucleotide composition, comparative genomics
- MeSH terms
- Animals, Drosophila melanogaster, Introns, Molecular Sequence Data, Polymerase Chain Reaction, Sequence Alignment, Genome, Conserved Sequence, Genes, Insect, Evolution, Molecular, DNA, Intergenic
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