Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor

D. E. Janes, C. Chapus, Y. Gondo, D. F. Clayton, S. Sinha, C. A. Blatti, C. L. Organ, M. K. Fujita, C. N. Balakrishnan, S. V. Edwards

Research output: Contribution to journalArticle

Abstract

Many noncoding regions of genomes appear to be essential to genome function. Conservation of large numbers of noncoding sequences has been reported repeatedly among mammals but not thus far among birds and reptiles. By searching genomes of chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and green anole (Anolis carolinensis), we quantified the conservation among birds and reptiles and across amniotes of long, conserved noncoding sequences (LCNS), which we define as sequences ≥500 bp in length and exhibiting ≥95% similarity between species. We found 4,294 LCNS shared between chicken and zebra finch and 574 LCNS shared by the two birds and Anolis. The percent of genomes comprised by LCNS in the two birds (0.0024%) is notably higher than the percent in mammals (<0.0003% to <0.001%), differences that we show may be explained in part by differences in genome-wide substitution rates. We reconstruct a large number of LCNS for the amniote ancestor (ca. 8,630) and hypothesize differential loss and substantial turnover of these sites in descendent lineages. By contrast, we estimated a small role for recruitment of LCNS via acquisition of novel functions over time. Across amniotes, LCNS are significantly enriched with transcription factor binding sites for many developmental genes, and 2.9% of LCNS shared between the two birds show evidence of expression in brain expressed sequence tag databases. These results show that the rate of retention of LCNS from the amniote ancestor differs between mammals and Reptilia (including birds) and that this may reflect differing roles and constraints in gene regulation.

Original languageEnglish (US)
Pages (from-to)102-113
Number of pages12
JournalGenome biology and evolution
Volume3
Issue number1
DOIs
StatePublished - 2011

Keywords

  • Blast
  • Dosage compensation
  • Regulatory element
  • Reptile
  • Transcription factor binding site

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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    Janes, D. E., Chapus, C., Gondo, Y., Clayton, D. F., Sinha, S., Blatti, C. A., Organ, C. L., Fujita, M. K., Balakrishnan, C. N., & Edwards, S. V. (2011). Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor. Genome biology and evolution, 3(1), 102-113. https://doi.org/10.1093/gbe/evq087