Evolutionary analysis of TATA-less proximal promoter function

Douglas L. Crawford, Jeff A. Segal, J. Lynn Barnett

Research output: Contribution to journalArticle

59 Scopus citations

Abstract

Many molecular studies describe how components of the proximal promoter affect transcriptional processes. However, these studies do not account for the likely effects of distant enhancers or chromatin structure, and thus it is difficult to conclude that the sequence variation in proximal promoters acts to modulate transcription in the natural context of the whole genome. This problem, the biological importance of proximal promoter sequence variation, can be addressed using a combination of molecular and evolutionary analyses. Provided here are molecular and evolutionary analyses of the variation in promoter function and sequence within and between populations of Fundulus heteroclitus for the lactate dehydrogenase-B (Ldh-B) proximal promoter. Approximately one third of the Ldh-B proximal promoter contains interspersed regions that are functionally important: (1) they bind transcription factors in vivo, (2) they effect a change in transcription as assayed by transient transfection into two different fish cell lines, and (3) they bind purified transcription factors in vitro. Evolutionary analyses that compare sequence variation in these functional regions versus the nonfunctional regions indicate that the changes in the Ldh-B proximal promoter sequences are due to directional selection. Thus, the Ldh-B proximal promoter sequence variations that affect transcriptional processes constitute a phenotypic change that is subject to natural selection, suggesting that proximal promoter sequence variation affects transcription in the natural context of the whole genome.

Original languageEnglish (US)
Pages (from-to)194-207
Number of pages14
JournalMolecular biology and evolution
Volume16
Issue number2
DOIs
StatePublished - Feb 1999

Keywords

  • Directional selection
  • Sp1
  • TATA-less
  • Transcription

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

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