Core promoter elements of eukaryotic genes have a highly distinctive mechanical property

Yoshiro Fukue, Noriyuki Sumida, Jun Ichi Nishikawa, Takashi Ohyama

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

In spite of the abundant data on DNA sequence, the mechanical aspects of promoter DNA remain poorly understood. We classified 1871 human and 196 mouse RNA polymerase II promoters and investigated average flexibility profiles of the human promoters containing either a TATA box or an initiator (Inr) sequence only. Here, we show that TATA boxes and Inr sequences have a common anomalous mechanical property: they are comprised of distinctively flexible and rigid sequences, compared with the other parts of the promoter region. The +2 position in the Inr consensus sequence does not favor adenine to keep the high flexibility and thus this position is more accurately represented as 'T, G, C ≫ A'. Additionally, it was also found that DNA region upstream of TATA box or Inr sequence is more rigid than region downstream of each element. These properties may function as a marker for recognition by TATA-binding protein and Inr-binding protein.

Original languageEnglish
Pages (from-to)5834-5840
Number of pages7
JournalNucleic Acids Research
Volume32
Issue number19
DOIs
Publication statusPublished - 2004
Externally publishedYes

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TATA Box
TATA-Box Binding Protein
Genes
RNA Polymerase II
DNA
Consensus Sequence
Adenine
Genetic Promoter Regions
Protein Binding
Carrier Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

Core promoter elements of eukaryotic genes have a highly distinctive mechanical property. / Fukue, Yoshiro; Sumida, Noriyuki; Nishikawa, Jun Ichi; Ohyama, Takashi.

In: Nucleic Acids Research, Vol. 32, No. 19, 2004, p. 5834-5840.

Research output: Contribution to journalArticle

Fukue, Yoshiro ; Sumida, Noriyuki ; Nishikawa, Jun Ichi ; Ohyama, Takashi. / Core promoter elements of eukaryotic genes have a highly distinctive mechanical property. In: Nucleic Acids Research. 2004 ; Vol. 32, No. 19. pp. 5834-5840.
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