A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance

Yoshiro Fukue, Noriyuki Sumida, Jun ichi Tanase, Takashi Ohyama

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

A recent study revealed that TATA boxes and initiator sequences have a common anomalous mechanical property, i.e. they comprise distinctive flexible and rigid sequences when compared with the other parts of the promoter region. In the present study, using the flexibility parameters from two different models, we calculated the average flexibility profiles of 1004 human promoters that do not contain canonical promoter elements, such as a TATA box, initiator (Inr) sequence, downstream promoter element or a GC box, and those of 382 human promoters that contain the GC box only. Here, we show that they have a common characteristic mechanical property that is strikingly similar to those of the TATA box-containing or Inr-containing promoters. Their most interesting feature is that the TATA- or Inr-corresponding region lies in the several nucleotides around the transcription start site. We have also found that a dinucleotide step from -1 to +1 (transcription start site) has a slight tendency to adopt CA that is known to be flexible. We also demonstrate that certain synthetic DNA fragments designed to mimic the average mechanical property of these 1386 promoters can drive transcription. This distinctive mechanical property may be the hallmark of a promoter.

Original languageEnglish
Pages (from-to)3821-3827
Number of pages7
JournalNucleic acids research
Volume33
Issue number12
DOIs
Publication statusPublished - 2005
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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