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 language | English |
|---|---|
| Pages (from-to) | 3821-3827 |
| Number of pages | 7 |
| Journal | Nucleic Acids Research |
| Volume | 33 |
| Issue number | 12 |
| DOIs | |
| Publication status | Published - 2005 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Genetics
Cite this
A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance. / Fukue, Yoshiro; Sumida, Noriyuki; Tanase, Jun ichi; Ohyama, Takashi.
In: Nucleic Acids Research, Vol. 33, No. 12, 2005, p. 3821-3827.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance
AU - Fukue, Yoshiro
AU - Sumida, Noriyuki
AU - Tanase, Jun ichi
AU - Ohyama, Takashi
PY - 2005
Y1 - 2005
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gki700
DO - 10.1093/nar/gki700
M3 - Article
C2 - 16027106
AN - SCOPUS:22444448187
VL - 33
SP - 3821
EP - 3827
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 12
ER -