TY - JOUR
T1 - A common feature shared by bent DNA structures locating in the eukaryotic promoter region
AU - Miyano, Masaru
AU - Kawashima, Tomo
AU - Ohyama, Takashi
N1 - Funding Information:
We thank Junko Ohyama for help in preparing the manuscript. This work was supported in part by a Grant-in-Aid from the Ministry of Education, Science, Sports and Culture of Japan, NIG Cooperative Research Program, and the Hirao Taro Foundation for Academic Research.
PY - 2001
Y1 - 2001
N2 - Eukaryotic promoters often contain a bent DNA structure, suggesting that this structure plays some role in transcription. To reveal the role, we need more information on the promoters that contain or flank a bent DNA structure. In this study, we collected such promoters by the following approach: we first isolated human genomic DNA fragments that contained at least one bent DNA structure, then shotgun cloned them into a promoter trap vector, screened DNA fragments that functioned as a promoter, and finally found the promoters of interest by determining the bent DNA locus and the region expressing promoter activity. From 1187 recombinant plasmids, we isolated 51 that showed promoter activity. Structural and functional analyses of randomly selected 10 clones with inserts of 548-913 bp demonstrated 11 sequences that could drive transcription. Unexpectedly, all of these clones met our purpose: i.e., each segment that showed a promoter activity (67-179 bp) was very close to the bent DNA structure (spanning about 150 bp in all clones), and in some cases overlapped it. More interestingly, these bent DNA structures all had a superhelical writhe. We propose a hypothesis that in the bent-DNA-containing eukaryotic promoters, bent DNA organizes local chromatin infrastructure appropriately for transcription initiation.
AB - Eukaryotic promoters often contain a bent DNA structure, suggesting that this structure plays some role in transcription. To reveal the role, we need more information on the promoters that contain or flank a bent DNA structure. In this study, we collected such promoters by the following approach: we first isolated human genomic DNA fragments that contained at least one bent DNA structure, then shotgun cloned them into a promoter trap vector, screened DNA fragments that functioned as a promoter, and finally found the promoters of interest by determining the bent DNA locus and the region expressing promoter activity. From 1187 recombinant plasmids, we isolated 51 that showed promoter activity. Structural and functional analyses of randomly selected 10 clones with inserts of 548-913 bp demonstrated 11 sequences that could drive transcription. Unexpectedly, all of these clones met our purpose: i.e., each segment that showed a promoter activity (67-179 bp) was very close to the bent DNA structure (spanning about 150 bp in all clones), and in some cases overlapped it. More interestingly, these bent DNA structures all had a superhelical writhe. We propose a hypothesis that in the bent-DNA-containing eukaryotic promoters, bent DNA organizes local chromatin infrastructure appropriately for transcription initiation.
KW - Bent DNA
KW - Chromatin
KW - Eukaryotic promoter
KW - Superhelical writhe
KW - Transcriptional regulation
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U2 - 10.1023/A:1011999730828
DO - 10.1023/A:1011999730828
M3 - Article
C2 - 11710566
AN - SCOPUS:0034777195
VL - 28
SP - 53
EP - 61
JO - Molecular Biology Reports
JF - Molecular Biology Reports
SN - 0301-4851
IS - 1
ER -