A novel feature of microsatellites in plants: A distribution gradient along the direction of transcription

Shigeo Fujimori; Takanori Washio; Kenichi Higo; Yasuhiro Ohtomo; Kazuo Murakami; Kenichi Matsubara; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki; Shoshi Kikuchi; Masaru Tomita

doi:10.1016/S0014-5793(03)01041-X

A novel feature of microsatellites in plants: A distribution gradient along the direction of transcription

Shigeo Fujimori, Takanori Washio, Kenichi Higo, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita

University

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Abstract

A computer-based analysis was conducted to assess the characteristics of microsatellites in transcribed regions of rice and Arabidopsis. In addition, two mammals were simultaneously analyzed for a comparative analysis. Our analyses confirmed a novel plant-specific feature in which there is a gradient in microsatellite density along the direction of transcription. It was also confirmed that pyrimidine-rich microsatellites are found intensively near the transcription start sites, specifically in the two plants, but not in the mammals. Our results suggest that microsatellites located at high frequency in the 5′-flanking regions of plant genes can potentially act as factors in regulating gene expression.

Original language	English
Pages (from-to)	17-22
Number of pages	6
Journal	FEBS Letters
Volume	554
Issue number	1-2
DOIs	https://doi.org/10.1016/S0014-5793(03)01041-X
Publication status	Published - 2003 Nov 6

Keywords

Full-length cDNA
Microsatellite
Tandem repeat
Transcribed region
Transcriptional regulation

ASJC Scopus subject areas

Biophysics
Structural Biology
Biochemistry
Molecular Biology
Genetics
Cell Biology

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10.1016/S0014-5793(03)01041-X

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title = "A novel feature of microsatellites in plants: A distribution gradient along the direction of transcription",

abstract = "A computer-based analysis was conducted to assess the characteristics of microsatellites in transcribed regions of rice and Arabidopsis. In addition, two mammals were simultaneously analyzed for a comparative analysis. Our analyses confirmed a novel plant-specific feature in which there is a gradient in microsatellite density along the direction of transcription. It was also confirmed that pyrimidine-rich microsatellites are found intensively near the transcription start sites, specifically in the two plants, but not in the mammals. Our results suggest that microsatellites located at high frequency in the 5′-flanking regions of plant genes can potentially act as factors in regulating gene expression.",

keywords = "Full-length cDNA, Microsatellite, Tandem repeat, Transcribed region, Transcriptional regulation",

author = "Shigeo Fujimori and Takanori Washio and Kenichi Higo and Yasuhiro Ohtomo and Kazuo Murakami and Kenichi Matsubara and Jun Kawai and Piero Carninci and Yoshihide Hayashizaki and Shoshi Kikuchi and Masaru Tomita",

note = "Funding Information: We would like to thank Keitaro Senda, Koji Numata, Atsushi Sakurai, Hiromi Kochiwa, Haruo Suzuki, Hitomi Ito and members of the Institute for Advanced Biosciences for their helpful discussion during the course of this work. We also thank TMRI for offering genomic sequence data. This work was supported by the Ministry of Agriculture, Forestry, and Fisheries of Japan (Rice Genome Project).",

year = "2003",

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doi = "10.1016/S0014-5793(03)01041-X",

language = "English",

volume = "554",

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T1 - A novel feature of microsatellites in plants

T2 - A distribution gradient along the direction of transcription

AU - Fujimori, Shigeo

AU - Washio, Takanori

AU - Higo, Kenichi

AU - Ohtomo, Yasuhiro

AU - Murakami, Kazuo

AU - Matsubara, Kenichi

AU - Kawai, Jun

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

AU - Kikuchi, Shoshi

AU - Tomita, Masaru

N1 - Funding Information: We would like to thank Keitaro Senda, Koji Numata, Atsushi Sakurai, Hiromi Kochiwa, Haruo Suzuki, Hitomi Ito and members of the Institute for Advanced Biosciences for their helpful discussion during the course of this work. We also thank TMRI for offering genomic sequence data. This work was supported by the Ministry of Agriculture, Forestry, and Fisheries of Japan (Rice Genome Project).

PY - 2003/11/6

Y1 - 2003/11/6

N2 - A computer-based analysis was conducted to assess the characteristics of microsatellites in transcribed regions of rice and Arabidopsis. In addition, two mammals were simultaneously analyzed for a comparative analysis. Our analyses confirmed a novel plant-specific feature in which there is a gradient in microsatellite density along the direction of transcription. It was also confirmed that pyrimidine-rich microsatellites are found intensively near the transcription start sites, specifically in the two plants, but not in the mammals. Our results suggest that microsatellites located at high frequency in the 5′-flanking regions of plant genes can potentially act as factors in regulating gene expression.

AB - A computer-based analysis was conducted to assess the characteristics of microsatellites in transcribed regions of rice and Arabidopsis. In addition, two mammals were simultaneously analyzed for a comparative analysis. Our analyses confirmed a novel plant-specific feature in which there is a gradient in microsatellite density along the direction of transcription. It was also confirmed that pyrimidine-rich microsatellites are found intensively near the transcription start sites, specifically in the two plants, but not in the mammals. Our results suggest that microsatellites located at high frequency in the 5′-flanking regions of plant genes can potentially act as factors in regulating gene expression.

KW - Full-length cDNA

KW - Microsatellite

KW - Tandem repeat

KW - Transcribed region

KW - Transcriptional regulation

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A novel feature of microsatellites in plants: A distribution gradient along the direction of transcription

Abstract

Keywords

ASJC Scopus subject areas

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