Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library

Jian Zhang, Dong Guo, Yuxiao Chang, Changjun You, Xingwang Li, Xiaoxia Dai, Qijun Weng, Jianwei - Zhang, Guoxing Chen, Xianghua Li, Huifang Liu, Bin Han, Qifa Zhang, Changyin Wu

Research output: Contribution to journalArticle

79 Citations (Scopus)

Abstract

We isolated 13 804 T-DNA flanking sequence tags (FSTs) from a T-DNA insertion library of rice. A comprehensive analysis of the 13 804 FSTs revealed a number of features demonstrating a highly non-random distribution of the T-DNA insertions in the rice genome: T-DNA insertions were biased towards large chromosomes, not only in the absolute number of insertions but also in the relative density; within chromosomes the insertions occurred more densely in the distal ends, and less densely in the centromeric regions; the distribution of the T-DNA insertions was highly correlated with that of full-length cDNAs, but the correlations were highly heterogeneous among the chromosomes; T-DNA insertions strongly disfavored transposable element (TE)-related sequences, but favored genic sequences with a strong bias toward the 5′ upstream and 3′ downstream regions of the genes; T-DNA insertions preferentially occurred among the various classes of functional genes, such that the numbers of insertions were in excess in certain functional categories but were deficient in other categories. The analysis of DNA sequence compositions around the T-DNA insertion sites also revealed several prominent features, including an elevated bendability from -200 to 200 bp relative to the insertion sites, an inverse relationship between the GC and TA skews, and reversed GC and TA skews in sequences upstream and downstream of the insertion sites, with both GC and TA skews equal to zero at the insertion sites. It was estimated that 365 380 insertions are needed to saturate the genome with P = 0.95, and that the 45 441 FSTs that have been isolated so far by various groups tagged 14 287 of the 42 653 non-TE related genes.

Original languageEnglish (US)
Pages (from-to)947-959
Number of pages13
JournalPlant Journal
Volume49
Issue number5
DOIs
StatePublished - Mar 2007
Externally publishedYes

Fingerprint

enhancer elements
Genome
nucleotide sequences
mutants
genome
DNA
Chromosomes
chromosomes
rice
Genes
genes
Specific Gravity
DNA Transposable Elements
T-DNA
transposons
Gene Library
DNA Sequence Analysis
Complementary DNA

Keywords

  • Flanking sequence tag
  • Insertion preference
  • Rice
  • T-DNA

ASJC Scopus subject areas

  • Plant Science

Cite this

Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library. / Zhang, Jian; Guo, Dong; Chang, Yuxiao; You, Changjun; Li, Xingwang; Dai, Xiaoxia; Weng, Qijun; Zhang, Jianwei -; Chen, Guoxing; Li, Xianghua; Liu, Huifang; Han, Bin; Zhang, Qifa; Wu, Changyin.

In: Plant Journal, Vol. 49, No. 5, 03.2007, p. 947-959.

Research output: Contribution to journalArticle

Zhang, Jian ; Guo, Dong ; Chang, Yuxiao ; You, Changjun ; Li, Xingwang ; Dai, Xiaoxia ; Weng, Qijun ; Zhang, Jianwei - ; Chen, Guoxing ; Li, Xianghua ; Liu, Huifang ; Han, Bin ; Zhang, Qifa ; Wu, Changyin. / Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library. In: Plant Journal. 2007 ; Vol. 49, No. 5. pp. 947-959.
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T1 - Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library

AU - Zhang, Jian

AU - Guo, Dong

AU - Chang, Yuxiao

AU - You, Changjun

AU - Li, Xingwang

AU - Dai, Xiaoxia

AU - Weng, Qijun

AU - Zhang, Jianwei -

AU - Chen, Guoxing

AU - Li, Xianghua

AU - Liu, Huifang

AU - Han, Bin

AU - Zhang, Qifa

AU - Wu, Changyin

PY - 2007/3

Y1 - 2007/3

N2 - We isolated 13 804 T-DNA flanking sequence tags (FSTs) from a T-DNA insertion library of rice. A comprehensive analysis of the 13 804 FSTs revealed a number of features demonstrating a highly non-random distribution of the T-DNA insertions in the rice genome: T-DNA insertions were biased towards large chromosomes, not only in the absolute number of insertions but also in the relative density; within chromosomes the insertions occurred more densely in the distal ends, and less densely in the centromeric regions; the distribution of the T-DNA insertions was highly correlated with that of full-length cDNAs, but the correlations were highly heterogeneous among the chromosomes; T-DNA insertions strongly disfavored transposable element (TE)-related sequences, but favored genic sequences with a strong bias toward the 5′ upstream and 3′ downstream regions of the genes; T-DNA insertions preferentially occurred among the various classes of functional genes, such that the numbers of insertions were in excess in certain functional categories but were deficient in other categories. The analysis of DNA sequence compositions around the T-DNA insertion sites also revealed several prominent features, including an elevated bendability from -200 to 200 bp relative to the insertion sites, an inverse relationship between the GC and TA skews, and reversed GC and TA skews in sequences upstream and downstream of the insertion sites, with both GC and TA skews equal to zero at the insertion sites. It was estimated that 365 380 insertions are needed to saturate the genome with P = 0.95, and that the 45 441 FSTs that have been isolated so far by various groups tagged 14 287 of the 42 653 non-TE related genes.

AB - We isolated 13 804 T-DNA flanking sequence tags (FSTs) from a T-DNA insertion library of rice. A comprehensive analysis of the 13 804 FSTs revealed a number of features demonstrating a highly non-random distribution of the T-DNA insertions in the rice genome: T-DNA insertions were biased towards large chromosomes, not only in the absolute number of insertions but also in the relative density; within chromosomes the insertions occurred more densely in the distal ends, and less densely in the centromeric regions; the distribution of the T-DNA insertions was highly correlated with that of full-length cDNAs, but the correlations were highly heterogeneous among the chromosomes; T-DNA insertions strongly disfavored transposable element (TE)-related sequences, but favored genic sequences with a strong bias toward the 5′ upstream and 3′ downstream regions of the genes; T-DNA insertions preferentially occurred among the various classes of functional genes, such that the numbers of insertions were in excess in certain functional categories but were deficient in other categories. The analysis of DNA sequence compositions around the T-DNA insertion sites also revealed several prominent features, including an elevated bendability from -200 to 200 bp relative to the insertion sites, an inverse relationship between the GC and TA skews, and reversed GC and TA skews in sequences upstream and downstream of the insertion sites, with both GC and TA skews equal to zero at the insertion sites. It was estimated that 365 380 insertions are needed to saturate the genome with P = 0.95, and that the 45 441 FSTs that have been isolated so far by various groups tagged 14 287 of the 42 653 non-TE related genes.

KW - Flanking sequence tag

KW - Insertion preference

KW - Rice

KW - T-DNA

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JO - Plant Journal

JF - Plant Journal

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