Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.

Lei Li, Xiangfeng Wang, Mian Xia, Viktor Stolc, Ning Su, Zhiyu Peng, Tongprasit Waraporn, Songgang Li, Jun Wang, Xiping Wang, Xing Wang Deng

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

BACKGROUND: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes. RESULTS: We report here an analysis of the chromosome 10 transcriptome of the two major rice subspecies, japonica and indica, using oligonucleotide tiling microarrays. This analysis detected expression of approximately three-quarters of the gene models without previous experimental evidence in both subspecies. Cloning and sequence analysis of the previously unsupported models suggests that the predicted gene structure of nearly half of those models needs improvement. Coupled with comparative gene model mapping, the tiling microarray analysis identified 549 new models for the japonica chromosome, representing an 18% increase in the annotated protein-coding capacity. Furthermore, an asymmetric distribution of genome elements along the chromosome was found that coincides with the cytological definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. CONCLUSION: These results demonstrated the utility of genome tiling microarray in evaluating annotated rice gene models and in identifying novel transcriptional units. The tiling microarray sanalysis further revealed a chromosome-wide transcription pattern that suggests a role for transposable element-enriched heterochromatin in shaping global transcription in response to environmental changes in rice.
Udgivelsesdato: 2005-null
OriginalsprogEngelsk
TidsskriftGenome Biology
Vol/bind6
Udgave nummer6
Sider (fra-til)R52
ISSN1465-6906
DOI
StatusUdgivet - 1. jan. 2005

Citer dette

Li, Lei ; Wang, Xiangfeng ; Xia, Mian ; Stolc, Viktor ; Su, Ning ; Peng, Zhiyu ; Waraporn, Tongprasit ; Li, Songgang ; Wang, Jun ; Wang, Xiping ; Deng, Xing Wang. / Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. I: Genome Biology. 2005 ; Bind 6, Nr. 6. s. R52.
@article{40f48f90def711dc860c000ea68e967b,
title = "Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.",
abstract = "BACKGROUND: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes. RESULTS: We report here an analysis of the chromosome 10 transcriptome of the two major rice subspecies, japonica and indica, using oligonucleotide tiling microarrays. This analysis detected expression of approximately three-quarters of the gene models without previous experimental evidence in both subspecies. Cloning and sequence analysis of the previously unsupported models suggests that the predicted gene structure of nearly half of those models needs improvement. Coupled with comparative gene model mapping, the tiling microarray analysis identified 549 new models for the japonica chromosome, representing an 18{\%} increase in the annotated protein-coding capacity. Furthermore, an asymmetric distribution of genome elements along the chromosome was found that coincides with the cytological definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. CONCLUSION: These results demonstrated the utility of genome tiling microarray in evaluating annotated rice gene models and in identifying novel transcriptional units. The tiling microarray sanalysis further revealed a chromosome-wide transcription pattern that suggests a role for transposable element-enriched heterochromatin in shaping global transcription in response to environmental changes in rice. Udgivelsesdato: 2005-null",
keywords = "Chromosomes, Plant, Cloning, Molecular, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Models, Genetic, Oligonucleotide Array Sequence Analysis, Oryza sativa, RNA, Messenger, Sequence Analysis, DNA, Transcription, Genetic",
author = "Lei Li and Xiangfeng Wang and Mian Xia and Viktor Stolc and Ning Su and Zhiyu Peng and Tongprasit Waraporn and Songgang Li and Jun Wang and Xiping Wang and Deng, {Xing Wang}",
year = "2005",
month = "1",
day = "1",
doi = "10.1186/gb-2005-6-6-r52",
language = "English",
volume = "6",
pages = "R52",
journal = "Genome Biology (Online Edition)",
issn = "1474-7596",
publisher = "BioMed Central",
number = "6",

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Li, L, Wang, X, Xia, M, Stolc, V, Su, N, Peng, Z, Waraporn, T, Li, S, Wang, J, Wang, X & Deng, XW 2005, 'Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.', Genome Biology, bind 6, nr. 6, s. R52. https://doi.org/10.1186/gb-2005-6-6-r52

Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. / Li, Lei; Wang, Xiangfeng; Xia, Mian; Stolc, Viktor; Su, Ning; Peng, Zhiyu; Waraporn, Tongprasit; Li, Songgang; Wang, Jun; Wang, Xiping; Deng, Xing Wang.

I: Genome Biology, Bind 6, Nr. 6, 01.01.2005, s. R52.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.

AU - Li, Lei

AU - Wang, Xiangfeng

AU - Xia, Mian

AU - Stolc, Viktor

AU - Su, Ning

AU - Peng, Zhiyu

AU - Waraporn, Tongprasit

AU - Li, Songgang

AU - Wang, Jun

AU - Wang, Xiping

AU - Deng, Xing Wang

PY - 2005/1/1

Y1 - 2005/1/1

N2 - BACKGROUND: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes. RESULTS: We report here an analysis of the chromosome 10 transcriptome of the two major rice subspecies, japonica and indica, using oligonucleotide tiling microarrays. This analysis detected expression of approximately three-quarters of the gene models without previous experimental evidence in both subspecies. Cloning and sequence analysis of the previously unsupported models suggests that the predicted gene structure of nearly half of those models needs improvement. Coupled with comparative gene model mapping, the tiling microarray analysis identified 549 new models for the japonica chromosome, representing an 18% increase in the annotated protein-coding capacity. Furthermore, an asymmetric distribution of genome elements along the chromosome was found that coincides with the cytological definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. CONCLUSION: These results demonstrated the utility of genome tiling microarray in evaluating annotated rice gene models and in identifying novel transcriptional units. The tiling microarray sanalysis further revealed a chromosome-wide transcription pattern that suggests a role for transposable element-enriched heterochromatin in shaping global transcription in response to environmental changes in rice. Udgivelsesdato: 2005-null

AB - BACKGROUND: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes. RESULTS: We report here an analysis of the chromosome 10 transcriptome of the two major rice subspecies, japonica and indica, using oligonucleotide tiling microarrays. This analysis detected expression of approximately three-quarters of the gene models without previous experimental evidence in both subspecies. Cloning and sequence analysis of the previously unsupported models suggests that the predicted gene structure of nearly half of those models needs improvement. Coupled with comparative gene model mapping, the tiling microarray analysis identified 549 new models for the japonica chromosome, representing an 18% increase in the annotated protein-coding capacity. Furthermore, an asymmetric distribution of genome elements along the chromosome was found that coincides with the cytological definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. CONCLUSION: These results demonstrated the utility of genome tiling microarray in evaluating annotated rice gene models and in identifying novel transcriptional units. The tiling microarray sanalysis further revealed a chromosome-wide transcription pattern that suggests a role for transposable element-enriched heterochromatin in shaping global transcription in response to environmental changes in rice. Udgivelsesdato: 2005-null

KW - Chromosomes, Plant

KW - Cloning, Molecular

KW - Gene Expression Profiling

KW - Gene Expression Regulation, Plant

KW - Genes, Plant

KW - Models, Genetic

KW - Oligonucleotide Array Sequence Analysis

KW - Oryza sativa

KW - RNA, Messenger

KW - Sequence Analysis, DNA

KW - Transcription, Genetic

U2 - 10.1186/gb-2005-6-6-r52

DO - 10.1186/gb-2005-6-6-r52

M3 - Journal article

VL - 6

SP - R52

JO - Genome Biology (Online Edition)

JF - Genome Biology (Online Edition)

SN - 1474-7596

IS - 6

ER -