Plant Mol Biol. 2005 Sep;59(1):137-49.

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder M, Gerstein M, Wang J, Deng XW.

Source

Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.

Abstract

As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcription units that will facilitate rice genome annotation.

PMID:: 16217608; [PubMed - indexed for MEDLINE]

LinkOut - more resources

Full Text Sources

Supplemental Content

Related citations

Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. [Genome Biol. 2005]
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.
Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Waraporn Tongprasit, Li S, Wang J, Wang X, et al. Genome Biol. 2005; 6(6):R52. Epub 2005 May 27.
Genome-wide transcription analyses in rice using tiling microarrays. [Nat Genet. 2006]
Genome-wide transcription analyses in rice using tiling microarrays.
Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, et al. Nat Genet. 2006 Jan; 38(1):124-9. Epub 2005 Dec 20.
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. [Plant Cell. 2005]
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.
Jiao Y, Jia P, Wang X, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, et al. Plant Cell. 2005 Jun; 17(6):1641-57. Epub 2005 Apr 29.
Review [Rice genome projects for gene discovery and functional analyses]. [Tanpakushitsu Kakusan Koso. 2003]
Review [Rice genome projects for gene discovery and functional analyses].
Higo K. Tanpakushitsu Kakusan Koso. 2003 Apr; 48(5):652-5.
Review From mapping to sequencing, post-sequencing and beyond. [Plant Cell Physiol. 2005]
Review From mapping to sequencing, post-sequencing and beyond.
Sasaki T, Matsumoto T, Antonio BA, Nagamura Y. Plant Cell Physiol. 2005 Jan; 46(1):3-13. Epub 2005 Jan 19.

See reviews... See all...

Cited by 4 PubMed Central articles

Rice molecular breeding laboratories in the genomics era: Current status and future considerations. [Int J Plant Genomics. 2008]
Rice molecular breeding laboratories in the genomics era: Current status and future considerations.
Collard BC, Vera Cruz CM, McNally KL, Virk PS, Mackill DJ. Int J Plant Genomics. 2008; 2008:524847.
Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. [Genome Biol. 2008]
Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays.
Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW. Genome Biol. 2008; 9(3):R57. Epub 2008 Mar 19.
High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. [Plant Cell. 2008]
High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression.
Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, et al. Plant Cell. 2008 Feb; 20(2):259-76. Epub 2008 Feb 8.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

A pilot study of transcription unit analysis in rice using oligonucleotide tilin...
A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.
Plant Mol Biol. 2005 Sep ;59(1):137-49.

PubMed
The adhesion molecule Necl-3/SynCAM-2 localizes to myelinated axons, binds to ol...
The adhesion molecule Necl-3/SynCAM-2 localizes to myelinated axons, binds to oligodendrocytes and promotes cell adhesion.
BMC Neurosci. 2007 Oct 29 ;8:90.

PubMed
Psychosocial aspects of patients with Niemann-Pick disease, type B.
Psychosocial aspects of patients with Niemann-Pick disease, type B.
Am J Med Genet A. 2009 Nov ;149A(11):2430-6.

PubMed
DNA microarray normalization methods can remove bias from differential protein e...
DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results.
Bioinformatics. 2004 Sep 1 ;20(13):2026-34. Epub 2004 Mar 25 .

PubMed
CAF1 plays an important role in mRNA deadenylation separate from its contact to ...
CAF1 plays an important role in mRNA deadenylation separate from its contact to CCR4.
Nucleic Acids Res. 2007 ;35(9):3002-15. Epub 2007 Apr 16 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to:

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

Source

Abstract

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Supplemental Content

Related citations

Cited by 4 PubMed Central articles

Related information

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information