ArticleThe Plant cell2005
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.
Article in The Plant cell, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
- Application of resequencing to rice genomics, functional genomics and evolutionary analysis.Rice (New York, N.Y.) · 2014Review
- Identification of gene modules associated with drought response in rice by network-based analysis.PloS one · 2012Article
- A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat.Plant physiology · 2011Article
- Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.Genome research · 2010Article
- High GC content: critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana.Bioinformation · 2009Article
- Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays.PloS one · 2009Article
- Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.BMC plant biology · 2009Article
- High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression.The Plant cell · 2008Article
- At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana.Genome biology · 2008Article
- A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies.Plant molecular biology · 2007Article
- Oryza sativa dicer-like4 reveals a key role for small interfering RNA silencing in plant development.The Plant cell · 2007Article
- Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus.Molecular genetics and genomics : MGG · 2007Article
- Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation.BMC genomics · 2007Article
- Rice functional genomics research in China.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2007Article
- Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice.Plant molecular biology · 2007Article
- A genome-wide transcriptional activity survey of rice transposable element-related genes.Genome biology · 2007Article
- Rice as a model for centromere and heterochromatin research.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2007Review
- Unraveling the dynamic transcriptome.The Plant cell · 2006Review
- Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome.Genetics · 2006Article
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15 authors.
Funding
Abstract
The complete genome sequence of cultivated rice (Oryza sativa) provides an unprecedented opportunity to understand the biology of this model cereal. An essential and necessary step in this effort is the determination of the coding information and expression patterns of each sequenced chromosome. Here, we report an analysis of the transcriptional activity of rice chromosome 4 using a tiling path microarray based on PCR-generated genomic DNA fragments. Six representative rice organ types were examined using this microarray to catalog the transcribed regions of rice chromosome 4 and to reveal organ- and developmental stage-specific transcription patterns. This analysis provided expression support for 82% of the gene models in the chromosome. Transcriptional activities in 1643 nonannotated regions were also detected. Comparison with cytologically defined chromatin features indicated that in juvenile-stage rice the euchromatic region is more actively transcribed than is the transposon-rich heterochromatic portion of the chromosome. Interestingly, increased transcription of transposon-related gene models in certain heterochromatic regions was observed in mature-stage rice organs and in suspension-cultured cells. These results suggest a close correlation between transcriptional activity and chromosome organization and the developmental regulation of transcription activity at the chromosome level.
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