A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.
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.
Jiao
Yuling
Y
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520-8014, USA.
Jia
Peixin
P
Wang
Xiangfeng
X
Su
Ning
N
Yu
Shuliang
S
Zhang
Dongfen
D
Ma
Ligeng
L
Feng
Qi
Q
Jin
Zhaoqing
Z
Li
Lei
L
Xue
Yongbiao
Y
Cheng
Zhukuan
Z
Zhao
Hongyu
H
Han
Bin
B
Deng
Xing Wang
XW
D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000032:analysis / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010940:Plant Proteins / Q000032:analysis / Q000235:genetics; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D036226:Seedlings / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic / Q000235:genetics*
D004251:DNA Transposable Elements; D018744:DNA, Plant; D010940:Plant Proteins