Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

被引:108
作者
Stolc, V [1 ]
Samanta, MP
Tongprasit, W
Sethi, H
Liang, SD
Nelson, DC
Hegeman, A
Nelson, C
Rancour, D
Bednarek, S
Ulrich, EL
Zhao, Q
Wrobel, RL
Newman, CS
Fox, BG
Phillips, GN
Markley, JL
Sussman, MR
机构
[1] NASA, Ames Res Ctr, Genome Res Facil, Moffett Field, CA 94035 USA
[2] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA
[3] NASA, Ames Res Ctr, Eloret Corp, Moffett Field, CA 94035 USA
[4] Univ Wisconsin, Ctr Eukaryot Struct Genom, Madison, WI 53706 USA
关键词
higher plant; transcriptome; maskless array synthesizer;
D O I
10.1073/pnas.0408203102
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Using a maskless photolithography method, we produced DNA oligonucleotide microarrays with probe sequences tiled throughout the genome of the plant Arabidopsis thaliana. RNA expression was determined for the complete nuclear, mitochondrial, and chloroplast genomes by tiling 5 million 36-mer probes. These probes were hybridized to labeled mRNA isolated from liquid grown T87 cells, an undifferentiated Arabidopsis cell culture line. Transcripts were detected from at least 60% of the nearly 26,330 annotated genes, which included 151 predicted genes that were not identified previously by a similar genome-wide hybridization study on four different cell lines. In comparison with previously published results with 25-mer tiling arrays produced by chromium masking-based photolithography technique, 36-mer oligonucleotide probes were found to be more useful in identifying intron-exon boundaries. Using two-dimensional HPLC tandem mass spectrometry, a small-scale proteomic analysis was performed with the same cells. A large amount of strongly hybridizing RNA was found in regions "antisense" to known genes. Similarity of antisense activities between the 25-mer and 36-mer data sets suggests that it is a reproducible and inherent property of the experiments. Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage.
引用
收藏
页码:4453 / 4458
页数:6
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