NASA Logo

NTRS

NTRS - NASA Technical Reports Server

Back to Results
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arraysUsing 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.
Document ID
20050172460
Acquisition Source
Legacy CDMS
Document Type
Reprint (Version printed in journal)
External Source(s)
Authors
Stolc, Viktor
(NASA Ames Research Center Moffett Field, CA United States)
Samanta, Manoj Pratim
Tongprasit, Waraporn
Sethi, Himanshu
Liang, Shoudan
Nelson, David C.
Hegeman, Adrian
Nelson, Clark
Rancour, David
Bednarek, Sebastian
Ulrich, Eldon L.
Zhao, Qin
Wrobel, Russell L.
Newman, Craig S.
Fox, Brian G.
Phillips, George N Jr
Markley, John L.
Sussman, Michael R.
Date Acquired
August 23, 2013
Publication Date
March 22, 2005
Publication Information
Publication: Proceedings of the National Academy of Sciences of the United States of America
Volume: 102
Issue: 12
ISSN: 0027-8424
Subject Category
Life Sciences (General)
Distribution Limits
Public
Copyright
Other

Available Downloads

There are no available downloads for this record.
No Preview Available