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PMID: 16244158 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants.

Plant physiology ·Vol. 139 ·No. 3 ·2005-11-00 ·Pages 1323-37

Xiao YL, Smith SR, Ishmael N, Redman JC, Kumar N, Monaghan EL, Ayele M, Haas BJ, Wu HC, Town CD

Abstract

In the fully sequenced Arabidopsis (Arabidopsis thaliana) genome, many gene models are annotated as "hypothetical protein," whose gene structures are predicted solely by computer algorithms with no support from either expressed sequence matches from Arabidopsis, or nucleic acid or protein homologs from other species. In order to confirm their existence and predicted gene structures, a high-throughput method of rapid amplification of cDNA ends (RACE) was used to obtain their cDNA sequences from 11 cDNA populations. Primers from all of the 797 hypothetical genes on chromosome 2 were designed, and, through 5' and 3' RACE, clones from 506 genes were sequenced and cDNA sequences from 399 target genes were recovered. The cDNA sequences were obtained by assembling their 5' and 3' RACE polymerase chain reaction products. These sequences revealed that (1) the structures of 151 hypothetical genes were different from their predictions; (2) 116 hypothetical genes had alternatively spliced transcripts and 187 genes displayed polyadenylation sites; and (3) there were transcripts arising from both strands, from the strand opposite to that of the prediction and possible dicistronic transcripts. Promoters from five randomly chosen hypothetical genes (At2g02540, At2g31270, At2g33640, At2g35550, and At2g36340) were cloned into report constructs, and their expressions are tissue or development stage specific. Our results indicate at least 50% of hypothetical genes on chromosome 2 are expressed in the cDNA populations with about 38% of the gene structures differing from their predictions. Thus, by using this targeted approach, high-throughput RACE, we revealed numerous transcripts including many uncharacterized variants from these hypothetical genes.

MeSH Terms
Alternative Splicing/genetics Arabidopsis/anatomy & histology,genetics Chromosomes, Plant/genetics Codon, Initiator/genetics Codon, Terminator/genetics DNA, Complementary/genetics Genes, Plant/genetics Genes, Reporter/genetics Genome, Plant Open Reading Frames/genetics Promoter Regions, Genetic/genetics Sequence Alignment Sequence Analysis, DNA Sequence Homology, Nucleic Acid Transcription, Genetic/genetics
Chemicals
Codon, Initiator Codon, Terminator DNA, Complementary
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Xiao Yong-Li
The Institute for Genomic Research, Rockville, MD 20850, USA. [email protected]
Smith Shannon R
Ishmael Nadeeza
Redman Julia C
Kumar Nihkil
Monaghan Erin L
Ayele Mulu
Haas Brian J
Wu Hank C
Town Christopher D
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Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.105.063479
Email
[email protected]
Published
2005-11-00
Epub
2005-00-21
Pages
1323-37
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC1283769
Subset
IM
External Links
PubMed source DOI: 10.1104/pp.105.063479 PMC Full Text View journal details
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