Amplification of plant U3 and U6 snRNA gene sequences using primers specific for an upstream promoter element and conserved intragenic regions

U-snRNA genes in higher plants contain two essential promoter elements, the USE with sequence RTCCCACATCG and the TATA-like box, positioned in the -70 and -30 regions, respectively. Using an oligodeoxynucleotide containing the USE motif and oligodeoxynucleotides specific for the intragenic regions c...

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Bibliographic Details
Published in:Nucleic acids research 1990-06, Vol.18 (12), p.3459-3466
Main Authors: Marshallsay, C, Kiss, T, Filipowicz, W
Format: Article
Language:English
Subjects:
Arabidopsis thaliana
Base Sequence
Gene Expression Regulation
Genes, Plant
Introns
Metazoa
Molecular Sequence Data
Nicotiana - genetics
Nicotiana plumbaginifolia
Nicotiana tabacum
Nucleic Acid Conformation
Plants - genetics
Plants, Toxic
Polymerase Chain Reaction
Promoter Regions, Genetic
RNA, Small Nuclear - genetics
Sequence Homology, Nucleic Acid
Templates, Genetic
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Summary:U-snRNA genes in higher plants contain two essential promoter elements, the USE with sequence RTCCCACATCG and the TATA-like box, positioned in the -70 and -30 regions, respectively. Using an oligodeoxynucleotide containing the USE motif and oligodeoxynucleotides specific for the intragenic regions conserved in U-snRNAs, several sequences encoding U6 and U3 snRNAs were determined by polymerase chain reaction (PCR) amplification of Arabidopsis thaliana and tobacco genomic DNAs. This method provides a simple and rapid procedure for characterisation of plant U-snRNA genes and their promoters. It could also be used for the characterisation of other genes containing conserved upstream promoter elements. PCR-derived fragments were used as probes for the isolation of the U3 snRNA genes from a genomic library of Arabidopsis. Two isolated U3 genes were shown to be active when transfected into protoplasts of Nicotiana plumbaginifolia. Both U3 genes contain the USE and TATA-like upstream elements located in similar positions to the U6 genes of Arabidopsis. The encoded Arabidopsis U3 snRNAs can be folded into a secondary structure which is more similar to that of U3 RNAs from lower eukaryotes rather than from metazoa.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/18.12.3459