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Nucleic Acids Research, 2001, Vol. 29, No. 7 1623-1630
© 2001 Oxford University Press

Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana

Qu Liang-Hu*, Meng Qing, Zhou Hui and Chen Yue-Qin

Key Laboratory of Gene Engineering of Education Ministry, Biotechnology Research Center, Zhongshan University, Guangzhou 510275, People’s Republic of China

Ten novel small nucleolar RNA (snoRNA) gene clusters, consisting of two or three snoRNA genes, respectively, were identified from Arabidopsis thaliana. Twelve of the 25 snoRNA genes in these clusters are homologous to those of yeast and mammals according to the conserved antisense sequences that guide 2'-O-ribose methylation of rRNA. The remaining 13 snoRNA genes, including two 5.8S rRNA methylation guides, are new genes identified from A.thaliana. Interestingly, seven methylated nucleotides, predicted by novel snoRNAs Z41a–Z46, are methylated neither in yeast nor in vertebrates. Using primer extension at low dNTP concentration the six methylation sites were determined as expected. These snoRNAs were recognized as specific guides for 2'-O-ribose methylation of plant rRNAs. Z42, however, did not guide the expected methylation of 25S rRNA in our assay. Thus, its function remains to be elucidated. The intergenic spacers of the gene clusters are rich in uridine (up to 40%) and most of them range in size from 35 to 100 nt. Lack of a conserved promoter element in each spacer and the determination of polycistronic transcription from a cluster by RT–PCR assay suggest that the snoRNAs encoded in the clusters are transcribed as a polycistron under an upstream promoter, and individual snoRNAs are released after processing of the precursor. Numerous snoRNA gene clusters identified from A.thaliana and other organisms suggest that the snoRNA gene cluster is an ancient gene organization existing abundantly in plants.

* To whom correspondence should be addressed. Tel: +86 20 8411 2399; Fax: +86 20 8403 6551; Email: lsbrc04{at}zsu.edu.cn +AJ010675, AJ224036, AJ240063–AJ240074, AJ240077, AJ240080, AJ242536, AJ242537, AJ276571–AJ276575, AJ440078, AJ440079


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