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Nucleic Acids Research, 1992, Vol. 20, No. 20 5435-5442
© 1992

MOLECULAR BIOLOGY

Genes for Xenopus laevis U3 small nuclear RNA

Rocco Savino1,2, Youssef Hitti1 and Susan A. Gerbi1,*

1Division of Biology and Medicine, Brown University Providence, RI 02912, USA 2Laboratori di Biologia Cellulare e dello Sviluppo, Universita di Pica 56010 Ghezzano (La Fontina), Pisa, Italy

* To whom correspondence should be addressed

Received June 23, 1992. Revised August 13, 1992. Accepted August 13, 1992.

Genomlc Southern blots showed there are only 14 to 20 copies of U3 snRNA genes per somatic genome in Xenopus laevis, unlike the highly repetitive, tandem arrangement of other snRNA genes in this organism. Sequencing of two U3 snRNA genes from {lambda} clones of a genomlc library revealed striking similarity upstream, but much more divergence downstream. Consensus motifs common to other U snRNA genes were also found: a distal sequence element (DSE, octamer motif at - 222 to - 215), a proximal sequence element (PSE, at - 62 to - 52) and a 3' Box (15 or 16 bp downstream of the U3 genes). The DSE of mammals also has an Inverted CCAAT motif specific for U3 snRNA genes, and we find this Is conserved in the amphibian U3 snRNA genes. The Xenopus inverted CCAAT motif is exactly one helical turn further upstream of the octamer motif than its mammalian counterpart, suggesting interaction of putative transcription factors bound to these motifs. Mutation of the inverted CCAAT motif and part of an adjacent Sp1 site greatly depresses transcription of the mutant U3 snRNA gene in Xenopus oocytes, implying a role in transcriptional efficiency. Electrophoretic mobility shift assays implicate transcription factor binding to this region.


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