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Nucleic Acids Research, 1985, Vol. 13, No. 2 537-556
© 1985

Articles

Structure of the sea urchin U1 RNA repeat

David T. Brown*, Gilbert F. Morris, Nunta Chodchoy, Cindy Sprecher and William F. Marzluff

Department of Chemistry, florida State University Tallahassee, FL 32306, USA

Received August 10, 1984. Revised December 27, 1984. Accepted December 27, 1984.

The genes coding for U1 RNA in the sea urchin L. variegatus are present in a 1400 base pair tandem repeat. One member of the repeat has been cloned and its sequence determined. The repeat unit contains a single copy of the gene for L.variegatus U1 RNA. This gene encodes an RNA which is 75% homologous to mammalian U1 RNAs. The L. variegatus U1 RNA could assume a secondary structure similar to that proposed for other U1 RNAs. In addition the L. variegatus U1 RNA is precipitated by anti-SM and anti-RNP anti-sera. Analysis of the L. variegatus genomic DNA using the cloned U1 gene as a probe reveals a major and a minor type of repeat unit. The two repeated units are the same length but differ in a number of restriction enzyme sites clustered 200–500 bases down stream from the gene. The monomer we have cloned and sequenced is a representative of the minor repeat. A sequence (GATAA) which is –41 to –37 bases 5' to the gene has homology to the putative RNA polymerase II promoter. Fifteen bases 3' of the gene is a sequence (CAAAGAAAGAAAA) which is very similar to the sequence found 3' of the sea urchin histone genes. The two Hha I, Hpa II and Ava I sites in the repeat are all unmethylated in sperm DNA.

*Present address: Department of Biochemistry, University of Mississippi Medical Center, 2500 N. State Street, Jackson, MS 39216, USA


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