Nucleic Acids Research, Vol 27, Issue 4 1070-1078, Copyright © 1999 by Oxford University Press
AD Farris, G Koelsch, GJ Pruijn, WJ van Venrooij and JB Harley
Y RNAs are small 'cytoplasmic' RNAs which are components of the Ro
ribonucleoprotein (RNP) complex. The core of this complex, which is found
in the cell nuclei of higher eukaryotes as well as the cytoplasm, is
composed of a complex between the 60 kDa Ro protein and Y RNAs. Human cells
contain four distinct Y RNAs (Y1, Y3, Y4 and Y5), while other eukaryotes
contain a variable number of Y RNA homologues. When detected in a
particular species, the Ro RNP has been present in every cell type within
that particular organism. This characteristic, along with its high
conservation among vertebrates, suggests an important function for Ro RNP
in cellular metabolism; however, this function has not yet been
definitively elucidated. In order to identify conserved features of Y RNA
sequences and structures which may be directly involved in Ro RNP function,
a phylogenetic comparative analysis of Y RNAs has been performed. Sequences
of Y RNA homologues from five vertebrate species have been obtained and,
together with previously published Y RNA sequences, used to predict Y RNA
secondary structures. A novel RNA secondary structure comparison algorithm,
the suboptimal RNA analysis program, has been developed and used in
conjunction with available algorithms to find phylogenetically conserved
secondary structure models for YI, Y3 and Y4 RNAs. Short, conserved
sequences within the Y RNAs have been identified and are invariant among
vertebrates, consistent with a direct role for Y RNAs in Ro function. A
subset of these are located wholly or partially in looped regions in the Y3
and Y4 RNA predicted model structures, in accord with the possibility that
these Y RNAs base pair with other cellular nucleic acids or are sites of
interaction between the Ro RNP and other macromolecules.
ARTICLES
Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis
Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA and Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands.
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