Av. Borovjagin et Sa. Gerbi, The spacing between functional cis-elements of U3 snoRNA is critical for rRNA processing, J MOL BIOL, 300(1), 2000, pp. 57-74
The sequences and structural features of Xenopus laevis U3 small nucleolar
RNA (snoRNA) necessary for pre-rRNA cleavage at sites 1 and 2 to form 18S r
RNA were assayed by depletion/rescue experiments in Xenopus oocytes. Mutage
nesis results demonstrated that the putative stem of U3 domain I is unneces
sary for 18 S rRNA processing. A model consistent with earlier experimental
data is proposed for the structure of domain I when U3 is not yet bound to
pre-rRNA. For its function in rRNA processing, a newly discovered element
(5' hinge) was revealed to be important but not as critical as the 3' hinge
region in Xenopus U3 snoRNA for 18 S rRNA formation. Base-pairing is propo
sed to occur between the U3 5' hinge and 3' hinge and complementary regions
in he external transcribed spacer (ETS); these interactions are phylogenet
ically conserved, and are homologous to those previously described in yeast
(5' hinge-ETS) and trypanosomes (3' hinge-ETS). A model is presented where
the base-pairing of the 5' hinge and 3' hinge of U3 snoRNA with the ETS of
pre-rRNA helps to correctly position U3 boxes A' + A for their function in
rRNA processing. Like an earlier proposal for yeast, boxes A' and A of Xen
opus may base-pair with 18 S sequences in pre-rRNA. We present the first di
rect experimental evidence in any system that box A' is essential for U3 sn
oRNA function in 18 S rRNA formation. The analysis of insertions and deleti
ons indicated that the spacing between the U3 elements is important, sugges
ting that they base-pair with the ETS and 18 S regions of pre-rRNA at the s
ame time. (C) 2000 Academic Press.