24 RNA SPLICING AND PROCESSING (Full Edition)
22 Small RNAs are required for rRNA processing
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- A snoRNA is a small nuclear RNA that is localized in the nucleolus.
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The C/D group of snoRNAs is required for modifying the 2' position of ribose with a methyl group.
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The H/ACA group of snoRNAs is required for converting uridine to pseudouridine.
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each case the snoRNA base pairs with a sequence of rRNA that contains
the target base to generate a typical structure that is the substrate
for modification.
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Processing and modification of rRNA requires a class of small RNAs called snoRNA
s (small nucleolar RNAs). There are 71 snoRNAs in the yeast (S. cerevisiae)
genome. They are associated with the protein fibrillarin, which is an
abundant component of the nucleolus (the region of the nucleus where
the rRNA genes are transcribed). Some snoRNAs are required for cleavage
of the precursor to rRNA; one example is U3 snoRNA, which is required
for the first cleavage event in both yeast and Xenopus (740).
We do not know what role the snoRNA plays in cleavage. It could be
required to pair with the rRNA sequence to form a secondary structure
that is recognized by an endonuclease.
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Two groups of snoRNAs are required for
the modifications that are made to bases in the rRNA. The members of
each group are identified by very short conserved sequences and common
features of secondary structure (1216; 1217).
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The C/D group of snoRNAs is required for
adding a methyl group to the 2' position of ribose. There are >100
2' -O-methyl groups at conserved locations in vertebrate rRNAs. This
group takes its name from two short conserved sequences motifs called
boxes C and D. Each snoRNA contains a sequence near the D box that is
complementary to a region of the 18S or 28S rRNA that is methylated.
Loss of a particular snoRNA prevents methylation in the rRNA region to
which it is complementary.
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Figure 24.39
A snoRNA base pairs with a region of rRNA that is to be methylated.
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Figure 24.39 suggests that the snoRNA base pairs with the rRNA to create the duplex
region that is recognized as a substrate for methylation. Methylation
occurs within the region of complementarity, at a position that is
fixed 5 bases on the 5' side of the D box (741; 1220).
Probably each methylation event is specified by a different snoRNA; ~40
snoRNAs have been characterized so far. The methylase(s) have not been
characterized; one possibility is that the snoRNA itself provides part
of the methylase activity.
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Figure 24.40
Uridine is converted to pseudouridine by replacing the
N1-sugar bond with a C5-sugar bond and rotating the base relative to
the sugar.
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Another group of snoRNAs is involved in
the synthesis of pseudouridine. There are 43 ? residues in yeast rRNAs
and ~100 in vertebrate rRNAs. The synthesis of pseudouridine involves
the reaction shown in Figure 24.40 in which the N1 bond from uridylic acid
to ribose is broken, the base is rotated, and C5 is rejoined to the sugar.
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Figure 24.41
H/ACA snoRNAs have two short conserved sequences and
two hairpin structures, each of which has regions in the stem that are
complementary to rRNA. Pseudouridine is formed by converting an
unpaired uridine within the complementary region of the rRNA.
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Pseudouridine formation in rRNA requires
the H/ACA group of ~20 snoRNAs. They are named for the presence of an
ACA triplet 3 nucleotides from the 3' end and a partially conserved
sequence (the H box) that lies between two stem-loop hairpin
structures. Each of these snoRNAs has a sequence complementary to rRNA
within the stem of each hairpin. Figure 24.41 shows
the structure that would be produced by pairing with the rRNA. Within
each pairing region, there are two unpaired bases, one of which is a
uridine that is converted to pseudouridine (742; 1218).
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The H/ACA snoRNAs are associated with a
nucleolar protein called Gar1p, which is required for pseudouridine
formation, but its function is unknown (1219). The known
pseudouridine synthases are proteins that function without an RNA
cofactor. Synthases that could be involved in snoRNA-mediated
pseudouridine synthesis have not been identified.
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The involvement of the U7 snRNA in 3' end
generation, and the role of snoRNAs in rRNA processing and
modification, is consistent with the view we develop in Catalytic RNA
that many — perhaps all — RNA processing events depend on RNA-RNA
interactions. As with splicing reactions, the snRNA probably functions
in the form of a ribonucleoprotein particle containing proteins as well
as the RNA. It is common (although not the only mechanism of action)
for the RNA of the particle to base pair with a short sequence in the
substrate RNA.
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Last Revised on August 9, 2004
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740 Kass, S. et al.
(1990).
The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing.
Cell 60, 897-908.
PubMed Journal
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741 Kiss-Laszlo, Z. et al.
(1996).
Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs.
Cell 85, 1077-1068.
PubMed Journal
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742 Ni, J., Tien, A. L., and Fournier, M. J.
(1997).
Small nucleolar RNAs direct site-specific synthesis of pseudouridine in rRNA.
Cell 89, 565-573.
PubMed Journal
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1216 Balakin, A. G., Smith, L., and Fournier, M.
J. (1996). The RNA world of the nucleolus: two major families of
small RNAs defined by different box elements with related functions.
Cell 86, 823-834. PubMed Journal
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1217 Ganot, P., Caizergues-Ferrer, M., and Kiss,
T. (1997). The family of box ACA small nucleolar RNAs is defined
by an evolutionarily conserved secondary structure and ubiquitous
sequence elements essential for RNA accumulation. Genes
Dev. 11, 941-956. PubMed
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1218 Ganot, P., Bortolin, M. L., and Kiss, T.
(1997).
Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs.
Cell 89, 799-809.
PubMed Journal
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1219 Bousquet-Antonelli, C., Henry, Y., G'elugne, J. P., Caizergues-Ferrer, M., and Kiss, T.
(1997).
A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs.
EMBO J. 16, 4770-4776.
PubMed Journal
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1220 Kiss-Laszlo, Z., Henry, Y., and Kiss, T.
(1998). Sequence and structural elements of methylation guide
snoRNAs essential for site-specific ribose methylation of pre-rRNA.
EMBO J. 17, 797-807. PubMed Journal
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© Jones and Bartlett Publishers (2007)
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