Small Nuclear RNAs: RNA Sequences, Structure, and

Modifications
RAM REDDY and HARRIS BUSCH 1

CONTENTS

Summary....................................................................... 1
1 Nomenclature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2 Occurrence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.1 Animal Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.2 Plant Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.3 Single Cell Eukaryotes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3 Diversity of Small RNAs .................................................... 5
4 Small RNAs of Normal and Thmor Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
5 Subcellular Localization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
5.1 Small RNAs in the Nucleoplasm............................................. 10
5.2 Small RNAs in the Nucleolus................................................ 10
5.3 Small RNAs in the Cytoplasm............................................... 10
5.4 Small RNAs in the Mitochondria............................................. 10
6 U-snRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
6.1 U-snRNAs of the Nucleoplasm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
6.2 U-snRNAs of the Nucleolus................................................. 16
7 Modified Nucleotides in U-snRNAs........................................... 18
8 Comparison of U-snRNAs from Higher and Lower Eukaryotes . . . . . . . . . . . . . . . . . . . 19
9 Conserved Features in U-snRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
9.1 m3G-cap Structure........ ... ... .............. ..... .. ...... ................. 20
9.2 Primary Sequence.......................................................... 21
9.3 Conserved Secondary Structures...... ... ..... ..... .............. ..... . ....... 21
9.4 Sm-Antigen Binding Site. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
9.5 Evolution of U-snRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
10 Conclusions and Prospects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
11 Appendix. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Summary
All eukaryotic cells contain multiple small nuclear RNAs, designated U-snRNAs.
At present ten U-snRNAs have been identified; they account for about 10J0 of the
total mammalian cellular RNA. Of these, the U1 to U8 snRNAs have been exten-
sively characterized. All the U-snRNAs contain a 5'-cap structure consisting of
a blocked 5'-terminal pyrophosphate linkage; except for U6 RNA, a trimethyl
guanosine-containing "cap" is the 5'-end. These U-snRNAs are confined to the
nucleus and are metabolically stable. They are synthesized by RNA polymerase

1 Baylor College of Medicine, Department of Pharmacology, Houston, Thxas 77030, USA

M. L. Birnstiel (ed.), Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein Particles
© Springer-Verlag Berlin Heidelberg 1988
2 R. Reddy and H. Busch

II. U6 snRNA, which has a non-nucleotide cap structure, is synthesized by RNA

polymerase III. All the U-snRNAs are present in the cells as small ribonucleopro-
tein particles (snRNPs), that are metabolically stable.
The U1, U2, U4/U6, and US snRNPs are localized in the nucleoplasm and
are involved in the maturation of pre-messenger RNAs as essential components
of the spliceosomes. The U3 and U8 snRNPs, which are localized to the
nucleolus, are implicated in processing of pre-ribosomal RNA.
The U-snRNAs have been characterized from animal cells, plant cells, smaller
eukaryotes like yeasts, slime molds, and dinoflagellates. The secondary structures
of individual U-snRNAs from distant species are virtually identical and some
regions of primary sequence are also conserved. The detailed mechanisms of in-
teractions between the U-snRNPs, mRNA, and rRNA precursors are currently
under intense investigation.
In addition to the U-snRNAs, eukaryotic cells also contain multiple other
distinct small RNAs. These RNAs, found mainly in the cytoplasm and synthesiz-
ed by RNA polymerase III, are involved in the protein synthesis. Although about
20 distinct small RNAs are characterized, the functions have been clearly
established for only 7SL RNA and RNase P RNA. 7SL RNA is an integral com-
ponent of the signal recognition particle and RNase P RNA is part of the RNase
P complex that cleaves the 5'-ends of precursor tRNA molecules. Understanding
the functions of these cytoplasmic small RNAs is a challenge for the future.

1 Nomenclature

The U-snRNAs were designated U1, U2, U3, etc. because these RNAs were
uridylic acid-rich when compared to ribosomal or messenger RNAs (Hodnett and
Busch 1968). The term small nuclear RNA (snRNA) was introduced by Weinberg
and Penman (1968) and the term small cytoplasmic RNAs (scRNAs) was added
later (Zieve and Penman 1976). The term small nucleolar RNAs (snoRNAs) was
suggested for U-snRNAs of the nucleolus (Reddyet al. 1981 e). The U-series of
small RNAs (U1 to U3) were found to contain a cap structure on their 5'-ends
(Reddyet al. 1974; Ro-Choi et al. 1974), and all the other capped small RNAs
are added to this series. U4, US, and U6 snRNAs were designated by M. R. Lerner
and Steitz (1979), U7 snRNA by Birnstiel (Strub et al. 1984) and U8 to U10
snRNAs by Reddy et al. ( 1985 b). U 11 RNA has recently been identified by Keller
(see chapter by Birnstiel, this Vol.). Recently, Guthrie and her co-workers (Riedel
et al. 1986) have suggested that there may be more than 20 U-snRNAs in yeast,
some of which may be present in as few as 50 copies per cell. The numbers for
the U-snRNAs were designated by order of discovery and not by size, location or
abundance. Only capped small RNAs are added to the U-snRNA series.
Although the term U-snRNAs originated because of high uridylic acid content
of the original small RNAs (Hodnett and Busch 1968), some of the newer U-series
of RNAs do not contain a high proportion of uridylic acid. The 5'-cap structure
is the most definitive structural criterion for the U-snRNAs. The U-snRNAs are
usually isolated from nuclear 4-8S RNA and the fractionation and the relative
electrophoretic migration of rat U-snRNAs is shown in Fig. 1.