A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3.

Abstract

A human small nucleolar RNA, identified previously in HeLa cells by anti-fibrillarin autoantibody precipitation and termed RNA X, has been characterized. It comprises two uridine-rich variants (148 and 146 nucleotides}, which we refer to as snRNA U15A and U15B. Secondary structure models predict for both variants a U15-specific stem-loop structure, as well as a new structural motif that contains conserved sequences and can also be recognized in the other fibrillarin-associated nucleolar snRNAs, U3, U14, and RNA Y. The single-copy gene for human U15A has been found unexpectedly to reside in intron 1 of the ribosomal protein $3 gene; the U15A sequence appears on the same strand as the $3 mRNA and does not exhibit canonical transcription signals for nuclear RNA polymerases. U15A RNA is processed in vitro from $3 intron 1 transcripts to yield the correct 5' end with a 5'-monophosphate; the in vitro system requires ATP for 3' cleavage, which occurs a few nucleotides downstream of the mature end. The production of a single primary transcript specifying the mRNA for a ribosomal or nucleolar protein and a nucleolar snRNA may constitute a general mechanism for balancing the levels of nucleolar components in vertebrate cells.

U17XS8, a small nucleolar RNA with a 12 nt complementarity to 18S rRNA and coded by a sequence repeated in the six introns ofXenopus laevisribosomal protein S8 gene

“…This peculiar mechanism has been demonstrated to be involved also in the production of the other snoRNAs recently found to be encoded in introns, U14, U15 U16 and HeLa U17 RNAs (7)(8)(9)41). In the case of U16 RNA, encoded in an intron of the Xenopus gene for r-protein L1, it has been shown that its production is alternative to that of the mature Li mRNA (8).…”

The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation.

“…The importance of this helix in accu mulation of a yeast ACA snoRNA, snRl 1, has been dem onstrated (Balakin et al 1996). Interestingly, many box C/D snoRNAs feature a stem structure similar to helix II (Tycowski et al 1993;Watkins et al 1996). Although this helix is dispensable for the accumulation of U14 snoRNA, it has been implicated in the processing of box C/D snoRNAs, which lack a 5',3' terminal stem struc ture (helix I) (Watkins et al 1996).…”

“…Accumulating evidence suggests that excision of intronic snoRNAs relies on exonucleolytic activities Filipowicz 1993, 1995;Xia et al 1997). The C, D, and ACA boxes of snoRNAs have been postulated to bind putative protein factor(s) which could delineate the terminal boundaries by protecting the snoRNAs from exonucleolytic degradation (Huang et al 1992;Tycowski et al 1993;Balakin et al 1994Balakin et al , 1996Caffarelli et al 1996;Watkins et al 1996;Xia et al 1997).…”

“…The U3 snoRNA is required for an early cleavage in the 5' external transcribed spacer (Kass et al 1990;Hughes and Ares 1991;Mougey et al 1993) and also for subsequent formation of mature 18S rRNA (Savino and Gerbi 1990;Hughes and Ares 1991). Likewise, the U14 and U22 snoRNAs are essential for the accumulation of IBS rRNA (Li et al 1990;Tycowski et al 1994), whereas the US snoRNA is implicated in the processing of 5.8S and 28S rRNAs (PecuUs and Steitz 1993). More recently, a large subset of box C/D snoRNAs have been demon strated to function as guide RNAs in site-specific ribose methylation of pre-rRNAs (Kiss-Laszlo et al 1996;Nicoloso et al 1996).…”

“…The snoRNAs are either tran scribed by RNA polymerase II (Pol II) from independent genes or they are processed from intron regions of premRNAs (for review, see Maxwell and Fournier 1995). The mature intron-encoded snoRNAs possess mono phosphates at their 5' ends (Kiss and Filipowicz 1993;Tycowski et al 1993), whereas the 5' termini of Pol IItranscribed snoRNAs are blocked by trimethylguanosine caps (Maxwell and Fournier 1995).…”