The external transcribed spacer and preceding region ofXenopus borealisrDNA: comparison with the corresponding region ofXenopus laevisrDNA

Abstract

We report sequence data from a cloned rDNA unit from Xenopus borealis, extending leftwards from the 18S gene to overlap a region previously sequenced by R.Bach, B.Allet and M.Crippa (Nucleic Acids Research 9,[5311][5312][5313][5314][5315][5316][5317][5318][5319][5320][5321][5322][5323][5324][5325][5326][5327][5328][5329][5330].Comparison with data from other species of Xenopus leads to the inference that the transcription initiation site in X.borealis is in the newly sequenced region and not, as was previously thought, in the region sequenced earlier.The X.borealis external transcribed spacer thus defined is some 612 nucleotides long, about 100 nucleotides shorter than in X.laevis. The X.borealis and X.laevis external transcribed spacers show a pattern of extensive but interrupted sequence divergence, with a large conserved tract starting about 100 nucleotides downstream from the transcription initiation site and shorter conserved tracts elsewhere.The regions in between the conserved tracts differ in length between the respective external transcribed spacers indicating that insertions and deletions have contributed to their divergence, as previously inferred for the internal transcribed spacers.Much of the overall length difference is in the region flanking the 18S gene, where there are also length microheterogeneities in X.laevis rDNA.As in X.laevis, the transcribed spacer sequences flanking the 18S gene in X.borealis contain no major tracts of mutual complementarity. The accumulated data on transcribed spacers in Xenopus render it unlikely that processing of ribosomal precursor RNA involves interaction between the regions flanking 18S RNA.

Nucleotide sequence determination and secondary structure ofXenopusU3 snRNA

“…However, processing cleavage has not been observed within the ETS of Xenopus (B. Sollner-Webb, personal communication). Moreover, there is no significant complementarity conserved between Box A of U3 snRNA and the ETS of X. laevis (61) or X. borealis (62). Therefore, the evidence is not compelling for base-pairing between Box A of U3 snRNA and the ETS in Xenopus.…”

Nucleolar Localization Elements ofXenopus laevisU3 Small Nucleolar RNA

“…In contrast, a mutant of the hinge region (Tag*) fully competed wild-type U3 for its nucleolar localization (Figure 6), as might be expected, because this mutant retains wild-type sequences for Boxes C and D that are the primary NoLEs. The reduced nucleolar labeling by the U3 hinge mutant (Tag*) when it is used as the probe ( Figure 5) may reflect a destabilization of nucleolar localization normally provided by base pairing between the U3 hinge region (nt 65-72 in Xenopus U3 snoRNA; Jeppesen et al, 1988) and sequences in the external transcribed spacer (ETS of 40S pre-rRNA; Xenopus nt 311-318) (Furlong et al, 1983). The possibility for base pairing between the U3 hinge region and the ETS was first noted by Maser and Calvet (1989), is phylogenetically conserved by compensatory mutations (our unpublished results), and has been substantiated by mutagenesis and cross-linking studies in yeast Tollervey, 1992, 1995;Beltrame et al, 1994).…”

The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA In higher eukaryotes

“…By their high potential to form self-contained very stable stem structures and by their history of repeated insertion and deletion events, the so-calLed "D" domains of 28S rRNA gene in higher eukaryotes are again closely related to the transcribed spacers of the ribosomal transcription unit (18,13,30,31). Although the presence of very short introns cannot definitely be ruled out so far, all the experimental evidences suggest that most (if not all) the transcripts of "D" domains are present in mature 28S rRNA of higher eukaryotes : very similar size and base content of sequenced genes and mature rRNAs, detection of the characteristic GC-rich giant stems (29) in mature 28S rRNA as mentioned above, protection from SI nuclease of rRNA-DNA hybrids (5).…”