The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs

Abstract

Eukaryote ribosomal RNAs (rRNAs) have expanded in the course of phylogeny by addition of nucleotides in specific insertion areas, the expansion segments. These number about 40 in the larger (25-28S) rRNA (up to 2,400 nucleotides), and about 12 in the smaller (18S) rRNA (<700 nucleotides). Expansion of the larger rRNA shows a clear phylogenetic increase, with a dramatic rise in mammals and especially in hominids. Substantial portions of expansion segments in this RNA are not bound to ribosomal proteins, and may engage extraneous interactants, including messenger RNAs (mRNAs). Studies on the ribosome-mRNA interaction have focused on proteins of the smaller ribosomal subunit, with some examination of 18S rRNA. However, the expansion segments of human 28S rRNA show much higher density and numbers of mRNA matches than those of 18S rRNA, and also a higher density and match numbers than its own core parts. We have studied that with frequent and potentially stable matches containing 7-15 nucleotides. The expansion segments of 28S rRNA average more than 50 matches per mRNA even assuming only 5% of their sequence as available for such interaction. Large expansion segments 7, 15, and 27 of 28S rRNA also have copious long (≥10-nucleotide) matches to most human mRNAs, with frequencies much higher than in other 28S rRNA parts. Expansion segments 7 and 27 and especially segment 15 of 28S rRNA show large size increase in mammals compared to other metazoans, which could reflect a gain of function related to interaction with non-ribosomal partners. The 28S rRNA expansion segment 15 shows very high increments in size, guanosine, and cytidine nucleotide content and mRNA matching in mammals, and especially in hominids. With these segments (but not with other 28S rRNA or any 18S rRNA expansion segments) the density and number of matches are much higher in 5'-terminal than in 3'-terminal untranslated mRNA regions, which may relate to mRNA mobilization via 5' termini. Matches in the expansion segments 7, 15, and 27 of human 28S rRNA appear as candidates for general interaction with mRNAs, especially those associated with intracellular matrices such as the endoplasmic reticulum.

Keywords: GC content; RNA expansion segment; RNA nucleotide bias; RNA nucleotide repeat; rRNA/mRNA matches.

Figure 1

Counts of canonical contiguous 7–15 nucleotide matches of human rRNA segments with human mRNA sectors. (A) Matches in 5′utr. (B) Matches in cds. (C) Matches in 3′utr. Percentages of the numbers of matches relative to ESL are shown in graph (D) for 5′utr, in graph (E) for cds, and in graph (F) for 3′utr. In Wilcoxon signed-rank (paired) test at p < 0.01 the numbers of matches in ESL were higher than those in ESS for all three sectors, and also higher for 5′utr and cds. The percentage of matches relative to ESL tested as lower in 5′utr for all other rRNA segments, and in cds and 3′utr for ESS. The percentage of CSL matches relative to ESL in 3′utr however tested as higher. Slopes of the linear regressions on number of nucleotides in segment vs. log₁₀ of match count for 5′utr, cds and 3′utr were: in ESL, −0.3402, −0.4087, and −0.4586; in CSL, −0.5551, −0.5851, and −0.5936; in ESS, −0.5204, −0.5631, and −0.6069; in CSS, −0.5356, −0.5748, and −0.6669. In linear regressions the ESL slopes were much lower than in other segment groups, with no overlaps at double SD (see Table 1). The r²-values were above 0.99 in all regressions.

Figure 2

Ratios of rRNA matches in 3′utr to other mRNA sectors. (A) 3′utr/5′utr match ratios. (B) 3′utr/cds match ratios. In Wilcoxon paired test at p < 0.01 the 3′utr/5′ utr ratios were lower for ESL relative to all other rRNA segments. The 3′utr/cds ratios for ESS were lower than those for CSS and CSL. Both 3′utr/5′utr and 3′utr/cds CSL ratios were lower than those for the corresponding CSS segments. All differences with ESL were significant at p < 0.01 in Monte Carlo t-tests.

Figure 3

Densities of 7- and 10-nucleotide matches to human mRNA sectors in segments of human 28S and 18S rRNAs. Total numbers of matches in segments are expressed per number of nucleotides in the segment and per 1,000 mRNAs (see section Methods). Upper row, 7-nt matches: (A) ESL, (B) CSL, (C) ESS, (D) CSS. Lower row, 10-nucleotide matches: (E) ESL, (F) CSL, (G) ESS, (H) CSS. Numbers of nucleotides in the segments are listed next to the segment labels. Average numbers of nucleotides in the examined mRNA sectors are listed in Methods. For 5′utr, the ESL densities were at least two-fold larger than in other segment groups and also significantly higher in Wilcoxon rank sum test (WRST) against all other groups for either the 7- or the 10-nt match length. For cds segments there were no significant density differences in WRST. For 3′utr the ESL densities were for both match sizes lower than in CSL, with significant difference in WRST. The above density differences showed closely similar confidence levels in Monte Carlo t-tests.

Figure 4

A comparison of size and GC content in ESL15 and the neighboring core segments of 25-28S rRNAs across the phylogenetic ladder. (A) Average number of nucleotides per CSL15, ESL15, and CSL19 segment. (B) Average number of 7-nt human mRNA matches per CSL15, ESL15, and CSL19 segment. (C) Overall 7-nt human mRNA matches by ESL15 segments. (D) Average GC content of 7-nt ES15L antisense matches in human mRNAs. Average GC contents (±SD) for entire segment sequences in all groups are: 54.9 ± 4.2 (46.6–60.4) for CSL15, 62.7 ± 16.6 (18.5–84.4) for ESL15, and 55.6 ± 5.1 (45–62.6) for CSL19. For details about the examined rRNAs see the Table S1.