Complementarity of sequences in low molecular weight RNAs to regions of messenger and ribosomal RNAs

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

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.

Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex

The crystal structure of the six NH2-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound with 31 bp of the 5S rRNA gene promoter has been determined at 3.1 A resolution. Individual zinc fingers are positioned differently in the major groove and across the minor groove of DNA to span the entire length of the duplex. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove.

Intermolecular hybridization of 5S rRNA with 18S rRNA: identification of a 5'-terminally-located nucleotide sequence in mouse 5S rRNA which base-pairs with two specific complementary sequences in 18S rRNA

Eukaryotic 5S rRNA hybridizes specifically with 18S rRNA in vitro to form a stable intermolecular RNA:RNA hybrid. We have used 5S rRNA/18S rRNA fragment hybridization studies coupled with ribonuclease digestion and primer extension/chain termination analysis of 5S rRNA:18S rRNA hybrids to more completely map those mouse 5S rRNA and 18S rRNA sequences responsible for duplex formation. Fragment hybridization analysis has defined a 5'-terminal region of 5S rRNA (nucleotides 6-27) which base-pairs with two independent sequences in 18S rRNA designated Regions 1 (nucleotides 1157-1180) and 2 (nucleotides 1324-1339). Ribonuclease digestion of isolated 5S rRNA:18S rRNA hybrids with both single-strand- and double-strand-specific nucleases supports the involvement of this 5'-terminal 5S rRNA sequence in 18S rRNA hybridization. Primer extension/chain termination analysis of isolated 5S rRNA:18S rRNA hybrids confirms the base-pairing of 5S rRNA to the designated Regions 1 and 2 of 18S rRNA. Using these results, 5S rRNA:18S rRNA intermolecular hybrid structures are proposed. Comparative sequence analysis revealed the conservation of these hybrid structures in higher eukaryotes and the same but smaller core hybrid structures in lower eukaryotes and prokaryotes. This suggests that the 5S rRNA:16S/18S rRNA hybrids have been conserved in evolution for ribosome function.

A simple and rapid method for the preparation of homologous DNA oligonucleotide hybridization probes from heterologous gene sequences and probes

We describe a simple and rapid method for the preparation of homologous DNA oligonucleotide probes for hybridization analysis and/or cDNA/genomic library screening. With this method, a synthetic DNA oligonucleotide derived from a known heterologous DNA/RNA/protein sequence is annealed to an RNA preparation containing the gene transcript of interest. Any unpaired 3'-terminal oligonucleotides of the heterologous DNA primer are then removed using the 3' exonuclease activity of the DNA Polymerase I Klenow fragment before primer extension/dideoxynucleotide sequencing of the annealed RNA species with AMV reverse transcriptase. From the determined RNA sequence, a completely homologous DNA oligonucleotide probe is then prepared. This approach has been used to prepare a homologous DNA oligonucleotide probe for the successful library screening of the yeast hybRNA gene starting with a heterologous mouse hybRNA DNA oligonucleotide probe.

Homologous genes for mouse 4.5S hybRNA are found in all eukaryotes and their low molecular weight RNA transcripts intermolecularly hybridize with eukaryotic 18S ribosomal RNAs

Previous work has reported the isolation and sequencing of a mouse low molecular weight RNA species designated 4.5S hybridizing RNA or hybRNA because of its ability to intermolecularly hybridize with mouse mRNA and 18S rRNA sequences. Using synthetic DNA oligonucleotide probes we have examined the conservation of this gene sequence and its expression as a lmwRNA transcript across evolution. Southern blot analysis has shown that homologous genes of single or low copy number are found in all eukaryotes examined as well as in E. coli. Northern blot analysis has demonstrated 4.5S hybRNA transcription in all mouse tissues as well as expression in yeast and Xenopus laevis as lmwRNAs of approximately 130 and 100 nucleotides, respectively, as compared with mouse/rat/hamster species of approximately 87 nucleotides. Yeast and X. laevis 4.5S hybRNA homologs, isolated by hybrid-selection, were shown by Northern blot analysis to intermolecularly hybridize with homologous as well as heterologous 18S rRNA sequences. The conservation of 4.5S hybRNA homologous genes and their expression as lmwRNA transcripts with common intermolecular RNA:RNA hybridization capabilities in fungi, amphibians, and mammals argues for a common, conserved and required biological function for this lmwRNA in all eukaryotes and potential utilization of its intermolecular RNA:RNA hybridization capabilities to carry out this function.

Description of putative ribosomal RNAs with low abundance, developmental regulation, and the identifier sequence

Three RNA species (5, 2, 0.15 kb) characterized by the repetitive identifier (ID) sequence, expressed constitutively, and at low abundance have been identified in rat L6 muscle cells by hybridization to cDNA pL6-411. Comigration of these three RNAs with 28, 18, and 5.8 S ribosomal RNAs (rRNAs) has suggested the possibility that pL6-411 RNAs are related to ribosomes or ribosome-like structures. Subsequent experiments showed that pL6-411-related RNAs could indeed be found in ribosome-like particles which were indistinguishable from ribosomes when separated on sucrose gradients under native (low salt, isolation of intact ribosomes) or denaturing conditions (detergent, high salt, isolation of ribosome subunits). Furthermore, we demonstrate that pL6-411-related RNAs are cytoplasmic in L6 cells, may be transcribed in nucleoli, and, based on their nucleotide sequence, have the potential of inter- and intramolecular hybridization. Expression of pL6-411 RNAs was also shown in adult as well as in fetal rat tissues after Day 14 of gestation. These above findings provide supportive evidence for the hypothesis that pL6-411 5- and 2-kb RNAs could exist in a subset of ribosomes. These ribosome-like pL6-411 particles nevertheless differ from ribosomes in that their associated RNAs have different nucleotide sequences, are of lower abundance, and are up-regulated later in development than rRNAs. We discuss our results in the context of a postulated ribosome subset containing RNAs other than rRNAs. These ribosome-like particles might be involved in the translational control of ID-positive mRNAs.

A low-molecular-weight RNA from mouse ascites cells that hybridizes to both 18S rRNA and mRNA sequences

A low-molecular-weight RNA species from mouse ascites cells has been selected and purified by its intermolecular RNA X RNA hybridization capabilities. This 4.5S RNA is able to base pair with poly(A)+ mRNA sequences and with 18S rRNA. Melting experiments have shown that the intermolecular hybrids formed with this complementary low-molecular-weight RNA are of comparable stability to other RNA X RNA interactions. Analysis has shown that this hybridizing RNA is 87 nucleotides long and has an unusual sequence structure. Located near the 3' terminus is an alternating pyrimidine dinucleotide region of UUCCUUCCUU. This region along with the 3'-adjacent nucleotides form a 14-nucleotide sequence that exhibits perfect complementarity with 18S rRNA. An additional region of 10 nucleotides at the 3' terminus is perfectly homologous to a similarly located sequence in 5.8S rRNA. An obvious RNA polymerase III binding site is not found internally in this low-molecular-weight RNA sequence. The complementary and homologous character of hybridizing RNA with respect to rRNA and mRNA sequences suggests a potential regulatory role for this RNA in the coupling of ribosome and mRNA functions.