Further studies on similarity of terminal nucleotide sequences of eukaryote mRNA-a possible mechanism of RNA splicing

hnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene

Exon 11 of the insulin receptor gene (INSR) is alternatively spliced in a developmentally and tissue-specific manner. Linker scanning mutations in a 5′ GA-rich enhancer in intron 10 identified AGGGA sequences that are important for enhancer function. Using RNA-affinity purification and mass spectrometry, we identified hnRNP F and hnRNP A1 binding to these AGGGA sites and also to similar motifs at the 3′ end of the intron. The hnRNPs have opposite functional effects with hnRNP F promoting and hnRNP A1 inhibiting exon 11 inclusion, and deletion of the GA-rich elements eliminates both effects. We also observed specific binding of hnRNP A1 to the 5′ splice site of intron 11. The SR protein SRSF1 (SF2/ASF) co-purified on the GA-rich enhancer and, interestingly, also competes with hnRNP A1 for binding to the splice site. A point mutation -3U→C decreases hnRNP A1 binding, increases SRSF1 binding and renders the exon constitutive. Lastly, our data point to a functional interaction between hnRNP F and SRSF1 as a mutant that eliminates SRSF1 binding to exon 11, or a SRSF1 knockdown, which prevents the stimulatory effect of hnRNP F over expression.

Comparative sequence analysis as a tool for studying the secondary structure of mRNAs

Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNAs and mRNA precursors. We observed many conserved helices in all mRNA groups analyzed. Three criteria were used to identify potential helices which were not conserved solely because of coding sequence constraints, and may therefore be important for the structure and function of the RNA. These results suggest that this approach will be useful in deriving secondary structure models for informational RNAs when used in conjunction with other complementary techniques, and in designing experiments to determine the functional significance of conserved base pairing interactions.

Alternative splicing caused by RNA secondary structure

mRNA precursors with stable hairpins were constructed by inserting inverted repeats into an adenovirus transcriptional template that encoded the three late leader exons. When the loop of the hairpin contained the second exon and the flanking splice sites, most of the RNA spliced in vitro had the first exon joined directly to the third exon. The remainder was spliced normally. The same types of alternatively spliced RNAs were formed when a similar template was introduced into HeLa cells by transfection. Thus both in extracts and in cells, an exon became optional when sequestered in a hairpin loop. Perhaps a related mechanism creates the alternative splicing patterns of complex transcription units.

Clustered genes require extragenic territorial DNA sequences

This paper is concerned with the basic question as to whether there exists a complex interaction between DNA sequences which have little specific function and functional genes regarding the spatial arrangement of the gene. Since gene clusters are a characteristic and basic feature of gene structure in higher eukaryotes, the size of extragenic DNA sequences surrounding the individual genes of various clustered gene families were compared. The size of the intergenic region, which is composed of the extragenic DNA sequences flanking the 3'-end of one gene and those flanking the 5'-end of the other gene, of the paired genes increases as the genes becomes larger. However, such a gene size-dependent increase is not seen if the total gene size of the paired genes is less than 0.3 kb or greater than 4 kb. The results suggests that a higher eukaryote gene requires extragenic territorial DNA sequences surrounding it, which presumably are necessary to maintain the gene's active functions.

Nucleotide sequence complementarity between adenovirus 2-coded VA RNA and host cell pre-mRNA. A possible regulatory mechanism of cellular RNA splicing by VA RNA

Using a computer program, complementary of nucleotide sequences was assessed between adenovirus 2-coded VA RNA and presumptive cellular and viral 'pre-mRNAs'. In this paper, the possibility is considered that the splicing of cellular 'pre-mRNA' can be regulated in such a way that the formation of the proper intramolecular double-stranded hairpin structures, key elements for RNA splicing, is prevented by the binding of VA RNAI or RNAII to the nucleotide sequences around the exon-intron and intron-exon joint sites of cellular 'pre-mRNA' molecules. Complementarity assessment showed that VA RNAI can bind to the joint sites in such a way as to form an omega shape at two separate regions around the joint sites of cellular 'pre-mRNA'. Whereas VA RNAI is not capable of binding to viral hexon 'pre-mRNA' in the same manner as it does to cellular 'pre-mRNA', the binding may occur in a different way. Such differential binding is discussed in relation to the post-transcriptional sequence selection which takes place during the late phase of adenovirus infection.

A possible regulatory mechanism in RNA processing and its implication for posttranscriptional sequence control during differentiation of cell function

1. This paper is concerned with the possible molecular mechanism for RNA processing including posttranscriptional sequence control underlying the differentiation of cell functions. 2. It was previously postulated that intramolecular double-stranded hairpin structures present at 5'- and 3'-terminal regions of a 'pre-mRNA' are key elements for RNA splicing [24]. 3. In this paper the possibility is considered that the splicing of 'pre-mRNA' can be regulated in such a way that the formation of the proper double-stranded hairpin structures is prevented by the binding of low-molecular-weight nuclear RNA (LnRNA) to the terminal regions and/or to the nucleotide sequences around the exon-intron and intron-exon joint sites of the 'pre-mRNA' molecules. 4. Complementarity assessment of nucleotide sequences of rat preproinsulin 'pre-mRNA' and rat LnRNA, i.e. Ul, showed that Ul RNA is capable of forming stable double-standard intermolecular structures around the joint sites of preproinsulin 'pre-mRNA' and may prevent the formation of intramolecular double-stranded structures required for RNA splicing. This may imply a regulatory (inhibitory) role for Ul RNA in the processing of 'pre-mRNA'. 5. A possible regulatory role of LnRNA in RNA splicing is discussed in relation to the determination of the mRNA population to be translated in the cytoplasm during differentiation of cell functions.

Electron microscopic observations of heterogeneous nuclear RNA of chicken reticulocytes

Secondary structures of annealed, snapped-back and untreated chicken reticulocyte poly(A)-containing nuclear RNA were investigated by electron microscopy. Three shapes of molecules were observed: 'coat'hanger' shaped, loop-bearing and filamentous molecules. The former two shaped molecules consist of a small and large fold-back or loop plus a short hook or tail, corresponding to the poly(A) segment at the apparent middle of the structure. The third shaped molecule, mainly seen after snap-back treatment, possesses a small fold-back structure at one end only. It is suggested that the small and large fold-backs or loops of the molecule represent the 5'- and 3'-terminal hairpin structures, respectively. Two distinct sizes of molecule, small and large, irrespective of molecule shape, were observed.