A diversity of U1 small nuclear RNAs in the silk moth Bombyx mori.

Variants of U1 small nuclear RNAs (snRNAs) have been previously detected in a permanent cell line (BmN) of the silk moth Bombyx mori. In this study, the existence of U1 snRNA isoforms in the silk gland (SG) of the organism is investigated. The polyploidy (approximately 200,000X the 2N somatic value) state of the B. mori silk gland cells represents a unique system to explore the potential presence and differential expression of multiple U1 variants in a normal tissue. B. mori U1-specific RT-PCR libraries from the silk gland were generated and five U1 isoforms were isolated and characterized. Nucleotide differences, structural alterations, as well as protein and RNA interaction sites were examined in these variants and compared to the previously reported isoforms from the transformed BmN cell line. In all these SG U1 variants, variant sites and inter-species differences are located in moderately conserved regions. Substitutional or compensatory changes were found in the double stranded areas and clustered in moderately conserved regions. Some of the changes generate stronger base pairing. Calculated free energy (DeltaG) values for the entire U1 snRNA secondary structures and for the individual stem/loops (I, II, III and IV) domains of the isoforms were generated and compared to determine their structural stability. Using phylogenetic analysis, an evolutionary parallelism is observed between the polymorphic sites in B. mori and variant locations found among animal and plant species.

Multiple forms of U2 snRNA coexist in the silk moth Bombyx mori.

Eight U2 snRNA variants were isolated from several Bombyx mori U2-specific RT-PCR libraries. U2 sequences and secondary structures were generated and examined in terms of potential RNA and protein interactions. Analysis indicated that nucleotide changes occurred in both stem/loop and single-stranded areas. Changes in the double stranded areas were either compensatory, single substitutions (e.g. C <--> U) or prevented the double-stranded formation of one or two base pairs. The polymorphisms were clustered in moderately conserved regions. Some of the changes observed generated stronger base pairing. Inter-species conserved protein or RNA-binding sites were relatively unaffected. No polymorphic sites were found in known functional sequences. Bombyx mori and Drosophila melanogaster U2 sequences are 95% and 70% similar at the 5'- and the 3'-ends of the molecule, respectively. Phylogenetic analysis of the U2 sequences demonstrates remarkable conservation across species.

An Alu insertion polymorphism in a baboon hybrid zone.

A novel polymerase chain reaction (PCR) primer pair was used to analyze the frequency of insertion of the first described, nonhuman, baboon-specific Alu repetitive element in populations from the Papio hamadryas anubis and the Papio hamadryas hamadryas subspecies, and from a number of anubis-hamadryas hybrids. The Alu insertion is found in intron 7 of the baboon lipoprotein lipase (LPL) gene. Each of the populations had different frequencies for the insertion, and the hybrids examined had a frequency intermediate to that of the parental populations. All hybrids and all P. h. anubis groups except the group of anubis sampled in 1973 exhibited higher-than-expected heterozygosity, while P. h. hamadryas and 1973 P. h. anubis showed lower-than-expected heterozygosity, supporting behavioral and other genetic observations of greater anubis outbreeding relative to hamadryas. This may include asymmetric introgression of the Alu insertion from hamadryas to the anubis population due to hybridization.

Effects of Alu insertions on gene function.

Alu elements are a family of short interspersed repetitive elements (SINEs) found exclusively in primates. These elements are around 300 base pairs long, are found in excess of one million copies per diploid genome, and are dispersed throughout the human genome. Alu elements are scattered by a mechanism called "retrotransposition". Three independent steps are involved in retrotransposition: transcription of the Alu repetitive element, reverse transcription of the Alu RNA and integration of the Alu cDNA. The fact that Alu elements retrotranspose so readily suggests that they have a myriad of effects on the genome, mostly by inactivating genes or altering their function. These characteristics of Alu repetitive elements point to these repetitive DNA fragments as a major driving force for evolution. In addition, Alu elements are known to adopt diverse functions depending on the context of the surrounding genetic material into which they insert. In this article, we review some of the evidence that demonstrates the functional significance of Alu repeats.