Small nuclear RNA variants of three Bombyx mori strains

The spliceosome is a high molecular weight cellular complex responsible for the removal of non-protein coding introns from pre-mRNA to form mature mRNA transcripts. It comprises five major uridine (U)-rich small nuclear (sn)RNAs, to which a number of proteins bind and interact. Variant snRNAs have been identified in several organisms, although it remains to be seen whether or not these isoforms have distinct cellular roles. Nevertheless, many of these sequences have spatio-temporal trends in expression, suggesting that the variant snRNAs are not functionally equivalent. In this report, we examine and contrast the available data on snRNAs in two strains of Bombyx mori: European 703 and Nistari from India. In addition, the genomic snRNA sequences from the p50T strain are described. Thus far, isoforms of U1, U2, U4 and U6 have been characterized in B. mori European 703 and/or Nistari strains using expression libraries. In this study, an in silico approach was used to identify the genomic counterparts of the U snRNA variants in the 6X Whole Genome Shotgun (WGS) of the B. mori p50T strain. The present study is the first comparison of snRNAs in different B. mori strains. Overall, we found that 46 full length U snRNA loci and 76 suspected truncated genes are present in the B. mori genome of the p50T strain. A total of 14 full length genes match previously identified snRNAs in either the Nistari and/or the European 703 strains. Multiple sequence alignments of upstream controlling elements revealed conserved boxes in a subset of U snRNA genes. The presence of divergent promoters within specific snRNA 5′-flanking sequences suggests that these loci may be transcribed from different controlling elements or are not expressed. The number of nucleotide differences within a given type of U snRNA is strongly correlated with its copy number in the genome (r2 = 77.8%) and it may reflect a relaxation of selection pressure on genes of higher copy number. The multiplicity in gene copy may provide for numerous, full length snRNA loci with variable sequences that adopt unique roles in pre-mRNA splicing, possibly by modulating protein-RNA and/or RNA-RNA interactions and in doing so affecting gene expression and development. © 2008 The Authors.

Duke Scholars

Author Jason Andrew Somarelli Medicine, Medical Oncology