Noncoding Y RNAs have been discovered in most vertebrates, and their homologs or similar molecules have also been discovered in other organisms. They have a typical secondary structure consisting of stems and loops and interact with many different proteins, mainly Ro60 and La. Although not all of their functions are known, they have been shown to play a role in the initiation of chromosomal DNA replication and, in a complex with Ro60, in the binding and degradation of misfolded RNAs. In the experimental part of the thesis, we incorporated the genes for all four human Y RNAs (hY1, hY3, hY4 and hY5) into the vector pcDNA3.1-U6 for expression in mammalian cells by in vivo assembly cloning (IVA cloning). The second part of the thesis is phylogenetic analyses of Y RNAs from different organisms and comparisons with mammalian relationships. We found that the sequences of RNY1 and RNY3 from different organisms are very similar, whereas the sequences of RNY4 and RNY5 are more different. In the phylogenetic analysis of human Y RNAs, we found that they most likely arose by gene duplications. First, the hY4 gene was duplicated to give rise to hY1, which also duplicated to give rise to the genes for hY3 and hY5. We found six different Y RNA sequences from rhesus macaque (Macaca mulatta) in which further gene duplication most likely occurred. Through phylogenetic analysis of the four Y RNA genes from different organisms, we found that the phylogeny of Y RNAs is not completely consistent with mammalian relationships. The sequences of Y RNAs were perhaps not the most appropriate choice for such analyses because they are short and very similar to each other. In addition, we had a very unbalanced set of sequences from different organisms (most of them were primate sequences that were mostly identical).
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