RNomics: Exploring the World of Non-Protein Coding (npc) RNAs

With experimental high-throughput cDNA library screening and biocomputational methods we identify and characterize novel npcRNAs from diverse model organisms. In contrast to mRNAs, which are templates for translating proteins, npcRNAs exhibit various functions in different compartments and developmental stages of the cell. Small nucleolar RNAs (snoRNAs), one of the largest classes of npcRNAs, guide post-transcriptional modifications of other RNAs that are crucial for appropriate RNA folding as well as for RNA-RNA and RNA-protein interactions. Detailed comparisons of paralog snoRNAs revealed, in addition to trans-duplication, a novel, cis-duplication distribution strategy with insertions near to the original loci. Some snoRNAs coevolved with their modification target sites, demonstrating the close interaction of complementary regions. Some target sites modified by snoRNAs are changed, added or lost, documenting a high degree of evolutionary plasticity of npcRNAs. The evolutionary history of npcRNAs in mammalian species is one of our main subjects to explore the world of RNomics.

Phylogenomics: Retroposed Elements as Archives for Evolutionary History

Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods as well as directional mutation pressure can produce molecular homoplasies, similar characteristics lacking common ancestors. Retroposed elements, by contrast, integrate randomly into genomes with negligible probabilities of the same element integrating independently into orthologous positions in different species. Thus, presence/absence analyses of these elements are a superior strategy for molecular systematics.

Functional Genomics: Retroposons - En Route to Protein-Coding Function

Exonization is defined as the creation of a new exon in response to changes in untranslated regions of a gene. Insertions of transposed elements are frequent flash points and substrates for exonizations. Exonized sequences of transposed elements are cotranscribed via alternative splicing and provide a potential source for novel genetic material.

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