Characterization of long noncoding RNAs in vertebrate brain development and evolution

• Main Author: Chodroff, Rebecca A.
• Published: University of Oxford 2011
• Subjects: 572.5
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.558292

Background: Long considered to be the building block of life, it is now apparent that protein is only one of many functional products generated by the eukaryotic genome. Indeed, more of the mammalian genome is transcribed into noncoding than into protein-coding sequence. This extensive and interleaved network of noncoding transcripts partially emerges from evolutionarily conserved genomic sequence, emphasizing its potential biological relevance. Nevertheless, the biological function of the vast majority of eutherian long intergenic noncoding RNAs (lincRNAs) has not been experimentally validated and the relationship between evolutionary sequence constraint and the role of non coding transcribed sequence remains unclear. To clarify the implications of evolutionary sequence conservation for biological function of lincRNAs, this thesis aims to (l) determine whether evolutionary sequence conservation is more often directed towards particular regions involved in the transcription of lincRNA loci, such as promoter and/or intron-exon boundaries; (2) identify and characterise the tissue expression patterns of lincRNA orthologs across diverse amniotes, ranging from mouse to chicken; and (3) describe the biological functions (if any) of four highly conserved brain-expressed lincRNAs. Results: Here, we performed a multi-disciplinary study of four highly conserved and brain-expressed transcripts selected from a list of mouse long intergenic noncoding RNA (lincRNA) loci that generally show pronounced evolutionary constraint within their putative promoter regions and across exon-intron boundaries. We identified some of the first lincRNA orthologs present in birds (chicken), marsupial (opossum) and eutherian mammals (mouse), and investigated whether they exhibit conservation of brain expression. In contrast to conventional protein-coding genes, the sequences, transcriptional start sites, exon structures and lengths for these noncoding genes are all highly variable. In a series of preliminary experiments, we found that these lincRNAs do not significantly contribute to global transcriptional regulation within a mouse cell line. Furthermore, a transgenic mouse model with a targeted deletion of one of these lincRNAs did not present a noticeable phenotype, suggesting that this lincRNA is not critical for survival. Conclusions: We identified four lincRNAs with evolutionary conservation in ex on structure and transcription, and similarities in brain expression pattern during embryonic and early postnatal stages across diverse amniotes. While tissue-specific expression patterns and evolutionary sequence constraint are suggestive of function, preliminary experiments investigating each transcripts' role did not provide significant proof for biological function. Nevertheless, the high levels of evolutionary sequence conservation and specific brain expression patterns among these four lincRNAs warrant further experimental inquiry.