Conservation and synteny of long non-coding RNAs invertebrate genomes and their identification in novel transcriptomes

Basu, Swaraj (2014). Conservation and synteny of long non-coding RNAs invertebrate genomes and their identification in novel transcriptomes. PhD thesis The Open University.

DOI: https://doi.org/10.21954/ou.ro.0000d5bd

Abstract

Long non-coding RNAs (IncRNAs) are a biological entity defined by what they are not, rather than by what they are. This indicates that our knowledge about them is sensibly limited. The aim of my PhD is to gain insights into the evolution and the functions of IncRNAs through computational approaches and the usage of large scale functional genomics dataset. I developed an annotation pipeline, which can effectively identify IncRNAs in entire transcriptomes. The pipeline is able to accurately annotate the coding genes while predicting a conservative estimate of the IncRNA population. It allowed me to show, for the first time, the presence of lncRNA transcription in a diverse range of organisms. Further, I analysed sequence and positional conservation of lncRNAs, demonstrating the presence of short segments of conserved sequence in IncRNAs and the existence of several syntenically conserved non-coding transcripts over large evolutionary distances. However, I also demonstrate that positional conservation of lncRNAs with a flanking coding gene is generally independent from the conservation of the lncRNA expression with respect to the coding gene. Finally, I have characterised the diversity of lncRNA transcription in specific cells and developmental stages of two teleost fishes. In summary, the work presented in the thesis provides novel findings and contributions in the field of lncRNAomics.

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