Identification of RNA editing in the human exome and development of DARNED DatabaseSF

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dc.check.date10000-01-01
dc.check.embargoformatBoth hard copy thesis and e-thesisen
dc.check.entireThesisEntire Thesis Restricted
dc.check.infoIndefiniteen
dc.check.opt-outNoen
dc.check.reasonThis thesis is due for publication or the author is actively seeking to publish this materialen
dc.contributor.advisorBaranov, Pavel V.en
dc.contributor.authorKiran, Anmol M.
dc.contributor.funderWellcome Trust, United Kingdomen
dc.contributor.funderScience Foundation Irelanden
dc.date.accessioned2014-06-11T11:53:52Z
dc.date.issued2014
dc.date.submitted2014
dc.description.abstractRNA editing is a biological phenomena that alters nascent RNA transcripts by insertion, deletion and/or substitution of one or a few nucleotides. It is ubiquitous in all kingdoms of life and in viruses. The predominant editing event in organisms with a developed central nervous system is Adenosine to Inosine deamination. Inosine is recognized as Guanosine by the translational machinery and reverse-transcriptase. In primates, RNA editing occurs frequently in transcripts from repetitive regions of the genome. In humans, more than 500,000 editing instances have been identified, by applying computational pipelines on available ESTs and high-throughput sequencing data, and by using chemical methods. However, the functions of only a small number of cases have been studied thoroughly. RNA editing instances have been found to have roles in peptide variants synthesis by non-synonymous codon substitutions, transcript variants by alterations in splicing sites and gene silencing by miRNAs sequence modifications. We established the Database of RNA EDiting (DARNED) to accommo-date the reference genomic coordinates of substitution editing in human, mouse and fly transcripts from published literatures, with additional information on edited genomic coordinates collected from various databases e.g. UCSC, NCBI. DARNED contains mostly Adenosine to Inosine editing and allows searches based on genomic region, gene ID, and user provided sequence. The Database is accessible at http://darned.ucc.ie RNA editing instances in coding region are likely to result in recoding in protein synthesis. This encouraged me to focus my research on the occurrences of RNA editing specific CDS and non-Alu exonic regions. By applying various filters on discrepancies between available ESTs and their corresponding reference genomic sequences, putative RNA editing candidates were identified. High-throughput sequencing was used to validate these candidates. All predicted coordinates appeared to be either SNPs or unedited.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Version
dc.format.mimetypeapplication/pdfen
dc.identifier.citationKiran, A. 2014. Identification of RNA editing in the human exome and development of DARNED DatabaseSF. PhD Thesis, University College Cork.en
dc.identifier.urihttps://hdl.handle.net/10468/1574
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.urihttp://darned.ucc.ie
dc.rights© 2014, Anmol Kiran.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/en
dc.subjectApoBen
dc.subjectDARNEDen
dc.subjectExomeen
dc.subjectHigh-throughput sequencingen
dc.subjectRNA editingen
dc.thesis.opt-outfalse
dc.titleIdentification of RNA editing in the human exome and development of DARNED DatabaseSFen
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD (Science)en
ucc.workflow.supervisorp.baranov@ucc.ie
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