Beyond the one-sequence-one-structure dogma : predicting and analysing transient and alternative RNA secondary structures that are evolutionarily conserved
department or school: Science, Faculty of
data provider: DSpace
degree campus: UBCV
creator: Zhu, Jing Yun Alice
issued: 2015-10-23T15:28:12
issued: 2015
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: State-of-the-art methods in RNA secondary structure prediction focus on predicting the final, functional structure. However, ample experimental and statistical evidence indicates that structure formation starts immediately during transcription and this co-transcriptional folding influences the resultant final RNA structure. Thus, identifying the transient structures that are formed co-transcriptionally may bring insight into understanding how co-transcriptional folding leads to the final conformation in vivo. As RNA secondary structures are currently best predicted by comparative approaches, we therefore investigated whether homologous RNA genes not only assume the same final structure, but also share structural features during the co-transcriptional folding in vivo. For this, we compiled a non-redundant data set of 32 transcripts deriving from six different RNA families which constitutes the most comprehensive data set with experimentally confirmed transient and alternative RNA structures so far. We present statistical evidence that homologous RNA genes from related organisms fold co-transcriptionally in a similar way. In particular, we show that some transient structures are highly conserved with levels similar to those of the final, functional structure. Moreover, we find that the predicted co-transcriptional folding pathways of homologous sequences encounter similar transient structure features, which often coincide with known transient features. We thus also predict candidates for these evolutionarily conserved transient features of co-transcriptional folding pathways in silico. We further expand 4 alignments from the aforementioned dataset by searching via covariance model and manual curation in order to share them with the RNA community. These alignments either update the existing Rfam datasets with annotation of transient structures, or introduce new RNA family: (1) Trp operon leader, where alternative structures are coordinated to regulate the operon transc…
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/54739
note: Beyond the one-sequence-one-structure dogma: predicting and analysingtransient and alternative RNA secondary structures that areevolutionarily conservedbyJing Yun Alice ZhuBSc, The University of British Columbia, 2012A THESIS SUBMITTED IN PARTIAL FULFILLMENT OFTHE REQUIREMENTS FOR THE DEGREE OFMASTER OF SCIENCEinTHE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES(Bioinformatics)THE UNIVERSITY OF BRITISH COLUMBIA(Vancouver)August, 2015c© Jing Yun Alice Zhu, 2015AbstractState-of-the-art methods in RNA secondary structure prediction focus on predicting the final, func-tional structure. However, ample experimental and statistical evidence indicates that structure formationstarts immediately during transcription and this co-transcriptional folding influences the resultant finalRNA structure. Thus, identifying the transient structures that are formed co-transcriptionally may bringinsight into understanding how co-transcriptional folding leads to the final conformation in vivo. As RNAsecondary structures are currently best predicted by comparative approaches, we therefore investigatedwhether homologous RNA genes not only assume the same final structure, but also share structural fea-tures during the co-transcriptional folding in vivo. For this, we compiled a non-redundant data set of 32transcripts deriving from six different RNA families which constitutes the most comprehensive data setwith experimentally confirmed transient and alternative RNA structures so far. We present statisticalevidence that homologous RNA genes from related organisms fold co-transcriptionally in a similar way.In particular, we show that some transient structures are highly conserved with levels similar to those ofthe final, functional structure. Moreover, we find that the predicted co-transcriptional folding pathwaysof homologous sequences encounter similar transient structure features, which often coincide with knowntransient features. We thus also predict candidates for these evolutionarily conserv…
has type: Thesis/Dissertation
date issued: 2015-11
is shown at: 10.14288/1.0220703
language: eng
degree discipline: Bioinformatics
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivs 2.5 Canada
rights URI: http://creativecommons.org/licenses/by-nc-nd/2.5/ca/
scholar level: Graduate
type: Text
identifier URI: http://hdl.handle.net/2429/54739