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Bioinformatic Methods for Identification of de novo TSM Mutations and Analysis of Ribosomal RNA Gene Variation

Show simple item record 2023-03-06T07:11:08Z 2023-03-06T07:11:08Z 2023-03-06
dc.title Bioinformatic Methods for Identification of de novo TSM Mutations and Analysis of Ribosomal RNA Gene Variation en
ethesis.faculty Bio- ja ympäristötieteellinen tiedekunta fi
ethesis.faculty Faculty of Biological and Environmental Sciences en
ethesis.faculty Bio- och miljövetenskapliga fakulteten sv
ethesis.faculty.URI Helsingin yliopisto fi University of Helsinki en Helsingfors universitet sv
dct.creator Dong, Junru
dct.issued 2022
dct.abstract Formation of template switching mutation has previously been proposed as a mechanism of RNA evolution. TSM mechanism may contribute to the creation, maintenance, and modification of the RNA Hairpin. The finding of de novo TSM in RNA sequences will provide evidence for this hypothesis. Ribosomal RNAs (rRNAs) appear in multicopy clusters on different chromosomes and evolve through concerted evolution. To study the properties of de novo TSM and the dynamics of the concerted evolution of rRNA, we developed a computational tool to analyze pairwise differences and the phylogenetic relationship of rRNA genes on different chromosomes. The genome assemblies that are based on traditional short-read sequencing methods have limitations on studying long tandem repeat rDNA, because the reading length is shorter than on the rRNA gene. To overcome this limitation. PacBio Hifi long-read sequencing data for human rRNA 18S and 28S genes were studied. By analyzing the diversity of rRNA genes between individuals and families, single nucleotide mutations, multiple nucleotide insertions, and deletions were identified. As expected, genetic variations in ribosomal genes were detected both within and between individuals. A larger sample size may be required for TSM identification. The finding of this research that related to the dynamics and concerted evolution of human rRNA may contribute to a better understanding of rRNA mutation-related genetic disorders. en
dct.subject Ribosomal RNA
dct.subject Template Switching Mutations
dct.subject Python Pipeline
ethesis.language englanti fi
ethesis.language English en
ethesis.language engelska sv
ethesis.supervisor Dr. Heli A.M. Mönttinen and Dr. Ari Löytynoja und
ethesis.thesistype pro gradu -tutkielmat fi
ethesis.thesistype master's thesis en
ethesis.thesistype pro gradu-avhandlingar sv
dct.identifier.ethesis E-thesisID:6793dc4b-804b-4f77-b05e-b0544065bd34
ethesis-internal.timestamp.reviewStep 2022-12-27 06:44:51:130
ethesis.principalprofessor Pia Siljander und
dct.identifier.urn URN:NBN:fi:hulib-202303061443
ethesis.facultystudyline Molecular and Analytical Health Biosciences fi
ethesis.facultystudyline Molecular and Analytical Health Biosciences en
ethesis.facultystudyline Molecular and Analytical Health Biosciences sv
ethesis.mastersdegreeprogram Genetiikan ja molekulaaristen biotieteiden maisteriohjelma fi
ethesis.mastersdegreeprogram Master's Programme in Genetics and Molecular Biosciences en
ethesis.mastersdegreeprogram Magisterprogrammet i genetik och molekylära biovetenskaper sv

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