Context dependent mutation biases in the human genome

Download
index.pdf
2017
Alıcı, Ahmet Yetkin
Show full item record
257
views
105
downloads
Different types of mutations occur and spread in the genome at varying rates. For instance, C->T transitions at CpG sites are the most frequent mutation in mammalian genomes. In contrast, GC-biased gene conversion causes A or T->G or C mutations to spread and fix rapidly in populations. Such fixation biases have not yet been investigated taking neighbouring sequence context into account. Using human population genomic data from the 1000 Genomes Project and comparative genomic data from other primates, possible fixation biases in the human genome at the level of quintuplets (5 bp sequences where the middle base is mutated) will be investigated. 
Genomes., Genomics., Human genome., Mutation (Biology).
http://etd.lib.metu.edu.tr/upload/12621301/index.pdf
https://hdl.handle.net/11511/26653
Graduate School of Natural and Applied Sciences, Thesis

Suggestions

Evaluating the effects of rescaling parameters in large-scale genomic simulations
Kıratlı, Ozan; Birand Özsoy, Ayşegül Ceren; Department of Biology (2016)
Computer simulations are widely used in many subdisciplines of biological sciences, which evolutionary biology. Large-scale genomic simulations, where several kb (kilo base) to several Mb (megabase) genomes are modeled, are being increasingly used. These simulations require high computing power. There are some methods proposed in the literature to decrease the time and memory demand of these simulations. This study is concentrated on one of those methods, where both the number of generation, and the number ...
PCR cloning and heterologous expression of Scytalidium thermophilum laccase gene in Aspergillus sojae
Koçlar, Gülden; Ögel, Zümrüt Begüm; Department of Biotechnology (2005)
In this study, Scytalidium thermophilum laccase gene was first cloned into E. coli and then heterologously expressed in A. sojae. S. thermophilum is a thermophilic fungus with an important role in determining selectivity of compost produced for growing Agaricus bisporus. S. thermophilum laccase gene was first cloned by Novo Nordisk Bio Tech, Inc. in 1998. This laccase gene (lccS) has an open reading frame of 2092bp. It is composed of five exons punctuated by four small introns. The coding region, excluding ...
Novel BRCA2 pathogenic genotype and breast cancer phenotype discordance in monozygotic triplets
Duzkale, Neslihan; EYERCİ, NİLNUR; Oksuzoglu, Berna; Teker, Taner; Kandemir, Olcay (Elsevier BV, 2020-04-01)
BRCA1/2 genes with high-penetrance are tumor suppressor and tumor susceptibility genes that play important roles in the homologous recombination mechanism in DNA repair and increase breast cancer risk. Variants in BRCA1 or BRCA2 are the main causes of familial and early-onset breast cancer. This study investigated pathogenic variant belonging to the BRCA2 gene splice region in monozygotic triplets. A 44-year-old woman was diagnosed with breast cancer when she was 32 years old. Her monozygotic sister had a h...
Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A center dot A base pairing and a putative structure of the coralyne-induced homo-adenine duplex
Joung, In Suk; Persil Çetinkol, Özgül; HUD, Nicholas V.; Cheatham, Thomas E. (Oxford University Press (OUP), 2009-12-01)
Coralyne is an alkaloid drug that binds homo-adenine DNA (and RNA) oligonucleotides more tightly than it does Watson-Crick DNA. Hud's laboratory has shown that poly(dA) in the presence of coralyne forms an anti-parallel duplex, however attempts to determine the structure by NMR spectroscopy and X-ray crystallography have been unsuccessful. Assuming adenine-adenine hydrogen bonding between the two poly(dA) strands, we constructed 40 hypothetical homo-(dA) anti-parallel duplexes and docked coralyne into the s...
Functional characterization of microrna-125b expression in MCF7 breast cancer cell line
Tuna, Serkan; Erson Bensan, Ayşe Elif; Department of Biology (2010)
microRNA dependent gene expression regulation has roles in diverse processes such as differentiation, proliferation and apoptosis. Therefore, deregulated miRNA expression has functional importance for various diseases, including cancer. miR-125b is among the commonly downregulated miRNAs in breast cancer cells . Therefore we aimed to characterize the effects of miR-125b expression in MCF7 breast cancer cell line (BCCL) to better understand its roles in tumorigenesis. Here, we investigated mir-125 family mem...
Citation Formats
A. Y. Alıcı, “Context dependent mutation biases in the human genome,” M.S. - Master of Science, Middle East Technical University, 2017.
METU IIS - Integrated Information Service open@metu.edu.tr