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200823270 Summary 3 Genomic Noise 1. Calculate how many times a sequence looking like a promoter with the specific sequence TATAT would appear randomly in a genome that is 3.3 billion base pairs long. Assume equal abundance of each nucleotide. There are 4 possible nucleotides within the genome having equal abundance, each of them having a 1/4 th probability of occurring randomly in any location within the genome. TATAT is a 5-base sequence, if it were to occur randomly within the nucleotide it has to be independent. If the genome is 3.3 million base pairs long, you will first multiply the probabilities together, it being 1/1024. Then multiply it with 3.3 million base pairs with the probability of the sequence resulting in 3,222,656.25. This results that the TATAT sequence would occur 3,222,656 times over the entire genome. This is an estimated amount of the sequence occurring within the genome including random insertions. (Ozbudak et al) 2. Would the number of sequences similar to a promoter be higher or lower if we allowed for some noise (variation) in the TATAT sequence? Promoters would be higher if there's noise in the TATAT sequence. This is because the chances for an insertion of a nucleotide at a certain part in a genome can be recognized by a promoter thus allowing for proteins to bind more and increasing the chances higher than ¼. Even with T/ A being interchangeable you can still get similar products. 3. Do you think that it is possible for false promoters* to be found in the human genome? (*Segments that would bind RNA polymerase but not be associated with genes.) Yes, it's possible for false promoters to occur in the human genome connecting to question 1&2 for the TATAT sequence occurring in the genome is common. It is typical for a promoter region to randomly occur in a non-coding region of DNA as this is what results in genomic noise. Promoter regions are also led to be recognized through transcription factors like RNA polymerase. Which helps in binding promoters. Since they don’t take over as a product of genomic noise and don’t have connections with functional genes, they don’t need to perform any extra activity. (Ozbudak et al) SNP s and Copy Number Variation 1. For a while the focus of human genome projects was to find Single Nucleotide Polymorphisms (SNP’S), what are these, and how do they compare to large genome insertions and deletions? SNPs are known as single nucleotide polymorphism that can vary in DNA sequences, it helps with single nucleotide substitutions like A, T, C, and G. This compares to large genome insertions and deletions as

they both contribute a lot towards genetic diversity. Studying these variations allows us to comprehend its role in health and disease. There are also many advances for genomic technologies, for example “next- generation sequencing” you're able to identify SNP’s and structural variations. (Nature publishing group) 2. In genetics terms, what's the difference between a Mendelian disease and that scientists are trying to find using Genome Wide Association Studies (GWAS)? Mendelian diseases are disorders that follow Mendelian inheritance patterns. This disease can be caused by mutations in a single gene. If one were to inherit the disease it can be predicted within the Mendelian principles since they're able to have a direct impact on phenotype. GWAS (Genome wide association studies) is used to identify specific genetic variants that’s linked with traits or diseases that don’t follow the mendelian principles. GWAS examines larger numbers of genetic markers to identify connections between a specific genetic trait and disease like diabetes, heart disease and psychological disorders. Key differences would be for Mendelian disease is that they are focusing on single genes that are responsible for inheritance (I.e. color blindness) Its more prevalent in men than women due to the sickle cell of one allele, or even with cystic fibrosis you need to two alleles to be sick. If it was GWAS it pinpoints genes that are related to a specific sickness within a population. (Shah et al) 3. How does Copy Number Variation happen? Why would they happen? CNV’s known as copy number variations are utilized for deletion/ duplication for larger portions of DNA. They're able to affect non-coding and coding regions. Their role is to help with genetic diversity and play a key role in phenotypic variation. Thus, can occur through NAHR (non-allelic homologous recombination) DNA sequences. Misalignment and recombination within DNA sequences is what allows for deletions and duplication to start. CNV’s can occur due to environmental factors such as exposure to radiation and increasing chances for DNA damage. With CNV’s can also implicate genetic disorders and intellectual disabilities. (Copy number variation) References Copy number variation (CNV) . Genome.gov. (n.d.). https://www.genome.gov/genetics-glossary/Copy- Number-Variation Shah, S., Henry, A., Roselli, C., Lin, H., Sveinbjörnsson, G., Fatemifar, G., Hedman, Å. K., Wilk, J. B., Morley, M. P., Chaffin, M. D., Helgadottir, A., Verweij, N., Dehghan, A., Almgren, P., Andersson, C., Aragam, K. G., Ärnlöv, J., Backman, J. D., Biggs, M. L., … Lumbers, R. T. (2020, January 9). Genome- wide association and mendelian randomisation analysis provide insights into the pathogenesis of heart failure . Nature News. https://www.nature.com/articles/s41467-019-13690-5 Nature Publishing Group. (n.d.). Nature news. https://www.nature.com/scitable/topicpage/using-snp- data-to-examine-human-phenotypic-706/

Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D., & van Oudenaarden, A. (2002, April 22). Regulation of noise in the expression of a single gene . Nature News. https://www.nature.com/articles/ng869z

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