Alzheimer’s Disease (AD) is one of the most common forms of dementia and a major cause of disability and dependency in older patients worldwide.Although there has been a lot of research done in the field of gene expression and possible drivers of AD, there has not been enough investigation into transcription start site and alternative promoter usage of AD. With relatively small genomes, species have evolved mechanisms for diversifying their transcriptome, which is the set of messenger mRNA transcripts produced in a given cell. While the most well-known mechanism of diversification is alternative splicing, another mechanism that has been less explored is alternative promoter (AP) usage, which generates different transcripts by selecting different transcription start sites (TSSs) upstream of a gene. More importantly, AP usage can bring about different coding sequences, which can in some cases lead to changes within the N-termini of the cognate proteins. Alternative promoter usage has the potential to regulate processes like alternative splicing, tissue specificity, regional specificity and subcellular specificity of gene expression and gene activation during development. In this study a customized pipeline for STRIPE-seq generated data was applied to AD and control data set and the first AD promoter atlas was generated. This atlas was used to generate list of genes with differentially used TSRs and biological pathways they are involved in. Finally, a consensus cluster set was created to investigate alternative promoter usage in AD patients and alternative promoter usage was shown in Alzheimer’s Disease related genes such as APOE and MAPT.

Regulation of transcription initiation is a critical factor in the emergence of diverse biological phenotypes, including the development of multiple cell types from a single genotype, the ability of organisms to respond to environmental cues, and the rise of heritable diseases. Transcription initiation is regulated in large part by promoter regions of DNA. The identification and characterization of cis-regulatory regions, and understanding how these sequences differ across species, is a question of interest in evolution. To address this topic, I used the model organism Daphnia pulex, a well-characterized microcrustacean with an annotated genome sequence and selected a distribution of well-defined populations geographically located throughout the Midwestern US, Oregon, and Canada. Using isolated total RNA from adult, female Daphnia originating from the selected populations as well as a related taxon, Daphnia pulicaria (200,000 years diverged from D. pulex), I identified an average of over 14,000 (n=14,471) promoter regions using a novel transcription start site (TSS) profiling method, STRIPE-seq. Through the identification of sequence architecture, promoter class, conservation, and transcription start region (TSR) width, of cis-regulatory regions across the aforementioned Daphnia populations, I constructed a system for the study of promoter evolution, enabling a robust interpretation of promoter evolution in the context of the population-genetic environment. The methodology presented, coupled with the generated dataset, provides a foundation for the study of the evolution of promoters across both species and populations.