Marín Maldonado, Frances M.

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    Comparative genomics of indels in primate lineages and the possible effect of the MET promoter indel on gene expression
    (2016) Marín Maldonado, Frances M.; Martínez Cruzado, Juan C.; College of Arts and Sciences - Sciences; Diffoot Carlo, Nanette; Oleksyk, Taras K.; Rodríguez Minguela, Carlos; Department of Biology; Carrasquillo, Arnaldo
    Approximately six million years ago, the human and chimpanzee lineages diverged from a common ancestor resulting in two distinct species with a great number of different morphological, behavioral, cognitive and other phenotypic traits. However, their genomes are more than 98.5% identical at protein-coding loci, and genomic differences between these two species hover around 2.4%, excluding repeats and low complexity DNA and including insertions and deletions (indels). It is believed that most of the genetic foundation for the differences among these two lineages lies at the level of gene regulation. Our work focused on lineagespecific large (> 10 bp) indels located in promoter regions that may affect gene expression and protein product levels. Our goal was to validate indels, in order to differentiate real features from computational artifacts. We started by identifying 64 indels, through the alignment of orthologous regions of human, chimpanzee, gorilla, orangutan and macaque (in-silico analysis), located at the 5’ side of the gene and at distance no more than 2 kb away from its nearest gene transcription start site. To validate the indels, PCR and electrophoresis (in-vitro) analysis was performed with all of them. We found two distinct indels, which were unique to the human lineage, in genes associated with neurodevelopment and the female-sexual development, MET and DMRTA2. Since previous studies suggest that most of the differences that exist between humans and chimpanzees are in areas related to the cognitive ability and fertility, our results could indicate that the derived variants observed in the human lineage might be important for processes that make the humans distinct to the other hominids. Moreover, given that most of the divergences that exist between humans and chimpanzees are due to differential gene expression, the promoters described herein could serve as models for in-vitro gene expression assays for evaluating how these fixed indels may affect gene expression in both species.