Characterization of the mechanisms of HERV-K (HML-2) transcription during human mammary epithelial cell transformation
Montesion, Meagan.
2017
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Abstract: Increasing evidence suggests that repetitive elements may play a role in host gene regulation, particularly through the donation of alternative promoters, enhancers, splice sites, and termination signals. Elevated transcript expression of the endogenous retrovirus group HERV-K (HML-2) is seen in many human cancers, although the identity of the individual proviral loci contributing to thi... read mores expression as well as their mechanism(s) of activation is unclear. Using a combination of reporter construct assays and RNA sequencing results, we characterized the HML-2 transcriptome and means of transcription in an in vitro model of human mammary epithelial cell transformation. RNA-Seq analysis showed transcription occurring through four different modes, with the majority of expression being in antisense orientation and from proviruses integrated within introns. Although we found two instances of LTR-driven provirus transcription, there was no evidence to suggest that these active 5' LTRs were influencing nearby host gene expression in the cell lines tested. Importantly, LTR-driven transcription was restricted to tumorigenic cells, suggesting that LTR promoter activity is dependent upon the transcriptional environment of a malignant cell. Using a transcription factor binding site prediction algorithm, we identified two unique binding sites on each 5' LTR of two highly active proviruses (3q12.3 and 11p15.4) that appear to be associated with inducing promoter activity during neoplasia. Genomic analyses of the homologous proviruses in several non-human primate species indicate genetic drift in two of the binding sites, away from the ancestral sequence and towards the active form. Based on the sequences of 2,504 individuals from the 1000 Genomes Project, one of these sites is polymorphic in the human population, with an allele frequency of 51%. These data suggest that cell-specific transcription factors at least partly contribute to LTR promoter activity during transformation and that transcription factor binding site polymorphisms may be responsible for the differential HML-2 activity often seen between individuals. These findings may provide implications for future studies investigating HML-2 as a target for immunotherapy or as a biomarker for disease.
Thesis (Ph.D.)--Tufts University, 2017.
Submitted to the Dept. of Genetics.
Advisor: John Coffin.
Committee: Naomi Rosenberg, Philip Hinds, and Charlotte Kuperwasser.
Keywords: Genetics, Virology, and Microbiology.read less - ID:
- fj236d75r
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