Characterization of the mechanisms of HERV-K (HML-2) transcription during human mammary epithelial cell transformation
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 t... read moreo this 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
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