Characterization of polymorphic HERV-K (HML-2) endogenous proviruses in human and gorilla genomes.
Freeman, Michael.
2019
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The HERV-K (HML-2)
endogenous retrovirus (ERV) family is the most recently active group of ERVs in humans,
being the only group with human-specific insertions. Some of the human-specific HERV-K
(HML-2) proviruses have retained one or more viral open reading frames (ORFs) and have
remained insertionally polymorphic in the human population, hinting at recent activity
in our lineage. Furthermore, ... read morethere is a strong correlation between HML-2 expression and
cancerous and inflammatory disease states. Though no naturally infectious HML-2
proviruses are known, there is the possibility that some undiscovered HML-2 proviruses
may still be active in the human population. Our group used publicly available human
genomic data from diverse populations in an effort to data-mine for these
uncharacterized, insertionally polymorphic HML-2 elements. This search resulted in the
discovery four non-reference HML-2 alleles that were carried at a very low frequency
within our population. One of these four alleles, Xq21.33, contained an ORF for every
viral gene, making it the second known example of a full-length endogenous HML-2
provirus. We investigated the function of this full-length provirus and found that it
retained some of the functions necessary for viral replication. Namely, the LTRs were
active promoters, the provirus could splice the three requisite viral transcripts, and
the provirus could produce retroviral-like particles and encapsidate the genomic viral
RNA. Unfortunately, the internal gag, pol, and env sequences of this provirus were found
to contain deleterious mutations that render Xq21.33 not infectious. Targeted reversion
of these substitutions revealed that only 6 point mutations distinguish Xq21.33 from a
replication-competent provirus, indicating that these elements may be closer to viable
than we expect. After data-mining over 2500 individual genomes, we were unable to
identify a viable HML-2 provirus in the human population. Since the HML-2 family is not
restricted to our lineage, we expanded the search to our close hominin relative, the
gorilla. Using a combination of the junction discovery method and linker-mediated
integration site analysis, we identified 31 novel 2-LTR proviruses in the gorilla
genome. We found that the gorilla-specific HML-2 elements contained many features that
are indicative of a recently active clade of endogenous retroviruses: there is little
divergence within the sequences of the proviruses, the proviruses remain insertionally
polymorphic in the population, and many proviruses encode intact ORFs for viral
proteins. We examined the 31 novel HML-2 elements and determined that the
gorilla-specific proviruses retained much more activity than their human counterparts.
Six gorilla HML-2 loci were found to have a functional, fusogenic envelope glycoprotein,
three loci were found to produce viral particles with an active reverse transcriptase,
and two loci could produce particles that mediated infectious gene transfer. Although no
provirus identified in the human or gorilla screens is expected to produce a replication
competent HML-2 element on its own, we did identify a number of partially functional
gorilla-specific HML-2 proviruses which retained an active envelope or viral core. Some
of these partially infectious HML-2 elements reside in the same gorilla genomes, hinting
at the potential for current replication in the gorilla
population.
Thesis (Ph.D.)--Tufts University, 2019.
Submitted to the Dept. of Biochemistry.
Advisor: John Coffin.
Committee: Jim Baleja, Claire Moore, and James Munro.
Keyword: Virology.read less - ID:
- 6395wm68w
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