Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections

Badarinarayan, Smitha Srinivasachar; Sauter, Daniel

doi:10.1128/jvi.02299-20

Cited by 46 publications

(34 citation statements)

References 110 publications

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“…HERVs are not only molecular ‘fossils’ of ancient retroviruses but are also functional in host genomes under certain circumstances [ 39 , 40 , 41 ]. One of the functions of HERVs is mediating host genomic recombination, leading to potential genomic rearrangement [ 26 , 42 , 43 ].…”

Section: Resultsmentioning

confidence: 99%

“…Recently, HERVs have been reported to be associated with many human diseases, including cancer and infectious and autoimmune diseases, and the mechanisms underlying the functions of HERVs in these illnesses also vary (e.g., acting as promoters or enhancers to regulate gene expression or encoding peptides that participate in immune regulation) [ 39 , 40 , 56 , 57 , 58 ]. Therefore, it is important to consider HERVs that have the potential to be expressed.…”

Section: Discussionmentioning

confidence: 99%

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Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates

Cui²

2022

Viruses

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Human endogenous retroviruses (HERVs) are viral “fossils” in the human genome that originated from the ancient integration of exogenous retroviruses. Although HERVs have sporadically been reported in nonhuman primate genomes, their deep origination in pan-primates remains to be explored. Hence, based on the in silico genomic mining of full-length HERVs in 49 primates, we performed the largest systematic survey to date of the distribution, phylogeny, and functional predictions of HERVs. Most importantly, we obtained conclusive evidence of nonhuman origin for most contemporary HERVs. We found that various supergroups, including HERVW9, HUERSP, HSERVIII, HERVIPADP, HERVK, and HERVHF, were widely distributed in Strepsirrhini, Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys and apes). We found that numerous HERVHFs are spread by vertical transmission within Catarrhini and one HERVHF was traced in 17 species, indicating its ancient nature. We also discovered that 164 HERVs were likely involved in genomic rearrangement and 107 HERVs were potentially coopted in the form of noncoding RNAs (ncRNAs) in humans. In summary, we provided comprehensive data on the deep origination of modern HERVs in pan-primates.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates

Cui²

2022

Viruses

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“…It did not include some relevant topics, such as solo LTR formation [67] and the currently ongoing ERV invasion in koalas [68]. Of particular interest for future study would be the programme's ability to cope with the shifting status of ERVs from potentially selfish genetic elements [69,70] to crucial contributors to the host's survival and reproduction [71][72][73].…”

Section: Discussionmentioning

confidence: 99%

How Well Does Evolution Explain Endogenous Retroviruses?—A Lakatosian Assessment

Jorritsma

2021

Viruses

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One of the most sophisticated philosophies of science is the methodology of scientific research programmes (MSRP), developed by Imre Lakatos. According to MSRP, scientists are working within so-called research programmes, consisting of a hard core of fixed convictions and a flexible protective belt of auxiliary hypotheses. Anomalies are accommodated by changes to the protective belt that do not affect the hard core. Under MSRP, research programmes are appraised as ‘progressive’ if they successfully predict novel facts but are judged as ‘degenerative’ if they merely offer ad hoc solutions to anomalies. This paper applies these criteria to the evolutionary research programme as it has performed during half a century of ERV research. It describes the early history of the field and the emergence of the endogenization-amplification theory on the origins of retroviral-like sequences. It then discusses various predictions and postdictions that were generated by the programme, regarding orthologous ERVs in different species, the presence of target site duplications and the divergence of long terminal repeats, and appraises how the programme has dealt with data that did not conform to initial expectations. It is concluded that the evolutionary research programme has been progressive with regard to the issues here examined.

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“…Transposable elements (TEs), which occupy half of the human genome, play critical roles as cis-regulatory elements in various human biological processes (Bourque, 2009;Bourque et al, 2018;Chuong et al, 2017). Notably, a particular subclass of TEs, Endogenous Retroviruses (ERVs), are derived from ancient retrovirus, suggesting a potential association with infection and immunity (Buttler and Chuong, 2021;Kassiotis and Stoye, 2016;Srinivasachar Badarinarayan and Sauter, 2021). Confirming this, an ERV family, MER41, was found to be co-opted as cisregulatory elements in the primate innate immune response (Bogdan et al, 2020;Chuong et al, 2016).…”

Section: Introductionmentioning

confidence: 89%

Transposable elements are associated with the variable response to influenza infection

Chen

Pacis

Aracena

et al. 2022

Preprint

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SUMMARYInfluenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Given that transposable elements (TEs) contribute to the activation of innate immunity, we wanted to explore their potential role in this variability. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using ATAC-seq we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators in stably enriched TE families and with other factors in variable families, including KRAB-ZNFs. We also observed a strong association between basal TE transcripts and viral load post infection. Finally, we built a predictive model suggesting that TEs, and host factors regulating TEs, contribute to the variable response to infection.

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Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections

Cited by 46 publications

References 110 publications

Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates

Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates

How Well Does Evolution Explain Endogenous Retroviruses?—A Lakatosian Assessment

Transposable elements are associated with the variable response to influenza infection

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