Novel Denisovan and Neanderthal Retroviruses

Lee, Adam F.; Huntley, Derek; Aiewsakun, Pakorn; Kanda, Ravinder K.; Lynn, Claire; Tristem, Michael

doi:10.1128/jvi.01825-14

Cited by 20 publications

(17 citation statements)

References 9 publications

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“…Eight of our validated loci have been recently reported in the genomes of two sequenced archaic samples (42,51) in addition to modern humans (12). We confirmed an additional three reported "archaic" sites in our data [19p12e and 10q24.2b, respectively: "De11" and "De12" in the study by Agoni et al (42); 19q13.43: "Ne5" in the study by Lee et al (51)], but found no evidence of the remaining eight reported archaic events.…”

Section: Discussionmentioning

confidence: 99%

Discovery of unfixed endogenous retrovirus insertions in diverse human populations

Wildschutte

Williams

Montesion

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

230

304

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Endogenous retroviruses (ERVs) have contributed to more than 8% of the human genome. The majority of these elements lack function due to accumulated mutations or internal recombination resulting in a solitary (solo) LTR, although members of one group of human ERVs (HERVs), HERV-K, were recently active with members that remain nearly intact, a subset of which is present as insertionally polymorphic loci that include approximately full-length (2-LTR) and solo-LTR alleles in addition to the unoccupied site. Several 2-LTR insertions have intact reading frames in some or all genes that are expressed as functional proteins. These properties reflect the activity of HERV-K and suggest the existence of additional unique loci within humans. We sought to determine the extent to which other polymorphic insertions are present in humans, using sequenced genomes from the 1000 Genomes Project and a subset of the Human Genome Diversity Project panel. We report analysis of a total of 36 nonreference polymorphic HERV-K proviruses, including 19 newly reported loci, with insertion frequencies ranging from <0.0005 to >0.75 that varied by population. Targeted screening of individual loci identified three new unfixed 2-LTR proviruses within our set, including an intact provirus present at Xq21.33 in some individuals, with the potential for retained infectivity.

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Section: Discussionmentioning

confidence: 99%

Discovery of unfixed endogenous retrovirus insertions in diverse human populations

Wildschutte

Williams

Montesion

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

230

304

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“…A small group of HERVs belonging to ERVK elements was actively proliferating in the genome after the divergence of human and chimpanzee ancestor lineages [19]. Few group members were even specific to non-human hominid genomes of Neanderthals and Denisovans [224]. Human specific HERVs, in turn, are presented by *130-140 members that shaped *330 kb of the human DNA.…”

Section: Impact On Human Evolutionmentioning

confidence: 99%

Molecular functions of human endogenous retroviruses in health and disease

Suntsova

Garazha

Ivanova

et al. 2015

Cell. Mol. Life Sci.

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Human endogenous retroviruses (HERVs) and related genetic elements form 504 distinct families and occupy ~8% of human genome. Recent success of high-throughput experimental technologies facilitated understanding functional impact of HERVs for molecular machinery of human cells. HERVs encode active retroviral proteins, which may exert important physiological functions in the body, but also may be involved in the progression of cancer and numerous human autoimmune, neurological and infectious diseases. The spectrum of related malignancies includes, but not limits to, multiple sclerosis, psoriasis, lupus, schizophrenia, multiple cancer types and HIV. In addition, HERVs regulate expression of the neighboring host genes and modify genomic regulatory landscape, e.g., by providing regulatory modules like transcription factor binding sites (TFBS). Indeed, recent bioinformatic profiling identified ~110,000 regulatory active HERV elements, which formed at least ~320,000 human TFBS. These and other peculiarities of HERVs might have played an important role in human evolution and speciation. In this paper, we focus on the current progress in understanding of normal and pathological molecular niches of HERVs, on their implications in human evolution, normal physiology and disease. We also review the available databases dealing with various aspects of HERV genetics.

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“…DNA sequences of these extinct hominins and those of present‐day humans share common ancestors on average about 800 000 years ago . Six of the HML‐2 loci identified in these archaic hominins appear to be absent in modern humans , but although highly suggestive, this does not necessarily mean that these retroviruses were still replicating and integrating into our hominin cousins after the presumed population split between modern humans on the one hand and Neanderthals and Denisovans on the other . They might simply be present at low frequencies in modern humans and have escaped discovery or have been completely lost as a result of genetic drift .…”

Section: Inventory Of the Hml‐2 Archivementioning

confidence: 99%

HERV‐K(HML‐2), a seemingly silent subtenant – but still waters run deep

Hanke

Hohn

Bannert

2016

APMIS

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A large proportion of the human genome consists of endogenous retroviruses, some of which are well preserved, showing transcriptional activity, and expressing retroviral proteins. The HERV‐K(HML‐2) family represents the most intact members of these elements, with some having open and intact reading frames for viral proteins and the ability to form virus‐like particles. Although generally suppressed in most healthy tissues by a variety of epigenetic processes and antiviral mechanisms, there is evidence that some members of this family are (at least partly) still active – particularly in certain stem cells and various tumors. This raises the possibility of their involvement in tumor induction or in developmental processes. In recent years, many new insights into this fascinating field have been attained, and this review focuses on new discoveries about coevolutionary events and intracellular defense mechanisms against HERV‐K(HML‐2) activity. We also describe what might occur when these mechanisms fail or become modulated by viral proteins or other viruses and discuss the new vistas opened up by the reconstitution of ancestral viral proteins and even complete HML‐2 viruses.

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Novel Denisovan and Neanderthal Retroviruses

Cited by 20 publications

References 9 publications

Discovery of unfixed endogenous retrovirus insertions in diverse human populations

Discovery of unfixed endogenous retrovirus insertions in diverse human populations

Molecular functions of human endogenous retroviruses in health and disease

HERV‐K(HML‐2), a seemingly silent subtenant – but still waters run deep

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