Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs?

Abstract

Endogenous retroviruses (ERVs) are long terminal repeat-containing virus-like elements that have colonized approximately 10 per cent of the present day mammalian genomes. The intracisternal A particles (IAPs) are a class of ERVs that is currently highly active in the rodents. IAP elements can influence the transcription profile of nearby genes by providing functional promoter elements and modulating local epigenetic landscape through changes in DNA methylation and histone (H3K9) modifications. Despite the potential role for IAPs in gene regulation, the precise genomic locations where these elements are integrated are not well understood. To address this issue, we have identified more than 400 novel IAP insertion sites within/near annotated genes by searching the murine genome, which suggests that the impact of IAP elements on local and/or global gene regulation could be more profound than was previously expected. On the basis of our independent analyses and already published reports, here we argue that IAPs and ERV elements in general could have an evolutionary role for modulating phenotypic plasticity upon environmental inputs, and that this could be mediated through specific stages of embryonic development such as placentation during which the epigenetic constraints on IAP elements are partially relaxed.

Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms

“…In addition, different classes of transposons may have evolved different roles in the evolutionary dynamics of germ lines and the plasticity of somatic cells in animals. 22 Preliminary evidence suggests that this may have been accompanied by the coevolution of genes, like the RNA-editing enzymes APOBEC (apolipoprotein B mRNA–editing enzyme, catalytic polypeptide-like) and the Rett syndrome–related MeCP2 (methyl CpG binding protein 2), to domesticate and regulate the process. 64,65 In any case, we suggest that the addition of transpositional experimentation and selection in sperm has been an important, and thus far unappreciated, aspect of the evolution of evolvability, especially in mammals.…”

“…21 TEs could therefore act as sensors and respond to sustained shortage of food with increased transposition and an intensified search for genomic innovation. 22 …”

Longitudinal epigenetic drift in mice perinatally exposed to lead

“…These commonly used biomarkers host CpG islands that are variably methylated 19 or differentially methylated, 18,20 respectively, and environmental exposures have been shown to stably influence their epigenetic marks and subsequent gene expression. [21][22][23][24] Therefore, measuring the relative change in DNA methylation from early to adult life in epigenetically labile regions is crucial to determining whether early life Pb exposure can alter the magnitude or direction of epigenetic drift.…”

Gene expression and epigenetic aberrations in F1‐placentas fathered by obese males

“…We performed real‐time PCR of a total of 22 genes—10 Peg s, 2 essential genes for transport of amino acids, 2 genes for transport of glucose, 7 developmental genes, and the IAP LTR and Gag regions—to determine if paternal obesity can affect expression of placental genes. Class II endogenous retroviruses are the second most‐abundant retrotransposon family in the mouse; the IAP elements left behind by this family of viruses represents up to 1000–2500 copies in the haploid genome, and are subject to DNA methylation, histone modifications, and activation that affect the transcription profile of nearby genes (Sharif, Shinkai, & Koseki, ).…”