Analysis of Simian Endogenous Retrovirus (SERV) Full-Length Proviruses in Old World Monkey Genomes

Abstract

Simian endogenous retrovirus, SERV, is a successful germ line invader restricted to Old World monkey (OWM) species. (1) Background: The availability of high-quality primate genomes warrants a study of the characteristics, evolution, and distribution of SERV proviruses. (2) Methods: Cercopithecinae OWM genomes from public databases were queried for the presence of full-length SERV proviruses. A dataset of 81 Cer-SERV genomes was generated and analyzed. (3) Results: Full-length Cer-SERV proviruses were mainly found in terrestrial OWM, and less so in arboreal, forest- dwelling monkeys. Phylogenetic analysis confirmed the existence of two genotypes, Cer-SERV-1 and Cer-SERV-2, with Cer-SERV-1 showing evidence of recent germ-line expansions. Long Terminal Repeat (LTR) variation indicated that most proviruses were of a similar age and were estimated to be between <0.3 and 10 million years old. Integrations shared between species were relatively rare. Sequence analysis further showed extensive CpG methylation-associated mutations, variable Primer Binding Site (PBS) use with Cer-SERV-1 using PBSlys3 and Cer-SERV-2 using PBSlys1,2, and the recent gain of LTR motifs for transcription factors active during embryogenesis in Cer-SERV-1. (4) Conclusions: sequence analysis of 81 SERV proviruses from Cercopithecinae OWM genomes provides evidence for the adaptation of this retrovirus to germ line reproduction.

Genome sequencing and application of Taiwanese macaque Macaca cyclopis

“…Previous studies have shown that many Old World Monkey species have either full length or near full-length simian endogenous retroviral sequences (SERSs) as a result of heterozygous integrations. As described by van der Kuyl and colleagues, most SERSs are of < 0.3 and 10 million years old 16 .…”

“…Most of the observed EVEs from simian virus (SIV), a retrovirus which relies on genomic insertion for replication, have undergone mutations for a long period of time. Thus, EVEs of SIV in macaques provide additional information for the study of primate evolution and medical application 16 . Previous studies have shown that many Old World Monkey species have either full length or near full-length simian endogenous retroviral sequences (SERSs) as a result of heterozygous integrations.…”

Species-Specific Transcription Factors Associated with Long Terminal Repeat Promoters of Endogenous Retroviruses: A Comprehensive Review

“…SERVs exist as two types: Cer-SERV-1 and Cer-SERV-2 [ 235 ]. The sequences within the LTR of Cer-SERV-1 are approximately 484 nt in length and encode five to eight TF-binding motifs (CREB, CDP, E2F, AREB6, FoxD3, FoxJ2, and Brn-2), shown in Table 2 [ 235 ].…”

“…SERVs exist as two types: Cer-SERV-1 and Cer-SERV-2 [ 235 ]. The sequences within the LTR of Cer-SERV-1 are approximately 484 nt in length and encode five to eight TF-binding motifs (CREB, CDP, E2F, AREB6, FoxD3, FoxJ2, and Brn-2), shown in Table 2 [ 235 ]. As FoxD3 and FoxJ2 are expressed in embryonic stem cells and during early embryonic development, respectively [ 234 , 257 ], Cer-SERV-1 may also be expressed in embryonic stem cell and during early embryonic development.…”

“…As FoxD3 and FoxJ2 are expressed in embryonic stem cells and during early embryonic development, respectively [ 234 , 257 ], Cer-SERV-1 may also be expressed in embryonic stem cell and during early embryonic development. Cer-SERV-2 encodes other TFs (AREB6, COMP1, CREB, NF-1, RFX1, Pax6, and v-Myb) than those encoded by Cer-SERV-1 [ 235 ]. Therefore, the transcription of Cer-SERV-2 may be regulated by other elements in different cells.…”