HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses

• DOI: 10.1101/gr.144303.112
• Publication Date: 2013-05-09T02:45:02Z
• Authors: Rafael Contreras-...; Mark H. Kaplan; Shirley He; Angie C. Contrera...; Marta J. Gonzalez...; Ferdinand Kappes; Derek Dube; Susana M. Chan; Dan Robinson; Fan Meng; Manhong Dai; Scott D. Gitlin; Arul M. Chinnaiyan; Gilbert S. Omenn; David M. Markovitz
• Keywords: Provirus; Endogenous retrovirus; Repeated sequence

Human endogenous retroviruses (HERVs) make up 8% of the human genome. The HERV-K (HML-2) family is most recent group these viruses to have inserted into genome, and we detected activation proviruses in blood patients with HIV-1 infection. We report that infection activates expression a novel provirus, termed K111, present multiple copies centromeres chromosomes throughout genome yet not annotated assembly. Infection or stimulation Tat protein leads K111 proviruses. as single copy chimpanzee, found genomes other primates. Remarkably, appear extinct Neanderthal Denisovan, while modern humans at least 100 spread across 15 chromosomes. Our studies suggest progenitor integrated before Homo-Pan divergence expanded number during evolution hominins, perhaps by recombination. expansion provides sequence evidence suggesting recombination between various took place humans. show significant variations each individual centromere, which may serve markers future efforts annotate centromere sequences. Further, this work an example potential discover previously unknown genomic sequences through analysis nucleic acids patients.