Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes.
Human endogenous retroviruses (HERVs) are ancient sequences integrated in the germ line cells and vertically transmitted through the offspring constituting about 8 % of our genome. In time, HERVs accumulated mutations that compromised their coding capacity. A prominent exception is HERV-W locus 7q21.2, producing a functional Env protein (Syncytin-1) coopted for placental syncytiotrophoblast formation. While expression of HERV-W sequences has been investigated for their correlation to disease, an exhaustive description of the group composition and characteristics is still not available and current HERV-W group information derive from studies published a few years ago that, of course, used the rough assemblies of the human genome available at that time. This hampers the comparison and correlation with current human genome assemblies.



In the present work we identified and described in detail the distribution and genetic composition of 213 HERV-W elements. The bioinformatics analysis led to the characterization of several previously unreported features and provided a phylogenetic classification of two main subgroups with different age and structural characteristics. New facts on HERV-W genomic context of insertion and co-localization with sequences putatively involved in disease development are also reported.



The present work is a detailed overview of the HERV-W contribution to the human genome and provides a robust genetic background useful to clarify HERV-W role in pathologies with poorly understood etiology, representing, to our knowledge, the most complete and exhaustive HERV-W dataset up to date.
Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SS554, 09042, Monserrato, Cagliari, Italy.
Nicole
0000-0003-0666-4361
N
Grandi
Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SS554, 09042, Monserrato, Cagliari, Italy.
Marta
0000-0002-7831-1648
M
Cadeddu
Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
Jonas
0000-0001-6492-2491
J
Blomberg
Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SS554, 09042, Monserrato, Cagliari, Italy. tramon@unica.it.|Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy. tramon@unica.it.
Enzo
0000-0002-4849-0980
E
Tramontano
D019295:Computational Biology; D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D005260:Female; D015686:Gene Products, env / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D010920:Placenta / Q000821:virology; D011247:Pregnancy; D011257:Pregnancy Proteins / Q000235:genetics; D011533:Proviruses / Q000235:genetics*; D011544:Pseudogenes; D014158:Transcription, Genetic
D015686:Gene Products, env; D011257:Pregnancy Proteins; C405335:syncytin
Endogenous retroviruses; HERV; HERV-W; Syncytin