Microarray-Based Sketches of the HERV Transcriptome Landscape

Abstract

Human endogenous retroviruses (HERVs) are spread throughout the genome and their long terminal repeats (LTRs) constitute a wide collection of putative regulatory sequences. Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. Herein, we have introduced a generic method aiming to optimally characterize individual loci associated with 25-mer probes by minimizing cross-hybridization risks. We therefore set up a microarray dedicated to a collection of 5,573 HERVs that can reasonably be assigned to a unique genomic position. We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment showed that almost one third of the HERV repertoire is indeed transcribed. The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. The probeset definition within the U3 and U5 regions was used to assign a function to some LTRs (i.e. promoter or polyA) and revealed that (i) autonomous active LTRs are broadly subjected to operational determinism (ii) the cellular gene density is substantially higher in the surrounding environment of active LTRs compared to silent LTRs and (iii) the configuration of neighboring cellular genes differs between active and silent LTRs, showing an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects.

Np9, a cellular protein of retroviral ancestry restricted to human, chimpanzee and gorilla, binds and regulates ubiquitin ligase MDM2

“…Especially the HERV-K(HML-2) group bears loci with ORFs for Gag (group-specific antigen), (Prot)ease, (Pol)ymerase and (Env)elope proteins, as well as for some regulatory accessory proteins (see ahead) 9,10 .…”

Comprehensive Analysis of Human Endogenous Retrovirus Group HERV-W Locus Transcription in Multiple Sclerosis Brain Lesions by High-Throughput Amplicon Sequencing

“…Employing microarray strategies, HERV-W was found to be transcribed in testicular cancer and the placenta (25,26) and in different human brain regions (27). High-resolution meltingtemperature analysis indicated nonrandom patterns of HERV-W transcription and also provided evidence for variable transcript levels between individuals (28).…”

“…Notably, no differences in relative transcript levels of specific HERV-W env loci were observed in PBMC from patients with MS and healthy controls in that study. Several HERV-W loci were also identified by a microarray-based strategy as being transcribed indirectly (26). In accordance with an initiative by the Human Gene Nomenclature Committee (HGNC) for assigning unique designations to transcribed HERV loci, several transcribed HERV-W loci were named ERVW-1 to ERVW-6 (34).…”

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer

“…Also ending by cloning and sequencing steps, the genome repeat expression monitoring technique aiming to identify promoters among repeats identified active HML-2 specific human solitary LTRs 32,33 . We successively developed two generations of high-density microarrays dedicated to the analysis of the HERV transcriptome, introducing methodologies suitable for repeated element probe design in order to minimize cross reactions between paralogous elements within a family 34,35 . The HERV-V2 chip which targets 2,690 distinct proviruses and 2,883 solo LTRs of the HERV-W, HERV-H, HERV-E 4.1, HERV-FRD, HERV-K HML-2 and HERV-K HML-5 families, unveiled the expression of 1,718 HERV loci (Figures 7A and B) in a wide range of tissues 35 , illustrated in this paper by the identification of putative prostate cancer biomarkers.…”

“…We successively developed two generations of high-density microarrays dedicated to the analysis of the HERV transcriptome, introducing methodologies suitable for repeated element probe design in order to minimize cross reactions between paralogous elements within a family 34,35 . The HERV-V2 chip which targets 2,690 distinct proviruses and 2,883 solo LTRs of the HERV-W, HERV-H, HERV-E 4.1, HERV-FRD, HERV-K HML-2 and HERV-K HML-5 families, unveiled the expression of 1,718 HERV loci (Figures 7A and B) in a wide range of tissues 35 , illustrated in this paper by the identification of putative prostate cancer biomarkers. In addition, the use of multiple probesets on a given locus is informative about its transcriptional regulation.…”