Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Dec;87(24):13837-52.
doi: 10.1128/JVI.02388-13. Epub 2013 Oct 9.

Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing

Katja Schmitt  1 , Christin Richter, Christina Backes, Eckart Meese, Klemens Ruprecht, Jens Mayer
Affiliations

Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing

Katja Schmitt et al. J Virol. 2013 Dec.

Abstract

Human endogenous retroviruses (HERVs) of the HERV-W group comprise hundreds of loci in the human genome. Deregulated HERV-W expression and HERV-W locus ERVWE1-encoded Syncytin-1 protein have been implicated in the pathogenesis of multiple sclerosis (MS). However, the actual transcription of HERV-W loci in the MS context has not been comprehensively analyzed. We investigated transcription of HERV-W in MS brain lesions and white matter brain tissue from healthy controls by employing next-generation amplicon sequencing of HERV-W env-specific reverse transcriptase (RT) PCR products, thus revealing transcribed HERV-W loci and the relative transcript levels of those loci. We identified more than 100 HERV-W loci that were transcribed in the human brain, with a limited number of loci being predominantly transcribed. Importantly, relative transcript levels of HERV-W loci were very similar between MS and healthy brain tissue samples, refuting deregulated transcription of HERV-W env in MS brain lesions, including the high-level-transcribed ERVWE1 locus encoding Syncytin-1. Quantitative RT-PCR likewise did not reveal differences in MS regarding HERV-W env general transcript or ERVWE1- and ERVWE2-specific transcript levels. However, we obtained evidence for interindividual differences in HERV-W transcript levels. Reporter gene assays indicated promoter activity of many HERV-W long terminal repeats (LTRs), including structurally incomplete LTRs. Our comprehensive analysis of HERV-W transcription in the human brain thus provides important information on the biology of HERV-W in MS lesions and normal human brain, implications for study design, and mechanisms by which HERV-W may (or may not) be involved in MS.

PubMed Disclaimer

Figures

Fig 1
Fig 1
Relative transcript levels of HERV-W loci in MS and healthy brain tissue samples. Shown are relative transcript levels of specific HERV-W loci in the various MS-derived and healthy brain tissue samples based on total numbers of cDNA sequences assignable to a locus relative to the total number of assignable cDNA sequences per sample. The numbers presented are from the 5′ env 454/FLX data set. The results from MS-derived (MS1 to MS7) and healthy-control (H1 to H7) brain tissue samples are presented in separate graphs that are further divided into sections depicting HERV-W loci with higher (top) and lower (<4%; bottom) relative cDNA sequence frequencies and thus transcript levels. HERV-W loci are designated according to their locations in chromosomal bands and HGNC-approved locus designations (Table 2; see the text and supplemental material).
Fig 2
Fig 2
Relative transcript levels of HERV-W loci in MS and healthy brain tissue samples based on the 3′ env amplicon data set. Depicted are relative transcript levels of specific HERV-W loci in MS lesion-derived and healthy brain tissue samples, basically as shown in Fig. 1 and the supplemental material.
Fig 3
Fig 3
No major differences were found in relative transcript levels of HERV-W loci for data sets generated by 454/FLX or Illumina/MiSeq amplicon-sequencing technology. Shown are the relative transcript levels of HERV-W loci obtained for the 5′ env data set generated by 454/FLX and Illumina/MiSeq amplicon sequencing deduced as described in the legend to Fig. 1. HERV-W loci with low relative cDNA frequencies are intentionally included to demonstrate results with little variation for those loci, as well. HERV-W loci are designated according to their locations in chromosomal bands and HGNC-approved locus designations (see the text). Detailed information on relative cDNA sequence frequencies in both data sets is provided in the supplemental material.
Fig 4
Fig 4
Relative transcript levels of HERV-W and specific HERV-W loci measured by qRT-PCR. The relative levels of HERV-W transcripts were determined by semiquantitative RT-PCR for the 5′ env amplicon, which can detect transcripts/cDNA from a greater number of HERV-W loci. Transcript levels of the HERV-W loci ERVWE1/ERVW-1 and ERVWE2/ERVW-2 specifically were likewise determined using locus-specific primer sets (see the text). Relative transcript levels are given as log2-transformed fold changes, with the healthy brain tissue sample H1 set as the reference. The whiskers depict maximum and minimum changes observed in replicates of the experiment. Note that seemingly different transcript levels between healthy control and MS brain tissue sample entities are not statistically significant.
Fig 5
Fig 5
HERV-W LTRs and remnants thereof often display promoter activity. Shown on the left is a representative result of normalized promoter activities of selected complete and incomplete HERV-W LTRs in the sense or antisense direction obtained from luciferase reporter gene assays in JEG-3 cells. LTR construct designations denote HGNC-approved locus names and the chromosomal position of a tested HERV-W 5′ or 3′ LTR, as well as the sense or antisense direction of the LTR within the luciferase reporter gene vector. A CMV-driven luciferase-expressing vector (pCMV-GLuc) served as the positive control and is presented separately to demonstrate ∼10-fold-higher promoter activity than the most active HERV-W LTR construct. A promoterless luciferase reporter vector (pGLuc-Basic) and untransfected JEG-3 cells served as negative controls. The error bars depict standard deviations observed for an experiment in triplicate. On the right are shown HERV-W LTRs or LTR portions, indicated by black bars, present within the various reporter gene constructs. HERV-W LTR sequences are depicted in comparison to the 780-bp-long HERV-W LTR17 reference sequence provided by Repbase (36). Note that some LTRs harbor insertions compared to the reference sequence. The HERV-W LTR U3 (harboring a TATA box toward the 3′ end), R (the boundaries of which define the start and endpoints of proviral transcription), and U5 regions are indicated at the top, further showing that several of the tested LTRs have been formed by L1-mediated retrotransposition and therefore lack certain LTR portions.
See this image and copyright information in PMC

References

    1. Jern P, Coffin JM. 2008. Effects of retroviruses on host genome function. Annu. Rev. Genet. 42:709–732 - PubMed
    1. Mayer J, Meese E. 2005. Human endogenous retroviruses in the primate lineage and their influence on host genomes. Cytogenet. Genome Res. 110:448–456 - PubMed
    1. Stoye JP. 2001. Endogenous retroviruses: still active after all these years? Curr. Biol. 11:R914–R916 - PubMed
    1. Kurth R, Bannert N. 2010. Beneficial and detrimental effects of human endogenous retroviruses. Int. J. Cancer 126:306–314 - PubMed
    1. Belshaw R, Katzourakis A, Paces J, Burt A, Tristem M. 2005. High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection. Mol. Biol. Evol. 22:814–817 - PubMed

Publication types

Associated data

LinkOut - more resources