At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription

Abstract

We report the first genome-wide comparison of in vivo promoter activities of a group of human-specific endogenous retroviruses in healthy and cancerous germ line tissues. To this end, we employed a recently developed technique termed genomic repeat expression monitoring. We found that at least 50% of human-specific long terminal repeats (LTRs) possessed promoter activity, and many of them were up- or downregulated in a seminoma. Individual LTRs were expressed at markedly different levels, ranging from approximately 0.001 to approximately 3% of the housekeeping beta-actin gene transcript level. We demonstrated that the main factors affecting the LTR promoter activity were the LTR type (5'-proviral, 3' proviral, or solitary) and position with regard to genes. The averaged promoter strengths of solitary and 3'-proviral LTRs were almost identical in both tissues, whereas 5'-proviral LTRs displayed two- to fivefold higher promoter activities. The relative content of promoter-active LTRs in gene-rich regions was significantly higher than that in gene-poor loci. This content was maximal in those regions where LTRs "overlapped" readthrough transcripts. Although many promoter-active LTRs were mapped near known genes, no clear-cut correlation was observed between transcriptional activities of genes and neighboring LTRs. Our data also suggest a selective suppression of transcription for LTRs located in gene introns.

FIG. 1.

Schematic representation of solitary (left) and proviral (right) LTR expression. The transcription driven from 5′-proviral LTRs results in mRNAs of viral genes, whereas the expression of either solitary or 3′-proviral LTRs results in the transcription of host nonrepetitive genomic sequences flanking the 3′ ends of the retroelements.

FIG. 2.

Proportions of promoter-active LTRs in four groups differing by the distance of the LTRs from known human genes or mapped cDNAs. (A) LTRs were grouped according to their distances from known human genes into four categories (C1 to C4) (see the text for details). The relative content of promoter-active LTRs in a group was calculated as the ratio of the number of LTRs in the group, for which the corresponding ELTs were obtained, to the total number of all LTRs in the group. (B) LTRs which were promoter active in at least one of the two tissues studied. (C) LTRs which were promoter active both in testicular parenchyma and in the seminoma. Averages and standard errors of the means (error bars) are presented.

FIG. 3.

Relative promoter strengths of 3′-proviral (gray) and solitary (black) LTRs grouped according to their distances from genes (groups C1 to C4) (see the text for details). (A) Testicular parenchyma; (B) seminoma. Averages and standard errors of the means (error bars) are presented.

FIG. 4.

Comparison of relative promoter strengths of solitary, 5′-proviral, and 3′-proviral LTRs (per LTR). Gray and black bars represent the relative LTR promoter strengths in the testicular parenchyma and seminoma, respectively. For details of relative promoter strength calculation, see the text. Averages and standard errors of the means (error bars) are presented.

FIG. 5.

Schematic representation of HS element 99 localization relative to its LIPH1 and SENP2 gene neighbors and their transcript levels in testicular parenchyma and seminoma.

FIG. 6.

Relative transcript levels of some human genes and LTRs. Relative transcript levels of randomly chosen HS LTRs and those of known human genes were measured using RT-PCR. (A) Testicular parenchyma; (B) seminoma.