Previous Article | Next Article ![]()
Journal of Virology, July 2007, p. 7805-7810, Vol. 81, No. 14
0022-538X/07/$08.00+0 doi:10.1128/JVI.02388-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Institute for Virology, Johannes Gutenberg-University, Mainz, Germany
Received 31 October 2006/ Accepted 30 April 2007
|
|
|---|
|
|
|---|
![]() View larger version (26K): [in a new window] |
FIG. 1. Models of MIE enhancer action in bidirectional gene pair transcription. (A) Synchronizer model. This model proposes that the enhancer region activates its flanking genes bidirectionally and simultaneously (the on-on state). As a consequence, transcriptions of ie1/3 and ie2 are expected to be correlated on the single genome level. (B) Switch model. This model proposes that the enhancer region activates its flanking genes bidirectionally but alternately (on-off and off-on states). As a consequence, transcriptions of ie1/3 and ie2 are expected to be anticorrelated on the single genome level, whereas alternate activation leads to correlated transcriptions on a multiple genome level. Bidirectional head-to-head architecture and exon-intron structure of the mCMV MIE locus (24, 35, 36) are illustrated. Open reading frames are designated according to the nomenclature proposed by Rawlinson et al. (37). Yellow and blue cylinders symbolize exons of ie1/3 and ie2, respectively. Yellow- and blue-colored arrows indicate the 5'-3' direction of transcription on the respective DNA strand. P, promoter; TF, transcription factor(s); TFBS, transcription factor binding site(s).
|
As shown by Trinklein et al. (44) for mammalian genes, bidirectional organization is associated mostly with coexpression of the gene pair, whereas in a minority of examples, transcription of one gene of the pair is induced while transcription of the other is inhibited. The bidirectional MIE locus architecture of mCMV prompted us to ask whether the enhancer region-flanking transcription units are transcribed synchronously upon activation of the enhancer region (on-on and off-off states of the gene pair), referred to here as the "synchronizer model" of enhancer action (Fig. 1A) or whether the enhancer operates as a genetic switch that decides between mutually exclusive but alternate states (on-off and off-on states of the gene pair), referred to here as the "switch model" of enhancer action (Fig. 1B).
The two models can be distinguished experimentally only on a single genome level, because statistical ensembles of high numbers of genomes or bidirectional reporter gene pair constructs, as is always the case in acute infection or upon transfection in cell culture models, would unavoidably mimic an on-on synchronicity due to the superposition of many individual on-off and off-on states. As discussed by Fiering et al. (14), this problem is inherent in all bulk read-out assays.
We have previously shown for the BALB/c mouse model of mCMV latency in the lungs that in situ MIE locus activity occurs randomly, is independently distributed, with a very low point prevalence of only 10 to 20 transcriptional events per 106 latent viral genomes (18, 26; reviewed in reference 41), and provides the molecular basis for immune surveillance of latency by IE1 epitope-specific CD8 T cells (39). This stochastic MIE locus activity can be described by Poisson distribution statistics (18) and is reminiscent of the variegated expression, also known as mosaic expression, of transgenes thought to involve chromatin remodeling (8, 14). Likewise, silencing and desilencing by local closing and opening of viral chromatin structure is thought to be the mechanistic basis for CMVs MIE locus activity (31, 38; for reviews, see references 5, 41, and 42). As the rare and stochastic transcription events most likely represent MIE locus activities from single viral genomes, the mouse model of pulmonary latency is unique in that it fulfills the conditions for testing the two proposed models of mCMV MIE enhancer action.
In our previous experiments, the question of whether the MIE enhancer was involved at all in the observed sporadic MIE locus activity remained an open one. Alternatively, it might have reflected a stochastic, basal activity of the independent core promoters P1/3 and P2 that did not involve the enhancer (18, 26). Thus, in order to decide between the two models, the enhancer must be activated experimentally. Tumor necrosis factor alpha (TNF-
) activates the mCMV enhancer through transcription factors NF-
B and AP-1 (20, 21), resulting in an enhanced frequency of MIE gene transcription in latently infected lungs (40; reviewed in reference 41). This established in vivo approach of TNF-induced enhancer activity was used here for a quantitative analysis of MIE gene transcription by real-time reverse transcriptase (RT)-PCRs specific for spliced IE1 and IE2 transcripts.
The sensitivity of the RT-PCR, which is defined mainly by the RT step rather than by cDNA amplification efficacy, was determined by a limiting dilution assay (27, 39) using graded numbers of synthetic transcripts (Fig. 2A to C). Although IE1 RT-PCR proved to be slightly more sensitive, cycle threshold (CT) values clearly discriminated between positive and negative samples for both types of RT-PCR. Transcript stability is another factor pertinent to transcript detectability. As shown in Fig. 2D for natural transcripts present in acutely infected fibroblasts, IE1 transcripts are extraordinarily stable, and IE2 transcripts are still fairly long-lived. Thus, a high-frequency oscillation between on-off and off-on states of the bidirectional gene pair should give an on-on result indistinguishable from the synchronizer model.
![]() View larger version (25K): [in a new window] |
FIG. 2. Detection limits of IE1- and IE2-specific real-time quantitative RT-PCRs. (A) Primers and probes. For, forward primer; Rev, reverse primer. Map positions are given according to GenBank accession no. L06816. RT-PCRs were performed on an ABI Prism 7500 (Applied Biosystems), with reaction conditions as described previously (39), except that the primer concentration was 0.6 µM and the 5-carboxy-X-rhodamine concentration was 0.132 µM. (B) Limiting dilution assay. Graded numbers of synthetic polyadenylated IE1 and IE2 transcripts (18) in 24 replicates were amplified by the respective real-time RT-PCRs. Dots represent the numbers of cDNA amplification CT values required for detection, with the median values for positive replicates marked by horizontal bars. The dotted lines indicate the cutoff CT value, defining a sample as negative if no signal above water control was obtained after 45 amplification cycles. (C) Poisson distribution analysis (27) based on the experimentally determined fractions of negative replicates (see panel B). The log-linear plots show the Poisson distribution graphs calculated with the maximum-likelihood method (13). Ninety-five percent confidence interval (CI) regions are shown shaded. The most probable number (MPN value) for the detection limit, representing the reciprocal of the Poisson distribution parameter , is revealed as the abscissa coordinate (dashed arrow) of the point of intersection between 1/e and the respective calculated regression line. CI, 95% confidence interval of MPN; P, probability value indicating the goodness of fit, which needs to be >0.05 for accepting the null hypothesis. (D) Transcript stability was measured as described previously in greater detail (39). The schedule for inhibitor treatment of infected mouse embryo fibroblasts is indicated: CH, cycloheximide for inhibition of protein synthesis restricting transcription to IE genes; V, infection with mCMV at a multiplicity of infection of 4 (centrifugal infection with 0.2 PFU/cell); ActD, actinomycin D to prevent further transcription. At the indicated time points after replacement of CH by ActD, total RNA was isolated from triplicate cultures, and IE1 and IE2 transcripts were quantitated by the respective real-time RT-PCRs. Dots represent data from triplicate cultures with the median value marked. Half-lives (HL; 95% confidence intervals of half-lives) HL-IE1 and HL-IE2 of the respective transcripts were determined from the negative slopes (95% confidence intervals of slopes) of the log-linear regression lines. Because of a gap period in the ActD effect, regression analysis included only data from day 2 onward (arrows). Calculations were performed using Mathematica Statistics linear-regression software, version 5.1 (Wolfram Research, Inc., Champaign, IL).
|
![]() View larger version (31K): [in a new window] |
FIG. 3. Contextual analysis of MIE locus transcription patterns in latently infected lungs. The BALB/c mouse model of syngeneic bone marrow transplantation and infection with the mCMV wild-type Smith (ATCC VR-194) strain was employed to establish viral latency in the lungs of transplantation recipients (41). Transcription analysis for five latently infected mice (designated LIM#1 through LIM#5) was performed at 12 months after transplantation and at 24 h after the in vivo activation of MIE gene expression by 1 µg of recombinant murine TNF- administered intravenously (40). For the analysis of variegated MIE gene expression, lungs were cut into pieces, specifically into nine pieces derived from the superior, middle, and inferior lobes of the right lung and seven pieces derived from the left lung. Two pieces (pieces 10 and 11) of the postcaval lobe were used to control for the presence and load of latent viral DNA (not shown). Transcripts IE1 and IE2 were quantified for each of the total number of 80 tissue pieces by the respective real-time RT-PCRs from 10% aliquots of the yields of total RNA purified with a QIAGEN RNeasy Plus kit. (Left panel) raw data given as CT values for the 16 lung pieces (pieces 1 to 9 and 12 to 18) tested per mouse. The dashed line marks the cutoff CT value separating negative from positive samples. Data for IE1 and IE2 are shown as yellow- and blue-filled circles, respectively. (Right panel) corresponding lung pictograms in anatomical view. Results are expressed in numbers of IE1/IE2 transcripts per test aliquot. In accordance with the MIE locus architecture illustrated in Fig. 1, yellow and blue boxes symbolize the presence of IE1 and IE2 transcripts, respectively. Open boxes symbolize the absence of transcripts.
|
![]() View larger version (13K): [in a new window] |
FIG. 4. Correlation analysis. The binary transcription-on and transcription-off data (dichotomous variables) derived from Fig. 3 were arranged in a two-by-two contingency table (Observed) and compared with those in the table expected for independent distribution (null hypothesis) of IE1 and IE2 transcription (Expected). Fisher's exact test was used to calculate the two-tailed P value (method of the sum of small P values) following the recommendations provided by Simple Interactive Statistical Analysis (2, 45). The variables are considered to be positively correlated only if the P value is <0.01 and under the condition that the number of double positives observed is greater than the number of double positives expected, both of which were not fulfilled. The hypothesis of independent distribution cannot be rejected if P is >0.05, which was the case.
|
Published ahead of print on 9 May 2007. ![]()
|
|
|---|
B. J. Virol. 72:180-190.
gene (ie2) is dispensable for growth. Virology 167:477-484.[Medline]This article has been cited by other articles:
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Copyright © 2009 by the American Society for Microbiology. For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»