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Microarray analysis reveals global modulation of endogenous retroelement transcription by microbes.

Young GR, Mavrommatis B, Kassiotis G - Retrovirology (2014)

Bottom Line: Modulated REs were frequently found near or embedded within similarly-modulated host genes.In line with these results, the transcriptional activity of numerous REs followed characteristics in different tissues according to exposure to environmental microbes and was further heavily altered during viral infection or imbalances with intestinal microbiota, both in mice and humans.More importantly, application of this methodology suggests that immune activation, as a result of infection with pathogens or dysbiosis with commensal microbes, causes global modulation of RE transcription.

View Article: PubMed Central - PubMed

Affiliation: Division of Immunoregulation, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK. gkassio@nimr.mrc.ac.uk.

ABSTRACT

Background: A substantial proportion of both the mouse and human genomes comprise of endogenous retroelements (REs), which include endogenous retroviruses. Over evolutionary time, REs accumulate inactivating mutations or deletions and thus lose the ability to replicate. Additionally, REs can be transcriptionally repressed by dedicated mechanisms of the host. Nevertheless, many of them still possess and express intact open reading frames, and their transcriptional activity has been associated with many physiological and pathological processes of the host. However, this association remains tenuous due to incomplete understanding of the mechanism by which RE transcription is regulated. Here, we use a bioinformatics tool to examine RE transcriptional activity, measured by microarrays, in murine and human immune cells responding to microbial stimulation.

Results: Immune cell activation by microbial signals in vitro caused extensive changes in the transcription not only of the host genes involved in the immune response, but also of numerous REs. Modulated REs were frequently found near or embedded within similarly-modulated host genes. Focusing on probes reporting single-integration, intergenic REs, revealed extensive transcriptional responsiveness of these elements to microbial signals. Microbial stimulation modulated RE expression in a cell-intrinsic manner. In line with these results, the transcriptional activity of numerous REs followed characteristics in different tissues according to exposure to environmental microbes and was further heavily altered during viral infection or imbalances with intestinal microbiota, both in mice and humans.

Conclusions: Together, these results highlight the utility of improved methodologies in assessing RE transcription profiles in both archived and new microarray data sets. More importantly, application of this methodology suggests that immune activation, as a result of infection with pathogens or dysbiosis with commensal microbes, causes global modulation of RE transcription. RE responsiveness to external stimuli should, therefore, be considered in any association between RE transcription and disease.

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Related in: MedlinePlus

Linkage of RE expression to activity of the nearest gene. Regression of RE-reporting probe values for heart tissue samples against the one-step Tukey’s biweight w-estimator value calculated for all probes corresponding to all probesets for the nearest 5′ or 3′ gene, omitting points where the nearest gene was not present on the microarray platform. (A) All RE-reporting probes, as identified using previously published methodologies, and (B) RE-reporting probes passing enhanced filtering, that were significantly regulated between B6 tissues for three independent experiments using the Mouse Genome 430 v2 microarray platform (p < 0.001 by ANOVA comparing tissues and eliminating experiment). Data are obtained from E-GEOD-1986, −9954, and −10246.
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Fig2: Linkage of RE expression to activity of the nearest gene. Regression of RE-reporting probe values for heart tissue samples against the one-step Tukey’s biweight w-estimator value calculated for all probes corresponding to all probesets for the nearest 5′ or 3′ gene, omitting points where the nearest gene was not present on the microarray platform. (A) All RE-reporting probes, as identified using previously published methodologies, and (B) RE-reporting probes passing enhanced filtering, that were significantly regulated between B6 tissues for three independent experiments using the Mouse Genome 430 v2 microarray platform (p < 0.001 by ANOVA comparing tissues and eliminating experiment). Data are obtained from E-GEOD-1986, −9954, and −10246.

Mentions: To assess the potential impact of such co-regulation, three independent experiments using MG430v2, originally designed to determine tissue-specific expression patterns, were analyzed for significantly regulated RE-reporting probes. While obvious clustering of tissues was observed (data not shown), the most highly expressed RE-reporting probes were members of probesets reporting the expression of known tissue specific genes, including Tnnt2 (troponin T2, cardiac) within heart tissue [35], Ldb3 (LIM domain binding 3) within skeletal muscle [36], and Ighv14-2 (immunoglobulin heavy variable 14–2) within the spleen [37]. Further supporting this observation, in a separate global analysis we found that when probesets contained a single RE-reporting probe, the behavior of the RE-reporting probe did not differ from that of the remainder of probes in the probeset across 9 tissues analyzed, in the vast majority of probesets (>86%) (p > 0.05, Holm-Bonferroni t test). To further investigate the extent of linkage between RE-reporting probe expression and that of a neighboring gene, correlation was assessed for heart tissue samples, which previously showed the greatest independence in RE-reporting probe expression. Varying significant (p < 0.0001) positive correlations were observed for LTR elements, LINEs and SINEs, suggesting expression patterns of neighboring genes explain ~30% of observed RE expression levels (Figure 2A).Figure 2


Microarray analysis reveals global modulation of endogenous retroelement transcription by microbes.

Young GR, Mavrommatis B, Kassiotis G - Retrovirology (2014)

Linkage of RE expression to activity of the nearest gene. Regression of RE-reporting probe values for heart tissue samples against the one-step Tukey’s biweight w-estimator value calculated for all probes corresponding to all probesets for the nearest 5′ or 3′ gene, omitting points where the nearest gene was not present on the microarray platform. (A) All RE-reporting probes, as identified using previously published methodologies, and (B) RE-reporting probes passing enhanced filtering, that were significantly regulated between B6 tissues for three independent experiments using the Mouse Genome 430 v2 microarray platform (p < 0.001 by ANOVA comparing tissues and eliminating experiment). Data are obtained from E-GEOD-1986, −9954, and −10246.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4222864&req=5

Fig2: Linkage of RE expression to activity of the nearest gene. Regression of RE-reporting probe values for heart tissue samples against the one-step Tukey’s biweight w-estimator value calculated for all probes corresponding to all probesets for the nearest 5′ or 3′ gene, omitting points where the nearest gene was not present on the microarray platform. (A) All RE-reporting probes, as identified using previously published methodologies, and (B) RE-reporting probes passing enhanced filtering, that were significantly regulated between B6 tissues for three independent experiments using the Mouse Genome 430 v2 microarray platform (p < 0.001 by ANOVA comparing tissues and eliminating experiment). Data are obtained from E-GEOD-1986, −9954, and −10246.
Mentions: To assess the potential impact of such co-regulation, three independent experiments using MG430v2, originally designed to determine tissue-specific expression patterns, were analyzed for significantly regulated RE-reporting probes. While obvious clustering of tissues was observed (data not shown), the most highly expressed RE-reporting probes were members of probesets reporting the expression of known tissue specific genes, including Tnnt2 (troponin T2, cardiac) within heart tissue [35], Ldb3 (LIM domain binding 3) within skeletal muscle [36], and Ighv14-2 (immunoglobulin heavy variable 14–2) within the spleen [37]. Further supporting this observation, in a separate global analysis we found that when probesets contained a single RE-reporting probe, the behavior of the RE-reporting probe did not differ from that of the remainder of probes in the probeset across 9 tissues analyzed, in the vast majority of probesets (>86%) (p > 0.05, Holm-Bonferroni t test). To further investigate the extent of linkage between RE-reporting probe expression and that of a neighboring gene, correlation was assessed for heart tissue samples, which previously showed the greatest independence in RE-reporting probe expression. Varying significant (p < 0.0001) positive correlations were observed for LTR elements, LINEs and SINEs, suggesting expression patterns of neighboring genes explain ~30% of observed RE expression levels (Figure 2A).Figure 2

Bottom Line: Modulated REs were frequently found near or embedded within similarly-modulated host genes.In line with these results, the transcriptional activity of numerous REs followed characteristics in different tissues according to exposure to environmental microbes and was further heavily altered during viral infection or imbalances with intestinal microbiota, both in mice and humans.More importantly, application of this methodology suggests that immune activation, as a result of infection with pathogens or dysbiosis with commensal microbes, causes global modulation of RE transcription.

View Article: PubMed Central - PubMed

Affiliation: Division of Immunoregulation, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK. gkassio@nimr.mrc.ac.uk.

ABSTRACT

Background: A substantial proportion of both the mouse and human genomes comprise of endogenous retroelements (REs), which include endogenous retroviruses. Over evolutionary time, REs accumulate inactivating mutations or deletions and thus lose the ability to replicate. Additionally, REs can be transcriptionally repressed by dedicated mechanisms of the host. Nevertheless, many of them still possess and express intact open reading frames, and their transcriptional activity has been associated with many physiological and pathological processes of the host. However, this association remains tenuous due to incomplete understanding of the mechanism by which RE transcription is regulated. Here, we use a bioinformatics tool to examine RE transcriptional activity, measured by microarrays, in murine and human immune cells responding to microbial stimulation.

Results: Immune cell activation by microbial signals in vitro caused extensive changes in the transcription not only of the host genes involved in the immune response, but also of numerous REs. Modulated REs were frequently found near or embedded within similarly-modulated host genes. Focusing on probes reporting single-integration, intergenic REs, revealed extensive transcriptional responsiveness of these elements to microbial signals. Microbial stimulation modulated RE expression in a cell-intrinsic manner. In line with these results, the transcriptional activity of numerous REs followed characteristics in different tissues according to exposure to environmental microbes and was further heavily altered during viral infection or imbalances with intestinal microbiota, both in mice and humans.

Conclusions: Together, these results highlight the utility of improved methodologies in assessing RE transcription profiles in both archived and new microarray data sets. More importantly, application of this methodology suggests that immune activation, as a result of infection with pathogens or dysbiosis with commensal microbes, causes global modulation of RE transcription. RE responsiveness to external stimuli should, therefore, be considered in any association between RE transcription and disease.

Show MeSH
Related in: MedlinePlus