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Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome.

Lim YW, Sanz LA, Xu X, Hartono SR, Chédin F - Elife (2015)

Bottom Line: Aicardi-Goutières syndrome (AGS) is a severe childhood inflammatory disorder that shows clinical and genetic overlap with systemic lupus erythematosus (SLE).AGS is thought to arise from the accumulation of incompletely metabolized endogenous nucleic acid species owing to mutations in nucleic acid-degrading enzymes TREX1 (AGS1), RNase H2 (AGS2, 3 and 4), and SAMHD1 (AGS5).However, the identity and source of such immunogenic nucleic acid species remain undefined.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States.

ABSTRACT
Aicardi-Goutières syndrome (AGS) is a severe childhood inflammatory disorder that shows clinical and genetic overlap with systemic lupus erythematosus (SLE). AGS is thought to arise from the accumulation of incompletely metabolized endogenous nucleic acid species owing to mutations in nucleic acid-degrading enzymes TREX1 (AGS1), RNase H2 (AGS2, 3 and 4), and SAMHD1 (AGS5). However, the identity and source of such immunogenic nucleic acid species remain undefined. Using genome-wide approaches, we show that fibroblasts from AGS patients with AGS1-5 mutations are burdened by excessive loads of RNA:DNA hybrids. Using MethylC-seq, we show that AGS fibroblasts display pronounced and global loss of DNA methylation and demonstrate that AGS-specific RNA:DNA hybrids often occur within DNA hypomethylated regions. Altogether, our data suggest that RNA:DNA hybrids may represent a common immunogenic form of nucleic acids in AGS and provide the first evidence of epigenetic perturbations in AGS, furthering the links between AGS and SLE.

No MeSH data available.


Related in: MedlinePlus

Canonical R-loop genomic patterns are not affected in AGS fibroblasts.(A) Representative screenshot of the broad genomic landscape of R-loop formation over a 2-Mb region. DRIP-seq signal is represented by the accumulation of sequence reads along the genomic sequence. Each sample is color-coded as indicated. CpG islands are indicated together with the positions of genes along the region. (B) A representative screenshot of R-loops formed at the 5′- and 3′-end of the DACT1 gene. (C) Pie chart depicting the distribution of common DRIP peaks at different genomic regions. (D) Percent length overlap of common and AGS-unique peaks over different genomic features. *p < 0.002 and fold change >20% relative to common peaks.DOI:http://dx.doi.org/10.7554/eLife.08007.007
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fig3s1: Canonical R-loop genomic patterns are not affected in AGS fibroblasts.(A) Representative screenshot of the broad genomic landscape of R-loop formation over a 2-Mb region. DRIP-seq signal is represented by the accumulation of sequence reads along the genomic sequence. Each sample is color-coded as indicated. CpG islands are indicated together with the positions of genes along the region. (B) A representative screenshot of R-loops formed at the 5′- and 3′-end of the DACT1 gene. (C) Pie chart depicting the distribution of common DRIP peaks at different genomic regions. (D) Percent length overlap of common and AGS-unique peaks over different genomic features. *p < 0.002 and fold change >20% relative to common peaks.DOI:http://dx.doi.org/10.7554/eLife.08007.007

Mentions: To identify other species of RNA:DNA hybrids that may be accumulating in AGS, we performed DRIP-seq, a technique originally developed to profile R-loop formation genome-wide (Ginno et al., 2012). R-loops are long RNA:DNA hybrid structures that form co-transcriptionally upon re-annealing of the RNA transcript to the template DNA strand, forcing the non-template strand into a single-stranded state. R-loops are enriched at the 5′- and 3′-ends of human genes where they play roles in epigenetic control and transcription regulation (Ginno et al., 2012, 2013). DRIP-seq revealed that AGS and control fibroblasts share a total of 15,897 DRIP peaks representing approximately 141 megabases of genomic space (Figure 3A,C, Figure 3—figure supplement 1A,B). Consistent with prior studies, 32% of these peaks mapped to promoters or gene ends, which represents a strong enrichment over expected genomic distribution and further indicates that gene ends correspond to R-loop formation hotspots (Ginno et al., 2013). Our high-coverage DRIP-seq data also revealed that 56% of the R-loop signal mapped onto gene bodies, suggesting that RNA–DNA entanglements during transcription are prevalent (Figure 3—figure supplement 1C). By contrast, only 15.6% of common R-loop peaks mapped to intergenic regions, consistent with a predominant genic origin for R-loop formation (Figure 3—figure supplement 1C). Overall, common DRIP peaks showed strong overlap with GC skew (Figure 3B), a key sequence determinant that favors co-transcriptional R-loop formation (Ginno et al., 2013). The observation that AGS samples display R-loop formation over expected R-loop forming, GC-skewed, regions indicates that canonical R-loop formation is not significantly altered in AGS patients (Figure 3—figure supplement 1A,B).10.7554/eLife.08007.006Figure 3.AGS fibroblasts accumulate RNA:DNA hybrids.


Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome.

Lim YW, Sanz LA, Xu X, Hartono SR, Chédin F - Elife (2015)

Canonical R-loop genomic patterns are not affected in AGS fibroblasts.(A) Representative screenshot of the broad genomic landscape of R-loop formation over a 2-Mb region. DRIP-seq signal is represented by the accumulation of sequence reads along the genomic sequence. Each sample is color-coded as indicated. CpG islands are indicated together with the positions of genes along the region. (B) A representative screenshot of R-loops formed at the 5′- and 3′-end of the DACT1 gene. (C) Pie chart depicting the distribution of common DRIP peaks at different genomic regions. (D) Percent length overlap of common and AGS-unique peaks over different genomic features. *p < 0.002 and fold change >20% relative to common peaks.DOI:http://dx.doi.org/10.7554/eLife.08007.007
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528086&req=5

fig3s1: Canonical R-loop genomic patterns are not affected in AGS fibroblasts.(A) Representative screenshot of the broad genomic landscape of R-loop formation over a 2-Mb region. DRIP-seq signal is represented by the accumulation of sequence reads along the genomic sequence. Each sample is color-coded as indicated. CpG islands are indicated together with the positions of genes along the region. (B) A representative screenshot of R-loops formed at the 5′- and 3′-end of the DACT1 gene. (C) Pie chart depicting the distribution of common DRIP peaks at different genomic regions. (D) Percent length overlap of common and AGS-unique peaks over different genomic features. *p < 0.002 and fold change >20% relative to common peaks.DOI:http://dx.doi.org/10.7554/eLife.08007.007
Mentions: To identify other species of RNA:DNA hybrids that may be accumulating in AGS, we performed DRIP-seq, a technique originally developed to profile R-loop formation genome-wide (Ginno et al., 2012). R-loops are long RNA:DNA hybrid structures that form co-transcriptionally upon re-annealing of the RNA transcript to the template DNA strand, forcing the non-template strand into a single-stranded state. R-loops are enriched at the 5′- and 3′-ends of human genes where they play roles in epigenetic control and transcription regulation (Ginno et al., 2012, 2013). DRIP-seq revealed that AGS and control fibroblasts share a total of 15,897 DRIP peaks representing approximately 141 megabases of genomic space (Figure 3A,C, Figure 3—figure supplement 1A,B). Consistent with prior studies, 32% of these peaks mapped to promoters or gene ends, which represents a strong enrichment over expected genomic distribution and further indicates that gene ends correspond to R-loop formation hotspots (Ginno et al., 2013). Our high-coverage DRIP-seq data also revealed that 56% of the R-loop signal mapped onto gene bodies, suggesting that RNA–DNA entanglements during transcription are prevalent (Figure 3—figure supplement 1C). By contrast, only 15.6% of common R-loop peaks mapped to intergenic regions, consistent with a predominant genic origin for R-loop formation (Figure 3—figure supplement 1C). Overall, common DRIP peaks showed strong overlap with GC skew (Figure 3B), a key sequence determinant that favors co-transcriptional R-loop formation (Ginno et al., 2013). The observation that AGS samples display R-loop formation over expected R-loop forming, GC-skewed, regions indicates that canonical R-loop formation is not significantly altered in AGS patients (Figure 3—figure supplement 1A,B).10.7554/eLife.08007.006Figure 3.AGS fibroblasts accumulate RNA:DNA hybrids.

Bottom Line: Aicardi-Goutières syndrome (AGS) is a severe childhood inflammatory disorder that shows clinical and genetic overlap with systemic lupus erythematosus (SLE).AGS is thought to arise from the accumulation of incompletely metabolized endogenous nucleic acid species owing to mutations in nucleic acid-degrading enzymes TREX1 (AGS1), RNase H2 (AGS2, 3 and 4), and SAMHD1 (AGS5).However, the identity and source of such immunogenic nucleic acid species remain undefined.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States.

ABSTRACT
Aicardi-Goutières syndrome (AGS) is a severe childhood inflammatory disorder that shows clinical and genetic overlap with systemic lupus erythematosus (SLE). AGS is thought to arise from the accumulation of incompletely metabolized endogenous nucleic acid species owing to mutations in nucleic acid-degrading enzymes TREX1 (AGS1), RNase H2 (AGS2, 3 and 4), and SAMHD1 (AGS5). However, the identity and source of such immunogenic nucleic acid species remain undefined. Using genome-wide approaches, we show that fibroblasts from AGS patients with AGS1-5 mutations are burdened by excessive loads of RNA:DNA hybrids. Using MethylC-seq, we show that AGS fibroblasts display pronounced and global loss of DNA methylation and demonstrate that AGS-specific RNA:DNA hybrids often occur within DNA hypomethylated regions. Altogether, our data suggest that RNA:DNA hybrids may represent a common immunogenic form of nucleic acids in AGS and provide the first evidence of epigenetic perturbations in AGS, furthering the links between AGS and SLE.

No MeSH data available.


Related in: MedlinePlus