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An Lnc RNA (GAS5)/SnoRNA-derived piRNA induces activation of TRAIL gene by site-specifically recruiting MLL/COMPASS-like complexes.

He X, Chen X, Zhang X, Duan X, Pan T, Hu Q, Zhang Y, Zhong F, Liu J, Zhang H, Luo J, Wu K, Peng G, Luo H, Zhang L, Li X, Zhang H - Nucleic Acids Res. (2015)

Bottom Line: However, its function in the mammalian somatic cells remains unknown.Interestingly, the PIWIL1/4 proteins, which bind with this piRNA, directly interact with WDR5, resulting in a site-specific recruitment of the hCOMPASS-like complexes containing at least MLL3 and UTX (KDM6A).We have indicated a novel pathway for piRNAs to specially activate gene expression.

View Article: PubMed Central - PubMed

Affiliation: Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China.

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pi-sno75 significantly affects the histone modifications of TRAIL promoter. (A) Schematic representation of the TRAIL gene and the predicted piRNA-targeting locations relative to the TSS. (B–D) Association of H3K4me3, H3K9me3 or H3K27me3 at the TRAIL gene with the overexpression of pi-sno75 was assayed by ChIP-qPCR. The relative enrichment was calculated by normalizing the quantity of TRAIL DNA against the quantity of input. (EandF) Association of PIWIL1 or PIWIL4 at the TRAIL promoter with the overexpression of pi-sno75 was assayed by ChIP-qPCR. (G–J) RNAi screening of various histone modifiers and PIWIL family proteins on the impact of pi-sno75 regulating TRAIL. GAPDH was set as the internal reference. Data in bar graphs in (B–J) represent mean ± SD (n = 3). *, statistically significant, ≤0.05.
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Figure 4: pi-sno75 significantly affects the histone modifications of TRAIL promoter. (A) Schematic representation of the TRAIL gene and the predicted piRNA-targeting locations relative to the TSS. (B–D) Association of H3K4me3, H3K9me3 or H3K27me3 at the TRAIL gene with the overexpression of pi-sno75 was assayed by ChIP-qPCR. The relative enrichment was calculated by normalizing the quantity of TRAIL DNA against the quantity of input. (EandF) Association of PIWIL1 or PIWIL4 at the TRAIL promoter with the overexpression of pi-sno75 was assayed by ChIP-qPCR. (G–J) RNAi screening of various histone modifiers and PIWIL family proteins on the impact of pi-sno75 regulating TRAIL. GAPDH was set as the internal reference. Data in bar graphs in (B–J) represent mean ± SD (n = 3). *, statistically significant, ≤0.05.

Mentions: Recent studies revealed that small RNAs can activate genes expression and modify the epigenetic status of the target genes (16,33,34). Meanwhile some reports also indicated that PIWI could regulate gene expression by altering the chromatin state (9,35,36). We initially tried to search for the possible binding sites of pi-sno75 on the region of TRAIL gene. A highly complementary binding site was predicted at position -169 bp of the transcription start site (TSS) on the TRAIL promoter through an online program RNAhybrid [Minimum Free Energy (MFE) -27.4 kcal/mol] (Supplementary Figure S4) (37). In addition, five other potential targets of pi-sno75 were also predicted with lower putative binding affinities (Figure 4A). Chromatin immunoprecipitation (ChIP) was conducted to detect the epigenetic states of TRAIL gene. The results showed that the H3K4me3 level was significantly increased and H3K27me3 level was significantly decreased in the area of -169 bp site of TRAIL promoter in the MCF7 cells with pi-sno75 overexpression (Figure 4B and D). However, no significant change was detected in H3K9me3 level and H3K9Ac level in the condition of pi-sno75 overexpression (Figure 4C and Supplementary Figure S5A). This pattern of histone modifications, H3K4 methylation and H3K27 demethylation, favored the activation of gene expression (38). Meanwhile, both PIWIL1 and PIWIL4 were associated with the area at -169 bp site of TRAIL promoter under the overexpression of pi-sno75 (Figure 4E and F). In addition, PIWIL1 or PIWIL4 knockdown by siRNA reduced TRAIL expression upregulated by pi-sno75 (Figure 4G). Taken together, these data indicated that the piRNA/PIWIL1 or piRNA/PIWIL4 complex specifically interacted with the area at -169 bp site on TRAIL promoter and was required for the upregulation of TRAIL expression by pi-sno75.


An Lnc RNA (GAS5)/SnoRNA-derived piRNA induces activation of TRAIL gene by site-specifically recruiting MLL/COMPASS-like complexes.

He X, Chen X, Zhang X, Duan X, Pan T, Hu Q, Zhang Y, Zhong F, Liu J, Zhang H, Luo J, Wu K, Peng G, Luo H, Zhang L, Li X, Zhang H - Nucleic Acids Res. (2015)

pi-sno75 significantly affects the histone modifications of TRAIL promoter. (A) Schematic representation of the TRAIL gene and the predicted piRNA-targeting locations relative to the TSS. (B–D) Association of H3K4me3, H3K9me3 or H3K27me3 at the TRAIL gene with the overexpression of pi-sno75 was assayed by ChIP-qPCR. The relative enrichment was calculated by normalizing the quantity of TRAIL DNA against the quantity of input. (EandF) Association of PIWIL1 or PIWIL4 at the TRAIL promoter with the overexpression of pi-sno75 was assayed by ChIP-qPCR. (G–J) RNAi screening of various histone modifiers and PIWIL family proteins on the impact of pi-sno75 regulating TRAIL. GAPDH was set as the internal reference. Data in bar graphs in (B–J) represent mean ± SD (n = 3). *, statistically significant, ≤0.05.
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Figure 4: pi-sno75 significantly affects the histone modifications of TRAIL promoter. (A) Schematic representation of the TRAIL gene and the predicted piRNA-targeting locations relative to the TSS. (B–D) Association of H3K4me3, H3K9me3 or H3K27me3 at the TRAIL gene with the overexpression of pi-sno75 was assayed by ChIP-qPCR. The relative enrichment was calculated by normalizing the quantity of TRAIL DNA against the quantity of input. (EandF) Association of PIWIL1 or PIWIL4 at the TRAIL promoter with the overexpression of pi-sno75 was assayed by ChIP-qPCR. (G–J) RNAi screening of various histone modifiers and PIWIL family proteins on the impact of pi-sno75 regulating TRAIL. GAPDH was set as the internal reference. Data in bar graphs in (B–J) represent mean ± SD (n = 3). *, statistically significant, ≤0.05.
Mentions: Recent studies revealed that small RNAs can activate genes expression and modify the epigenetic status of the target genes (16,33,34). Meanwhile some reports also indicated that PIWI could regulate gene expression by altering the chromatin state (9,35,36). We initially tried to search for the possible binding sites of pi-sno75 on the region of TRAIL gene. A highly complementary binding site was predicted at position -169 bp of the transcription start site (TSS) on the TRAIL promoter through an online program RNAhybrid [Minimum Free Energy (MFE) -27.4 kcal/mol] (Supplementary Figure S4) (37). In addition, five other potential targets of pi-sno75 were also predicted with lower putative binding affinities (Figure 4A). Chromatin immunoprecipitation (ChIP) was conducted to detect the epigenetic states of TRAIL gene. The results showed that the H3K4me3 level was significantly increased and H3K27me3 level was significantly decreased in the area of -169 bp site of TRAIL promoter in the MCF7 cells with pi-sno75 overexpression (Figure 4B and D). However, no significant change was detected in H3K9me3 level and H3K9Ac level in the condition of pi-sno75 overexpression (Figure 4C and Supplementary Figure S5A). This pattern of histone modifications, H3K4 methylation and H3K27 demethylation, favored the activation of gene expression (38). Meanwhile, both PIWIL1 and PIWIL4 were associated with the area at -169 bp site of TRAIL promoter under the overexpression of pi-sno75 (Figure 4E and F). In addition, PIWIL1 or PIWIL4 knockdown by siRNA reduced TRAIL expression upregulated by pi-sno75 (Figure 4G). Taken together, these data indicated that the piRNA/PIWIL1 or piRNA/PIWIL4 complex specifically interacted with the area at -169 bp site on TRAIL promoter and was required for the upregulation of TRAIL expression by pi-sno75.

Bottom Line: However, its function in the mammalian somatic cells remains unknown.Interestingly, the PIWIL1/4 proteins, which bind with this piRNA, directly interact with WDR5, resulting in a site-specific recruitment of the hCOMPASS-like complexes containing at least MLL3 and UTX (KDM6A).We have indicated a novel pathway for piRNAs to specially activate gene expression.

View Article: PubMed Central - PubMed

Affiliation: Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China.

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Related in: MedlinePlus