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FUS-regulated RNA metabolism and DNA damage repair: Implications for amyotrophic lateral sclerosis and frontotemporal dementia pathogenesis.

Zhou Y, Liu S, Oztürk A, Hicks GG - Rare Dis (2014)

Bottom Line: Our recent discovery of a FUS autoregulatory mechanism and its dysregulation in ALS-FUS mutants demonstrated that dysregulated alternative splicing can directly exacerbate the pathological FUS accumulation.We show here that FUS targets RNA for pre-mRNA alternative splicing and for the processing of long intron-containing transcripts, and that these targets are enriched for genes in neurogenesis and gene expression regulation.We also identify that FUS RNA targets are enriched for genes in the DNA damage response pathway.

View Article: PubMed Central - PubMed

Affiliation: Manitoba Institute of Cell Biology; Department of Biochemistry & Medical Genetics; Regenerative Medicine Program; University of Manitoba; Winnipeg, MB Canada.

ABSTRACT
Cytoplasmic inclusion of RNA binding protein FUS/TLS in neurons and glial cells is a characteristic pathology of a subgroup of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Dysregulation of RNA metabolism caused by FUS cytoplasmic inclusion emerges to be a key event in FUS-associated ALS/FTD pathogenesis. Our recent discovery of a FUS autoregulatory mechanism and its dysregulation in ALS-FUS mutants demonstrated that dysregulated alternative splicing can directly exacerbate the pathological FUS accumulation. We show here that FUS targets RNA for pre-mRNA alternative splicing and for the processing of long intron-containing transcripts, and that these targets are enriched for genes in neurogenesis and gene expression regulation. We also identify that FUS RNA targets are enriched for genes in the DNA damage response pathway. Together, the data support a model in which dysregulated RNA metabolism and DNA damage repair together may render neurons more vulnerable and accelerate neurodegeneration in ALS and FTD.

No MeSH data available.


Related in: MedlinePlus

Figure 3. FUS targets RNA of genes in DNA damage response and repair pathways. (A) Ingenuity Pathways Analysis (IPA) of FUS RNA targets that fall into the GO functional category of “cellular response to DNA damage stimulus” (GO: 0006974). FUS RNA targets from ours12 and five others’ CLIP-seq assays were analyzed.18-22 The RNA targets that fall into the GO: 006974 category and were also identified by at least two research groups are used for IPA. The blue bars represent P values. The pink line represents the ratio of FUS RNA targets over the total number of genes in each pathway. (B) FUS RNA targets that map to the ATM signaling pathway by IPA analysis. FUS RNA targets are highlighted in purple.
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Figure 3: Figure 3. FUS targets RNA of genes in DNA damage response and repair pathways. (A) Ingenuity Pathways Analysis (IPA) of FUS RNA targets that fall into the GO functional category of “cellular response to DNA damage stimulus” (GO: 0006974). FUS RNA targets from ours12 and five others’ CLIP-seq assays were analyzed.18-22 The RNA targets that fall into the GO: 006974 category and were also identified by at least two research groups are used for IPA. The blue bars represent P values. The pink line represents the ratio of FUS RNA targets over the total number of genes in each pathway. (B) FUS RNA targets that map to the ATM signaling pathway by IPA analysis. FUS RNA targets are highlighted in purple.

Mentions: The function of FUS in DNA damage repair on the molecular level is not yet clear. In response to DNA damage, FUS is rapidly recruited to DNA damage sites prior to H2AX phosphorylation, and interacts with HDAC1.17 FUS may be recruited to modulate chromatin conformation changes, stabilize DNA damage repair complexes, or regulate transcription and alternative splicing. Our recent analysis of CLIP-seq data suggests that FUS may regulate the alternative splicing of genes crucial in DNA damage response and repair pathways. We searched for FUS RNA targets that fall into the GO functional category of cellular response to DNA damage stimulus (GO: 0006974) in ours and five other previously published FUS CLIP-seq data.12,18-22 We identified 382 genes that were detected in at least two studies (data not shown) and applied Ingenuity Pathway Analysis (IPA) to these genes. The top 20 statistically significant (P ≤ 0.05) pathways are shown in Figure 3A. BRCA1 breast cancer signaling, ATM signaling (Fig. 3B), DNA double-strand break repair and cell cycle checkpoints are among the most enriched pathways. Remarkably, about 60% of the genes in the DNA double-strand break repair HR pathway (Fig. S2A) and NHEJ pathway (Fig. S2B) are FUS RNA targets. These data suggest that FUS may regulate the alternative splicing of these DNA damage response or repair genes in response to DNA double strand breaks. It was reported that EWS, a family member closely related to FUS, modulates the alternative splicing of ABL1, CHEK2, and MAP4K2 in response to UV-induced single strand DNA damage and genotoxic stress signaling.27 A similar mechanism likely exists for FUS-dependent DNA damage response. Our analysis here suggests for the first time that RNA metabolism may represent a novel mechanism underlying FUS-dependent DNA damage response and repair. Given that FUS is phosphorylated by ATM in response to DNA double-strand breaks,28 it is tempting to speculate that FUS may link the ATM signaling pathway to RNA metabolism. FUS may modulate alternative splicing to coordinate crucial DNA damage response and repair pathways. Genetic lesions in DNA damage repair and DNA damage response signaling genes are well known to cause cell death and neurodegeneration.13 Defective DNA damage repair caused by ALS-associated FUS mutations may render neurons more vulnerable to stress and promote neurodegeneration. In line with this notion, ALS with FUS mutations, in general, show an earlier disease onset when compared with other ALS mutations.29


FUS-regulated RNA metabolism and DNA damage repair: Implications for amyotrophic lateral sclerosis and frontotemporal dementia pathogenesis.

Zhou Y, Liu S, Oztürk A, Hicks GG - Rare Dis (2014)

Figure 3. FUS targets RNA of genes in DNA damage response and repair pathways. (A) Ingenuity Pathways Analysis (IPA) of FUS RNA targets that fall into the GO functional category of “cellular response to DNA damage stimulus” (GO: 0006974). FUS RNA targets from ours12 and five others’ CLIP-seq assays were analyzed.18-22 The RNA targets that fall into the GO: 006974 category and were also identified by at least two research groups are used for IPA. The blue bars represent P values. The pink line represents the ratio of FUS RNA targets over the total number of genes in each pathway. (B) FUS RNA targets that map to the ATM signaling pathway by IPA analysis. FUS RNA targets are highlighted in purple.
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Related In: Results  -  Collection

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Figure 3: Figure 3. FUS targets RNA of genes in DNA damage response and repair pathways. (A) Ingenuity Pathways Analysis (IPA) of FUS RNA targets that fall into the GO functional category of “cellular response to DNA damage stimulus” (GO: 0006974). FUS RNA targets from ours12 and five others’ CLIP-seq assays were analyzed.18-22 The RNA targets that fall into the GO: 006974 category and were also identified by at least two research groups are used for IPA. The blue bars represent P values. The pink line represents the ratio of FUS RNA targets over the total number of genes in each pathway. (B) FUS RNA targets that map to the ATM signaling pathway by IPA analysis. FUS RNA targets are highlighted in purple.
Mentions: The function of FUS in DNA damage repair on the molecular level is not yet clear. In response to DNA damage, FUS is rapidly recruited to DNA damage sites prior to H2AX phosphorylation, and interacts with HDAC1.17 FUS may be recruited to modulate chromatin conformation changes, stabilize DNA damage repair complexes, or regulate transcription and alternative splicing. Our recent analysis of CLIP-seq data suggests that FUS may regulate the alternative splicing of genes crucial in DNA damage response and repair pathways. We searched for FUS RNA targets that fall into the GO functional category of cellular response to DNA damage stimulus (GO: 0006974) in ours and five other previously published FUS CLIP-seq data.12,18-22 We identified 382 genes that were detected in at least two studies (data not shown) and applied Ingenuity Pathway Analysis (IPA) to these genes. The top 20 statistically significant (P ≤ 0.05) pathways are shown in Figure 3A. BRCA1 breast cancer signaling, ATM signaling (Fig. 3B), DNA double-strand break repair and cell cycle checkpoints are among the most enriched pathways. Remarkably, about 60% of the genes in the DNA double-strand break repair HR pathway (Fig. S2A) and NHEJ pathway (Fig. S2B) are FUS RNA targets. These data suggest that FUS may regulate the alternative splicing of these DNA damage response or repair genes in response to DNA double strand breaks. It was reported that EWS, a family member closely related to FUS, modulates the alternative splicing of ABL1, CHEK2, and MAP4K2 in response to UV-induced single strand DNA damage and genotoxic stress signaling.27 A similar mechanism likely exists for FUS-dependent DNA damage response. Our analysis here suggests for the first time that RNA metabolism may represent a novel mechanism underlying FUS-dependent DNA damage response and repair. Given that FUS is phosphorylated by ATM in response to DNA double-strand breaks,28 it is tempting to speculate that FUS may link the ATM signaling pathway to RNA metabolism. FUS may modulate alternative splicing to coordinate crucial DNA damage response and repair pathways. Genetic lesions in DNA damage repair and DNA damage response signaling genes are well known to cause cell death and neurodegeneration.13 Defective DNA damage repair caused by ALS-associated FUS mutations may render neurons more vulnerable to stress and promote neurodegeneration. In line with this notion, ALS with FUS mutations, in general, show an earlier disease onset when compared with other ALS mutations.29

Bottom Line: Our recent discovery of a FUS autoregulatory mechanism and its dysregulation in ALS-FUS mutants demonstrated that dysregulated alternative splicing can directly exacerbate the pathological FUS accumulation.We show here that FUS targets RNA for pre-mRNA alternative splicing and for the processing of long intron-containing transcripts, and that these targets are enriched for genes in neurogenesis and gene expression regulation.We also identify that FUS RNA targets are enriched for genes in the DNA damage response pathway.

View Article: PubMed Central - PubMed

Affiliation: Manitoba Institute of Cell Biology; Department of Biochemistry & Medical Genetics; Regenerative Medicine Program; University of Manitoba; Winnipeg, MB Canada.

ABSTRACT
Cytoplasmic inclusion of RNA binding protein FUS/TLS in neurons and glial cells is a characteristic pathology of a subgroup of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Dysregulation of RNA metabolism caused by FUS cytoplasmic inclusion emerges to be a key event in FUS-associated ALS/FTD pathogenesis. Our recent discovery of a FUS autoregulatory mechanism and its dysregulation in ALS-FUS mutants demonstrated that dysregulated alternative splicing can directly exacerbate the pathological FUS accumulation. We show here that FUS targets RNA for pre-mRNA alternative splicing and for the processing of long intron-containing transcripts, and that these targets are enriched for genes in neurogenesis and gene expression regulation. We also identify that FUS RNA targets are enriched for genes in the DNA damage response pathway. Together, the data support a model in which dysregulated RNA metabolism and DNA damage repair together may render neurons more vulnerable and accelerate neurodegeneration in ALS and FTD.

No MeSH data available.


Related in: MedlinePlus