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Protein–protein interactions mediate the cotranscriptional assembly of ribonucleoprotein complexes that are targets of DNA damage-induced signaling pathways. (A) Schematic representation of the communication between the transcriptional and splicing machineries mediated by RPB7, EWS, and YB-1. Camptothecin inhibits the interaction between Ewing’s sarcoma proto-oncoprotein (EWS), an RNAPII-associated factor, and YB-1, a spliceosome-associated factor. This results in the cotranscriptional skipping of several exons of the MDM2 gene (Dutertre et al., 2010). (B) The PRP19 complex functions in transcription and is recruited to the transcription machinery by the C terminus of its component Syf1, the yeast homolog of human XAB2 (adapted from Chanarat et al., 2011). Human XAB2 co-purifies both with factors involved in transcription (RNAPII), splicing (PRP19), and TCR (XPA, CSA and CSB; Kuraoka et al., 2008). The PRP19 complex is required for the recruitment of the THO/TREX complex to nascent transcripts after the switch from the B to the C splicing complex. Thick and thin black lines represent exons and introns, respectively.
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It is well-known that DNA-damaging agents induce genome instability, but only recently have we begun to appreciate that chromosomes are fragile per se and frequently subject to DNA breakage. DNA replication further magnifies such fragility, because it leads to accumulation of single-stranded DNA. Recent findings suggest that chromosome fragility is...
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RNA helicase A (RHA) promotes multiple steps in HIV-1 production including transcription and translation of viral RNA, annealing of primer tRNA(Lys3) to viral RNA, and elevating the ratio of unspliced to spliced viral RNA. At its amino terminus are two double-stranded RNA binding domains (dsRBDs) that are essential for RHA-viral RNA interaction. Li...
Citations
... Also, the alteration of HNRNPA3, SRSF7, and SRSF4 expression levels, as well as the disruption of transcriptome-wide splicing patterns using a pharmacological inhibitor of SF3B1, is also associated with the induction of senescence [149]. On the other hand, the restoration of splicing factor expression levels has been shown to rescue various aspects of the senescent cell phenotype [150][151][152]. In fact, not only was overexpression of the RNA processing factor PRP19 able to extend the lifespan of human endothelial cells in vitro by enhancing stress resilience and DNA repair capacity [150], but it has also demonstrated the ability to increase lifespan in a Drosophila systemic model [153]. ...
... On the other hand, the restoration of splicing factor expression levels has been shown to rescue various aspects of the senescent cell phenotype [150][151][152]. In fact, not only was overexpression of the RNA processing factor PRP19 able to extend the lifespan of human endothelial cells in vitro by enhancing stress resilience and DNA repair capacity [150], but it has also demonstrated the ability to increase lifespan in a Drosophila systemic model [153]. ...
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
... Sridhara et al. (2017) reported that SRPK2 phosphorylates the DDX23 helicase, thus suppressing the formation of R-loops. However, RNA processing defects result in elevated levels of R-loops (Stirling et al., 2012;Montecucco and Biamonti, 2013). Hence, signals that promote the nuclear accumulation of SRPK2 and the subsequent dysregulation of the splicing machinery would also be anticipated to lead to the formation of R-loop structures. ...
SR Protein Kinases (SRPKs), discovered approximately 30 years ago, are widely known as splice factor kinases due to their decisive involvement in the regulation of various steps of mRNA splicing. However, they were also shown to regulate diverse cellular activities by phosphorylation of serine residues residing in serine-arginine/arginine-serine dipeptide motifs. Over the last decade, SRPK1 has been reported as both tumor suppressor and promoter, depending on the cellular context and has been implicated in both chemotherapy sensitivity and resistance. Moreover, SRPK2 has been reported to exhibit contradictory functions in different cell contexts promoting either apoptosis or tumor growth. The aim of the current review is to broaden and deepen our understanding of the SRPK function focusing on the subcellular localization of the kinases. There is ample evidence that the balance between cytoplasmic and nuclear SRPK levels is tightly regulated and determines cell response to external signals. Specific cell states coupled to kinase levels, spatial specific interactions with substrates but also changes in the extent of phosphorylation that allow SRPKs to exhibit a rheostat-like control on their substrates, could decide the proliferative or antiproliferative role of SRPKs.
... Telomere shortening and initiation of replicating senescence [89][90][91] Decreased plasticity and adaptability of transcriptome Decreased molecular stress resilience [117] Uncoupling of DNA damage response and splicing regulation Accumulation and faulty repair of DNA damage [70,95] 1227 ...
... RNA molecules may exist in a state where there may be interactions between not only RNA and mRNA processing factors, but also between nascent transcripts and DNA. Evidence is mounting that dysregulated coordination between different RNA processing steps may facilitate introduce defects in genome stability by disrupting the interactions between nascent RNA and the DNA template [95]. DNA damage is also able to directly modify splicing proteins via PARylation, arginine methylation, acetylation, ubiquitination/sumoylation or phosphorylation [70]. ...
... Similarly, genetic perturbation of HNRNPA3, SRSF7 and SRSF4 expression levels was sufficient to provoke senescence, as was disruption of transcriptome wide splicing patterns using a pharmacological inhibitor of SF3B1, an important component of the U2 snRNP involved in branch site recognition [53]. Similarly, depletion of the pre-mRNA processing factor Prp19 promotes cellular senescence and premature ageing in mouse skin [95]. The third criteria of a hallmark of ageing is that its experimental abrogation should bring about improvement to aspects of the ageing phenotype. ...
The human genome is capable of producing hundreds of thousands of different proteins and non‐coding RNAs from <20 000 genes, in a co‐ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence‐associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
... While many proteins showed similar interaction with LMNA, regardless of the SIRT6 allele present, a large group of proteins showed enhanced interaction with LMNA in the presence of centSIRT6 (Fig 6G; Data S3). LMNA-interaction partners enhanced by sentSIRT6 included ELAVL1, FUS, PCBP2, SAFB, SRSF1, SRSF3, TFIP11, THRAP3, BCLAF1, and U2AFBP all proteins that facilitate the coordination of the DNA damage response with RNA processing (Beli, Lukashchuk et al., 2012, Montecucco & Biamonti, 2013, Naro, Bielli et al., 2015, Vohhodina, Barros et al., 2017. Many of the proteins identified in SIRT6 and LMNA IPs are ADP-ribosylated (Bilan, Leutert et al., 2017, Hendriks et al., 2019, Jungmichel, Rosenthal et al., 2013, Leslie Pedrioli, Leutert et al., 2018, Martello, Leutert et al., 2016, Vivelo, Wat et al., 2017) (shown as hexagons in Fig 6G), ...
Sirtuin 6 (SIRT6) is a deacylase and mono-ADP ribosyl transferase (mADPr) enzyme involved in multiple cellular pathways implicated in the regulation of aging and metabolism. Targeted sequencing identified a SIRT6 allele containing two linked substitutions (N308K/A313S) as enriched in Ashkenazi Jewish (AJ) centenarians as compared to AJ control individuals. Characterization of this SIRT6 (centSIRT6) allele demonstrated it to be a stronger suppressor of LINE1 retrotransposons, confer enhanced stimulation of DNA double strand break repair, and more robust cancer cell killing compared to the wild type. Surprisingly, centSIRT6 displayed weaker deacetylase activity, but stronger mADPr activity, over a range of NAD+ concentrations and substrates. Additionally, centSIRT6 displayed a stronger interaction with Lamin A/C (LMNA), which correlated with enhanced ribosylation of LMNA. Our results suggest that enhanced SIRT6 function contributes to human longevity by improving genome maintenance via increased mADPr activity and enhanced interaction with LMNA.
... The second is homologous recombination repair (HR), an errorfree process that functions in late S and G2 phases, when an intact chromatid is available (4)(5)(6)(7)(8). Work from our lab and many others revealed a prevalent role of RNA binding proteins and pre-mRNA processing factors in DDR including DSB repair (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23). Remarkably, splicing factors were shown to accumulate at DNA damage sites, suggesting that they may play a direct role in DDR beside their canonical function in pre-mRNA splicing (17,(24)(25)(26)(27)(28). ...
RNA-binding proteins regulate mRNA processing and translation and are often aberrantly expressed in cancer. The RNA-binding motif protein 6, RBM6, is a known alternative splicing factor that harbors tumor suppressor activity and is frequently mutated in human cancer. Here, we identify RBM6 as a novel regulator of homologous recombination (HR) repair of DNA double-strand breaks (DSBs). Mechanistically, we show that RBM6 regulates alternative splicing-coupled nonstop-decay of a positive HR regulator, Fe65/APBB1. RBM6 knockdown leads to a severe reduction in Fe65 protein levels and consequently impairs HR of DSBs. Accordingly, RBM6-deficient cancer cells are vulnerable to ATM and PARP inhibition and show remarkable sensitivity to cisplatin. Concordantly, cisplatin administration inhibits the growth of breast tumor devoid of RBM6 in mouse xenograft model. Furthermore, we observe that RBM6 protein is significantly lost in metastatic breast tumors compared with primary tumors, thus suggesting RBM6 as a potential therapeutic target of advanced breast cancer. Collectively, our results elucidate the link between the multifaceted roles of RBM6 in regulating alternative splicing and HR of DSBs that may contribute to tumorigenesis, and pave the way for new avenues of therapy for RBM6-deficient tumors.
... Besides, our MS analysis suggests that La inhibits gene expression through forming two protein groups: the RBP group and ribosome structure protein group. As an RBP, it is possible for La to interact with other RBPs to assemble into RNP complexes (35). Cotranscriptional assembly of RNP complex is important for the maintenance of genome integrity by preventing the formation of R-loop during transcription (35,36), which might simultaneously suppress the chromatin accessibility and shut down the transcription. ...
... As an RBP, it is possible for La to interact with other RBPs to assemble into RNP complexes (35). Cotranscriptional assembly of RNP complex is important for the maintenance of genome integrity by preventing the formation of R-loop during transcription (35,36), which might simultaneously suppress the chromatin accessibility and shut down the transcription. On the other hand, noncanonical function of ribosome constituents in gene expression has also been found. ...
Significance
Epithelial cell–mediated chemokine production and subsequent neutrophil recruitment are important for pathogen clearance, which, however, are also closely related to severe inflammatory tissue damage during lung infection, especially influenza virus infection and the current pandemic coronavirus infection. Certain regulation and underlying mechanisms of chemokine expression in epithelial cells remain largely unknown. Here, by identifying the mouse long noncoding RNA lnc-Cxcl2 and human lnc-CXCL2-4-1 in virus-infected lung epithelial cells, we demonstrated a self-protecting mechanism in host lung epithelial cells for restraining viral infection–induced lung inflammation through feedback-suppressing chemokine expression. These findings provide better understandings of chemokine regulation and epithelial cell function during lung viral infection and will benefit the treatment of related lung infectious diseases.
... Recent findings support the notion that DNA damage is inherently linked to splicing [9][10][11] . The presence of irreparable DNA lesions may influence RNA splicing through the selective nuclear transport of splicing factors 12,13 , the inhibition of the elongating RNAPII 9 , the interaction of RNAPIIand spliceosome-associated factors 14 or the displacement of the spliceosome when RNAPII is stalled at DNA damage sites 11 . ...
RNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csb m/m developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for transcription-coupled DNA repair disorders.
... Moreover, alteration in the phosphorylation of SRSF1 subsequent to DNA damages alters the alternative splicing pattern in caspase 9. This signifies the active influence of etoposide on alternative splicing mechanisms and its correlation with the modulation of apoptosis in target cells [274][275][276][277] . ...
Chemotherapeutic drugs kill cancer cells or control their progression all over the patient's body, while radiation- and surgery-based treatments perform in a particular site. Based on their mechanisms of action, they are classified into different groups, including alkylating substrates, antimetabolite agents, anti-tumor antibiotics, inhibitors of topoisomerase I and II, mitotic inhibitors, and finally, corticosteroids. Although chemotherapeutic drugs have brought about more life expectancy, two major and severe complications during chemotherapy are chemoresistance and tumor relapse. Therefore, we aimed to review the underlying intracellular signaling pathways involved in cell death and resistance in different chemotherapeutic drug families to clarify the shortcomings in the conventional single chemotherapy applications. Moreover, we have summarized the current combination chemotherapy applications, including numerous combined-, and encapsulated-combined-chemotherapeutic drugs. We further discussed the possibilities and applications of precision medicine, machine learning, next-generation sequencing (NGS), and whole-exome sequencing (WES) in promoting cancer immunotherapies. Finally, some of the recent clinical trials concerning the application of immunotherapies and combination chemotherapies were included as well, in order to provide a practical perspective toward the future of therapies in cancer cases.
... DNA/RNA metabolism-related cellular pathways or biological processes, especially the base excision repair, were both involved in the potential role of SNRPA in the pathogenesis of LUAD and LUSC. Considering the essential role of SNRPA in the cellular pre-mRNA splicing process (Singh and Singh, 2019) and the association between pre-mRNA processing factors and DNA damage response (Montecucco and Biamonti, 2013), it is meaningful to analyze the potential functional link of SNPRA with DNA damage repair pathway during tumorigenesis. Further, cell cycle and ubiquitin mechanism-associated issues may be involved in the LUAD pathogenesis, whereas RNA splicingrelated cellular issues seem to be important for LUSC. ...
SNRPA (small nuclear ribonucleoprotein polypeptide A) gene is essential for the pre-mRNA splicing process. Using the available datasets of TCGA or GEO, we aimed at exploring the potential association between the SNRPA gene and lung cancer by several online tools (such as GEIPA2, MEXPRESS, Oncomine) and bioinformatics analysis software (R or GSEA). SNRPA was highly expressed in the tissues of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma tissue (LUSC), compared with control tissues. The high SNRPA expression was associated with a poor survival prognosis of LUAD cases, while the genetic alteration within SNRPA was linked to the overall survival prognosis of LUSC cases. There was a potential correlation between promoter methylation and the expression of SNRPA for LUAD. Compared with normal tissues, we observed a higher phosphorylation level at the S115 site of SNRPA protein (NP_004587.1) (p = 0.002) in the primary LUAD tissues. The potential ATR kinase of the S115 site was predicted. Besides, SNRPA expression in lung cancer was negatively correlated with the infiltration level of M2 macrophage but positively correlated with that of Follicular B helper T cells, in both LUAD and LUSC. The enrichment analysis of SNRPA-correlated genes showed that cell cycle and ubiquitin mechanism-related issues were mainly observed for LUAD; however, RNA splicing-related cellular issues were mainly for LUSC. In summary, the SNRPA gene was identified as a potential prognosis biomarker of lung cancer, especially lung adenocarcinoma, which sheds new light on the association between the spliceosomal complex component and tumorigenesis.
... It is an integral protein that helps with the formation and maintenance of paraspeckles in mammalian cells 5 . SFPQ is also speculated to play a vital role in other biological processes such as DNA repair, RNA splicing and transport [6][7][8][9] . In another study in mice, knocking out of the gene that encodes Nuclear Enriched Abundant Transcript 1 (NEAT1) RNA, another core component of paraspeckles, resultant in a complete loss of paraspeckles, but no apparent phenotypic changes were observed in mice 5 . ...
CRISPR-Cas9 is widely used for targeted genome editing for a wide range of organisms. In this study, we used CRISPR interference (CRISPRi) which employs a catalytically inactive version of Cas9 (known as Dead Cas9 or dCas9) fused to KRAB a chromatin modifier. Similar to Cas9, the dCas9 protein forms a complex along with single guide RNA (sgRNA) and binds desired DNA sequences in the presence of a protospacer adjacent motif (PAM). However, unlike Cas9, dCas9 doesn’t cleave the DNA sequence but can repress gene expression when fused with KRAB. The role of paraspeckles in human cell biology is relatively unknown. In this study, we used CRISPRi to investigate the role of splicing factor proline and glutamine rich (SFPQ), also known as PSF (PTB-associated splicing factor), which is a conserved and core component of paraspeckles. We designed and constructed six different sgRNAs to target different locations of the SFPQ gene in Human induced Pluripotent Stem Cells (HiPSCs). The most effective sgRNA (sgRNA #5) knocked down the expression of SFPQ up to > 99%. We also observed that the knockdown of SFPQ exhibits severe cell-death phenotype in HiPSCs. This finding suggests that CRISPRi based SFPQ repression can modulate stem cell proliferation and maintenance. This study also suggests that SFPQ could play a vital role in proliferating cells such as cancer cells. Most importantly, these results are significant because in mice, knocking out another core component of paraspeckles results in no apparent phenotype despite the complete loss of paraspeckles. Given that traditional drug testing approaches rely on animal models, it is consequential to consider that human cell biology is more distinct than previously imagined. This study provides a new insight for role and function of SFPQ in iPSCs.
