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Karen L. Beemon - One of the best experts on this subject based on the ideXlab platform.
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rous sarcoma virus RNA Stability element inhibits deadenylation of mRNAs with long 3 utrs
Viruses, 2017Co-Authors: Vidya Balagopal, Karen L. BeemonAbstract:All retroviruses use their full-length primary transcript as the major mRNA for Group-specific antigen (Gag) capsid proteins. This results in a long 3′ untranslated region (UTR) downstream of the termination codon. In the case of Rous sarcoma virus (RSV), there is a 7 kb 3′UTR downstream of the gag terminator, containing the pol, env, and src genes. mRNAs containing long 3′UTRs, like those with premature termination codons, are frequently recognized by the cellular nonsense-mediated mRNA decay (NMD) machinery and targeted for degradation. To prevent this, RSV has evolved an RNA Stability element (RSE) in the RNA immediately downstream of the gag termination codon. This 400-nt RNA sequence stabilizes premature termination codons (PTCs) in gag. It also stabilizes globin mRNAs with long 3′UTRs, when placed downstream of the termination codon. It is not clear how the RSE stabilizes the mRNA and prevents decay. We show here that the presence of RSE inhibits deadenylation severely. In addition, the RSE also impairs decapping (DCP2) and 5′-3′ exonucleolytic (XRN1) function in knockdown experiments in human cells.
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the structure and function of the rous sarcoma virus RNA Stability element
Journal of Cellular Biochemistry, 2011Co-Authors: Johanna B Withers, Karen L. BeemonAbstract:Rous sarcoma virus (RSV) is an avian retrovirus originally discovered by Peyton Rous in 1911 as a filterable transmissible agent isolated from a sarcoma of the common fowl [Rous, 1911]. All retroviruses have two copies of a plus strand RNA genome, which is capped and polyadenylated [Beemon et al., 1974; Furuichi et al., 1975]. Upon entry into a receptive host cell, the genomic RNA is reverse transcribed into a proviral DNA copy. This proviral DNA is stably integrated into the host cell chromosomal DNA by the viral integrase. After integration, the provirus is treated as a cellular gene where subsequent steps of viral gene expression are completed by the machinery associated with cellular RNA polymerase II and ribosomes [Coffin et al., 1997]. RSV is a simple avian retrovirus with a genome containing four main open reading frames (ORFs) 5′-gag-pol-env-src-3′ (Fig. 1). The first three genes (gag, pol, and env) are minimally required to generate a functional retrovirus. These proteins are expressed from three viral RNAs [Hayward, 1977]. The first is a full-length, unspliced RNA, which is the RNA genome for progeny virions and the mRNA for Gag and Pol proteins [Coffin et al., 1997]. Gag and Pol are expressed as polyproteins that are later cleaved by a viral protease into their individual functional polypeptides. In alpha retroviruses such as RSV, gag encodes the main structural components of the viral capsid and the viral protease. Pol encodes the reverse transcriptase and integrase. The gag and pol ORFs are separated by a −1 frameshift that is facilitated by a pseudoknot that lies just downstream of the gag ORF [Coffin et al., 1997]. Fig. 1 The RSV genome and viral mRNAs. RSV contains three uORFS and four ORFs (gag, pol, env, and src) that are expressed from the proviral DNA in three RNA isoforms. The direct repeats (DRs) are required for export of the unspliced RNA. The long terminal repeats ... The first spliced RNA allows for expression of env, which encodes the glycoproteins that stud the outside of the retroviral lipid bilayer and interact with host cell surface receptors to facilitate cell entry. The second spliced RNA encodes for Src, which is the viral counterpart to the cellular proto-oncogene c-Src [Coffin et al., 1981; Martin, 2004]. Viral Src, contains several point mutations and a C-terminal substitution that results in its deregulation within host cells. In addition, RSV contains three short ORFs upstream of gag, of unknown function [Petersen et al., 1984; Petersen and Hackett, 1985]. Mutational studies suggest that these ORFs regulate the efficiency of translation at the gag start codon [Donze and Spahr, 1992; Donze et al., 1995]. Additionally, mutation of either the first or the third upstream ORF (uORFS) inhibits RNA encapsidation into the viral particle by up to 50-fold [Donze et al., 1995]. Upon infection of a receptive avian host cell, the integrated provirus is transcribed by cellular RNA polymerase II. Although this helps mask the viral RNA to make it resemble a cellular mRNA, in that it is capped and polyadenylated, there are many features of the unspliced viral mRNA that make it unique. First, the longest, most abundant viral RNA is unspliced. Typically, unspliced cellular pre-mRNAs are retained in the nucleus for degradation by the nuclear exosome [Bousquet-Antonelli et al., 2000]. Despite the presence of splice donor and acceptor sequences within the viral RNA, the full-length RSV RNA is maintained due to weak 3′ splice sites and a negative regulator of splicing (NRS)[Gontarek et al., 1993]. The RSV NRS forms a pre-splicing complex that is not competent to facilitate the first transesterification reaction, thereby preventing splicing [Giles and Beemon, 2005]. Export of this unspliced RNA is mediated in part by interactions between the RSV direct repeat (DR) sequences flanking the src gene and the cellular export factors Tap and Dbp5 [Ogert et al., 1996; Leblanc et al., 2007]. Second, the unspliced RNA is polycistronic. Normally mRNAs with multiple ORFs and consequently, multiple translation termination codons, are targets for nonsense-mediated mRNA decay (NMD). Third, the unspliced RNA primarily expresses the first long ORF (gag), in accordance with 5′ loading of the eukaryotic ribosome. This means that the 6.9 kb after gag is presented to cellular factors as a 3′ UTR. In aves, the average 3′ UTR is 650 nts, with the longest observed 3′ UTR being 3.3 kb [Pesole et al., 2001; Caldwell et al., 2005]. This means that the 3′ UTR of RSV gag is abnormally large. Long 3′ UTRs are also commonly targets of NMD [Hilleren and Parker, 1999]. Despite these unique attributes of RSV unspliced RNA, it still has a half-life of 10–20 h and during an infection can represent as much as 5% of the total cellular RNA [Baltimore, 1975; Stoltzfus et al., 1983; Weil and Beemon, 2006].
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structural characterization of the rous sarcoma virus RNA Stability element
Journal of Virology, 2009Co-Authors: Jason E Weil, Michalis Hadjithomas, Karen L. BeemonAbstract:In eukaryotic cells, an mRNA bearing a premature termination codon (PTC) or an abnormally long 3′ untranslated region (UTR) is often degraded by the nonsense-mediated mRNA decay (NMD) pathway. Despite the presence of a 5- to 7-kb 3′ UTR, unspliced retroviral RNA escapes this degradation. We previously identified the Rous sarcoma virus (RSV) Stability element (RSE), an RNA element downstream of the gag natural translation termination codon that prevents degradation of the unspliced viral RNA. Insertion of this element downstream of a PTC in the RSV gag gene also inhibits NMD. Using partial RNAse digestion and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, we determined the secondary structure of this element. Incorporating RNAse and SHAPE data into structural prediction programs definitively shows that the RSE contains an AU-rich stretch of about 30 single-stranded nucleotides near the 5′ end and two substantial stem-loop structures. The overall secondary structure of the RSE appears to be conserved among 20 different avian retroviruses. The structural aspects of this element will serve as a tool in the future design of cis mutants in addressing the mechanism of stabilization.
Yikai Luo - One of the best experts on this subject based on the ideXlab platform.
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rbms1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon
Cancer Discovery, 2020Co-Authors: Albertas Navickas, Hosseinali Asgharian, Bruce Culbertson, Lisa Fish, Kristle Garcia, John Paolo Olegario, Maria Dermit, Martin Dodel, Benjamin Hanisch, Yikai LuoAbstract:Identifying master regulators that drive pathological gene expression is a key challenge in precision oncology. Here, we have developed an analytical framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a post-transcriptional regulator of RNA Stability by directly binding its target mRNAs. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA Stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.
Albertas Navickas - One of the best experts on this subject based on the ideXlab platform.
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rbms1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon
Cancer Discovery, 2020Co-Authors: Albertas Navickas, Hosseinali Asgharian, Bruce Culbertson, Lisa Fish, Kristle Garcia, John Paolo Olegario, Maria Dermit, Martin Dodel, Benjamin Hanisch, Yikai LuoAbstract:Identifying master regulators that drive pathological gene expression is a key challenge in precision oncology. Here, we have developed an analytical framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a post-transcriptional regulator of RNA Stability by directly binding its target mRNAs. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA Stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.
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rbms1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon
bioRxiv, 2020Co-Authors: Bruce Culbertson, Robert S Warren, Albertas Navickas, Hosseinali Asgharian, Lisa Fish, John Paolo Olegario, Benjamin Hanisch, Ethan M Weinberg, Rodrigo Dienstmann, Hani GoodarziAbstract:Broad dysregulation of gene expression control is a hallmark of cancer progression. Identifying the underlying master regulators that drive pathological gene expression is a key challenge in precision oncology. Here, we have developed a network analytical framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a post-transcriptional regulator of RNA Stability by directly binding and stabilizing ~80 target mRNAs. Measurements in more than 180 clinical samples as well as survival analyses in publicly available datasets, have shown that RBMS1 silencing and the subsequent downregulation of its targets are strongly associated with disease progression and poor survival in colon cancer patients. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA Stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.
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nuclear tarbp2 drives oncogenic dysregulation of RNA splicing and decay
Molecular Cell, 2019Co-Authors: Lisa Fish, Albertas Navickas, Bruce Culbertson, Steven Zhang, Hoang C B Nguyen, Myles Hochman, Ross A Okimoto, Brian D Dill, Henrik Molina, Hamed S NajafabadiAbstract:Post-transcriptional regulation of RNA Stability is a key step in gene expression control. We describe a regulatory program, mediated by the RNA binding protein TARBP2, that controls RNA Stability in the nucleus. TARBP2 binding to pre-mRNAs results in increased intron retention, subsequently leading to targeted degradation of TARBP2-bound transcripts. This is mediated by TARBP2 recruitment of the m6A RNA methylation machinery to its target transcripts, where deposition of m6A marks influences the recruitment of splicing regulators, inhibiting efficient splicing. Interactions between TARBP2 and the nucleoprotein TPR then promote degradation of these TARBP2-bound transcripts by the nuclear exosome. Additionally, analysis of clinical gene expression datasets revealed a functional role for TARBP2 in lung cancer. Using xenograft mouse models, we find that TARBP2 affects tumor growth in the lung and that this is dependent on TARBP2-mediated destabilization of ABCA3 and FOXN3. Finally, we establish ZNF143 as an upstream regulator of TARBP2 expression.
Lisa Fish - One of the best experts on this subject based on the ideXlab platform.
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rbms1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon
Cancer Discovery, 2020Co-Authors: Albertas Navickas, Hosseinali Asgharian, Bruce Culbertson, Lisa Fish, Kristle Garcia, John Paolo Olegario, Maria Dermit, Martin Dodel, Benjamin Hanisch, Yikai LuoAbstract:Identifying master regulators that drive pathological gene expression is a key challenge in precision oncology. Here, we have developed an analytical framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a post-transcriptional regulator of RNA Stability by directly binding its target mRNAs. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA Stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.
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rbms1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon
bioRxiv, 2020Co-Authors: Bruce Culbertson, Robert S Warren, Albertas Navickas, Hosseinali Asgharian, Lisa Fish, John Paolo Olegario, Benjamin Hanisch, Ethan M Weinberg, Rodrigo Dienstmann, Hani GoodarziAbstract:Broad dysregulation of gene expression control is a hallmark of cancer progression. Identifying the underlying master regulators that drive pathological gene expression is a key challenge in precision oncology. Here, we have developed a network analytical framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a post-transcriptional regulator of RNA Stability by directly binding and stabilizing ~80 target mRNAs. Measurements in more than 180 clinical samples as well as survival analyses in publicly available datasets, have shown that RBMS1 silencing and the subsequent downregulation of its targets are strongly associated with disease progression and poor survival in colon cancer patients. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA Stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.
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nuclear tarbp2 drives oncogenic dysregulation of RNA splicing and decay
Molecular Cell, 2019Co-Authors: Lisa Fish, Albertas Navickas, Bruce Culbertson, Steven Zhang, Hoang C B Nguyen, Myles Hochman, Ross A Okimoto, Brian D Dill, Henrik Molina, Hamed S NajafabadiAbstract:Post-transcriptional regulation of RNA Stability is a key step in gene expression control. We describe a regulatory program, mediated by the RNA binding protein TARBP2, that controls RNA Stability in the nucleus. TARBP2 binding to pre-mRNAs results in increased intron retention, subsequently leading to targeted degradation of TARBP2-bound transcripts. This is mediated by TARBP2 recruitment of the m6A RNA methylation machinery to its target transcripts, where deposition of m6A marks influences the recruitment of splicing regulators, inhibiting efficient splicing. Interactions between TARBP2 and the nucleoprotein TPR then promote degradation of these TARBP2-bound transcripts by the nuclear exosome. Additionally, analysis of clinical gene expression datasets revealed a functional role for TARBP2 in lung cancer. Using xenograft mouse models, we find that TARBP2 affects tumor growth in the lung and that this is dependent on TARBP2-mediated destabilization of ABCA3 and FOXN3. Finally, we establish ZNF143 as an upstream regulator of TARBP2 expression.
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nuclear tarbp2 drives oncogenic dysregulation of RNA splicing and decay
bioRxiv, 2018Co-Authors: Lisa Fish, Steven Zhang, Hoang C B Nguyen, Myles Hochman, Brian D Dill, Henrik Molina, Hamed S Najafabadi, Claudio R Alarcon, Hani GoodarziAbstract:Post-transcriptional regulation of RNA Stability is a key step in gene expression control. We describe a regulatory program, mediated by the double-stranded RNA binding protein TARBP2, that controls RNA Stability in the nucleus. TARBP2 binding to pre-mRNAsresults in increased intron retention, subsequently leading to targeted degradation of TARBP2-bound transcripts. This is mediated by TARBP2 recruitment of the m6A RNA methylation machinery to its target transcripts, where deposition of m6A marks influences the recruitment of splicing regulators, inhibiting efficient splicing. Interactions between TARBP2 and the nucleoprotein TPR then promote degradation of these TARBP2-bound transcripts by the nuclear exosome. Additionally, analysis of clinical gene expression datasets revealed a functional role for this TARBP2 pathway in lung cancer. Using xenograft mouse models, we find that TARBP2 impacts tumor growth in the lung, and that this function is dependent on TARBP2-mediated destabilization of ABCA3 and FOXN3. Finally, we establish the transcription factor ZNF143 as an upstream regulator of TARBP2 expression.
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metastasis suppressor transcript destabilization through tarbp2 binding of mRNA hairpins
Nature, 2014Co-Authors: Hani Goodarzi, Lisa Fish, Steven Zhang, Colin G Buss, Saeed TavazoieAbstract:Aberrant regulation of RNA Stability has an important role in many disease states. Deregulated post-transcriptional modulation, such as that governed by microRNAs targeting linear sequence elements in messenger RNAs, has been implicated in the progression of many cancer types. A defining feature of RNA is its ability to fold into structures. However, the roles of structural mRNA elements in cancer progression remain unexplored. Here we performed an unbiased search for post-transcriptional modulators of mRNA Stability in breast cancer by conducting whole-genome transcript Stability measurements in poorly and highly metastatic isogenic human breast cancer lines. Using a computational framework that searches RNA sequence and structure space, we discovered a family of GC-rich structural cis-regulatory RNA elements, termed sRSEs for structural RNA Stability elements, which are significantly overrepresented in transcripts displaying reduced Stability in highly metastatic cells. By integrating computational and biochemical approaches, we identified TARBP2, a double-stranded RNA-binding protein implicated in microRNA processing, as the trans factor that binds the sRSE family and similar structural elements--collectively termed TARBP2-binding structural elements (TBSEs)--in transcripts. TARBP2 is overexpressed in metastatic cells and metastatic human breast tumours and destabilizes transcripts containing TBSEs. Endogenous TARBP2 promotes metastatic cell invasion and colonization by destabilizing amyloid precursor protein (APP) and ZNF395 transcripts, two genes previously associated with Alzheimer's and Huntington's disease, respectively. We reveal these genes to be novel metastasis suppressor genes in breast cancer. The cleavage product of APP, extracellular amyloid-α peptide, directly suppresses invasion while ZNF395 transcriptionally represses a pro-metastatic gene expression program. The expression levels of TARBP2, APP and ZNF395 in human breast carcinomas support their experimentally uncovered roles in metastasis. Our findings establish a non-canonical and direct role for TARBP2 in mammalian gene expression regulation and reveal that regulated RNA destabilization through protein-mediated binding of mRNA structural elements can govern cancer progression.
Bruce Culbertson - One of the best experts on this subject based on the ideXlab platform.
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rbms1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon
Cancer Discovery, 2020Co-Authors: Albertas Navickas, Hosseinali Asgharian, Bruce Culbertson, Lisa Fish, Kristle Garcia, John Paolo Olegario, Maria Dermit, Martin Dodel, Benjamin Hanisch, Yikai LuoAbstract:Identifying master regulators that drive pathological gene expression is a key challenge in precision oncology. Here, we have developed an analytical framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a post-transcriptional regulator of RNA Stability by directly binding its target mRNAs. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA Stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.
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rbms1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon
bioRxiv, 2020Co-Authors: Bruce Culbertson, Robert S Warren, Albertas Navickas, Hosseinali Asgharian, Lisa Fish, John Paolo Olegario, Benjamin Hanisch, Ethan M Weinberg, Rodrigo Dienstmann, Hani GoodarziAbstract:Broad dysregulation of gene expression control is a hallmark of cancer progression. Identifying the underlying master regulators that drive pathological gene expression is a key challenge in precision oncology. Here, we have developed a network analytical framework, named PRADA, that identifies oncogenic RNA-binding proteins through the systematic detection of coordinated changes in their target regulons. Application of this approach to data collected from clinical samples, patient-derived xenografts, and cell line models of colon cancer metastasis revealed the RNA-binding protein RBMS1 as a suppressor of colon cancer progression. We observed that silencing RBMS1 results in increased metastatic capacity in xenograft mouse models, and that restoring its expression blunts metastatic liver colonization. We have found that RBMS1 functions as a post-transcriptional regulator of RNA Stability by directly binding and stabilizing ~80 target mRNAs. Measurements in more than 180 clinical samples as well as survival analyses in publicly available datasets, have shown that RBMS1 silencing and the subsequent downregulation of its targets are strongly associated with disease progression and poor survival in colon cancer patients. Together, our findings establish a role for RBMS1 as a previously unknown regulator of RNA Stability and as a suppressor of colon cancer metastasis with clinical utility for risk stratification of patients.
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nuclear tarbp2 drives oncogenic dysregulation of RNA splicing and decay
Molecular Cell, 2019Co-Authors: Lisa Fish, Albertas Navickas, Bruce Culbertson, Steven Zhang, Hoang C B Nguyen, Myles Hochman, Ross A Okimoto, Brian D Dill, Henrik Molina, Hamed S NajafabadiAbstract:Post-transcriptional regulation of RNA Stability is a key step in gene expression control. We describe a regulatory program, mediated by the RNA binding protein TARBP2, that controls RNA Stability in the nucleus. TARBP2 binding to pre-mRNAs results in increased intron retention, subsequently leading to targeted degradation of TARBP2-bound transcripts. This is mediated by TARBP2 recruitment of the m6A RNA methylation machinery to its target transcripts, where deposition of m6A marks influences the recruitment of splicing regulators, inhibiting efficient splicing. Interactions between TARBP2 and the nucleoprotein TPR then promote degradation of these TARBP2-bound transcripts by the nuclear exosome. Additionally, analysis of clinical gene expression datasets revealed a functional role for TARBP2 in lung cancer. Using xenograft mouse models, we find that TARBP2 affects tumor growth in the lung and that this is dependent on TARBP2-mediated destabilization of ABCA3 and FOXN3. Finally, we establish ZNF143 as an upstream regulator of TARBP2 expression.
