Regulation of constitutive and alternative splicing by PRMT5 reveals a role for <i>Mdm4</i> pre-mRNA in sensing defects in the spliceosomal machinery

Bezzi, Marco; Teo, Shun Xie; Müller, Julius; Mok, Wei Chuen; Sahu, Sanjeeb Kumar; Vardy, Leah A.; Bonday, Zahid; Guccione, Ernesto

doi:10.1101/gad.219899.113

Cited by 220 publications

(306 citation statements)

References 72 publications

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“…S6D). PRMT5 can symmetrically dimethylate the C-terminal tails of the U snRNP Sm proteins B/B′, D1, D3, and LSm4 in multiple organisms, which may facilitate the recognition of a subset of 5′ splice sites (10,11,(33)(34)(35)(36). Here atprmt5 mutants show a dramatic impairment of the interaction between Prp19C/NTC and AtSmD3b, revealing a previously unidentified function of symmetric arginine dimethylation in the recruitment of Prp19C/ NTC to the spliceosome.…”

Section: Discussionmentioning

confidence: 99%

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Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

Deng

Wang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Protein arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), is involved in a multitude of biological processes in eukaryotes. Symmetric arginine dimethylation mediated by PRMT5 modulates constitutive and alternative pre-mRNA splicing of diverse genes to regulate normal growth and development in multiple species; however, the underlying molecular mechanism remains largely unknown. A genetic screen for suppressors of an Arabidopsis symmetric arginine dimethyltransferase mutant, atprmt5, identified two gain-of-function alleles of pre-mRNA processing factor 8 gene (prp8-8 and prp8-9), the highly conserved core component of the U5 small nuclear ribonucleoprotein (snRNP) and the spliceosome. These two atprmt5 prp8 double mutants showed suppression of the developmental and splicing alterations of atprmt5 mutants. In atprmt5 mutants, the NineTeen complex failed to be assembled into the U5 snRNP to form an activated spliceosome; this phenotype was restored in the atprmt5 prp8-8 double mutants. We also found that loss of symmetric arginine dimethylation of Sm proteins prevents recruitment of the NineTeen complex and initiation of spliceosome activation. Together, our findings demonstrate that symmetric arginine dimethylation has important functions in spliceosome assembly and activation, and uncover a key molecular mechanism for arginine methylation in pre-mRNA splicing that impacts diverse developmental processes.arginine methylation | protein arginine methyltransferase | AtPRMT5 | pre-mRNA splicing | Prp19C/NTC P rotein arginine methyltransferase 5 (PRMT5), a highly conserved type II protein arginine methyltransferase, transfers methyl groups to arginine residues, generating monomethylarginine and symmetric ω-N G , N′ G -dimethylarginine (SDMA) (1-3). In mammals, PRMT5 methylates and interacts with diverse proteins, including histones and other proteins, and has long been implicated in the modulation of a variety of processes, such as transcriptional regulation, RNA metabolism (4), apoptosis (5), signal transduction (6), and germ cell development (7). Both loss-of-function and overexpression of PRMT5 are fatal in mammals (8). AtPRMT5, the Arabidopsis homolog of PRMT5, regulates multiple aspects of plant growth and development, such as flowering time, growth rate, leaf morphology, sensitivity to stress conditions, and circadian rhythm, by modulating transcription, constitutive and alternative precursor mRNA (pre-mRNA) splicing of diverse genes (9-13). AtPRMT5 also mediates the symmetric arginine dimethylation of uridine-rich small nuclear ribonucleoproteins (U snRNPs) AtSmD1, D3, and AtLSm4 proteins, thus linking arginine methylation and splicing (10,11,13). However, the exact mechanism remains elusive.Pre-mRNA splicing occurs in the nucleus, removing introns and ligating exons (14). In eukaryotes, most introns are spliced in a series of reactions catalyzed by the spliceosome, which consists of five subcomplexes of U snRNPs and several non-snRNP factors. Each U snRNP contains distinct splicing...

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Section: Discussionmentioning

confidence: 99%

“…We and others have demonstrated that AtPRMT5 is essential for constitutive and alternative pre-mRNA splicing of diverse genes, but how AtPRMT5 functions in pre-mRNA splicing has remained unclear (10)(11)(12)33). …”

Section: Discussionmentioning

confidence: 99%

Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

Deng

Wang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Consistent with the up-regulation of p53 protein, Clk inhibition was shown previously to induce an increase in the NMD isoform of Mdm4, a negative regulator of p53 (Allende-Vega et al 2013;Bezzi et al 2013). We identified the introns flanking the Mdm4 NMD switch exon as DIs and therefore reasoned that their splicing might be regulated under physiological conditions that induce p53, such as DNA damage.…”

Section: Dna Damage Triggers Changes In Splicing Of a Subset Of Dismentioning

confidence: 66%

“…It has previously been observed that a small-molecule Clk inhibitor triggered an increase in Mdm4 NMD isoform splicing, a corresponding decrease in Mdm4 protein, and up-regulation of p53 protein levels (Allende-Vega et al 2013;Bezzi et al 2013). This effect was attributed to induction of stress due to a general inhibition of splicing; however, to date, there has been no global analysis of splicing in cells treated with Clk inhibitors.…”

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confidence: 99%

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

2015

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Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts; we classified these as ''detained'' introns (DIs). We identified thousands of DIs, many of which are evolutionarily conserved, in human and mouse cell lines as well as the adult mouse liver. DIs can have half-lives of over an hour yet remain in the nucleus and are not subject to nonsense-mediated decay (NMD). Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs; half showed increased splicing, and half showed increased intron detention, altering transcript pools of >300 genes. Srsf4, which undergoes a dramatic phosphorylation shift in response to Clk kinase inhibition, regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. The splicing of some DIs-including those in Mdm4, a negative regulator of p53-was also altered following DNA damage. After 4 h of Clk inhibition, the expression of >400 genes changed significantly, and almost one-third of these are p53 transcriptional targets. These data suggest a widespread mechanism by which the rate of splicing of DIs contributes to the level of gene expression.

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“…We found altered expression of the regulators serine/arginine-rich splicing factor 3 (SRSF3), splicing factor 3A3 (SF3A3), heterogeneous nuclear ribonuclear proteins Q and A1, small nuclear ribonuclear proteins A′ and E, regulation of nuclear pre-mRNA domain-containing protein 2 (RPRD2), RNA-binding proteins 22, 4b, 39, 47, and MS, and the RNA helicase DHX30 (Table 1). Perturbation of the splicing machinery also can activate the p53 pathway (71,72).…”

Section: Functional Classes Of Proteins and Pathways Changed By Exposmentioning

confidence: 99%

Quantitative proteomic analyses of mammary organoids reveals distinct signatures after exposure to environmental chemicals

Williams

Lemieux

Hassis

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Common environmental contaminants such as bisphenols and phthalates and persistent contaminants such as polychlorinated biphenyls are thought to influence tissue homeostasis and carcinogenesis by acting as disrupters of endocrine function. In this study we investigated the direct effects of exposure to bisphenol A (BPA), mono-n-butyl phthalate (Pht), and polychlorinated biphenyl 153 (PCB153) on the proteome of primary organotypic cultures of the mouse mammary gland. At low-nanomolar doses each of these agents induced distinct effects on the proteomes of these cultures. Although BPA treatment produced effects that were similar to those induced by estradiol, there were some notable differences, including a reduction in the abundance of retinoblastomaassociated protein and increases in the Rho GTPases Ras-related C3 botulinum toxin substrate 1 (Rac1) and cell division cycle protein CDC42. Both Pht and PCB153 induced changes that were distinct from those induced by estrogen, including decreased levels of the transcriptional corepressor C-terminal binding protein 1. Interestingly, the three chemicals appeared to alter the abundance of distinct splice forms of many proteins as well as the abundance of several proteins that regulate RNA splicing. Our combined results indicate that the three classes of chemical have distinct effects on the proteome of normal mouse mammary cultures, some estrogen-like but most estrogen independent, that influence diverse biological processes including apoptosis, cell adhesion, and proliferation.proteomics | mammary epithelium | environmental chemicals | organotypic culture | estrogen B reast cancers are caricatures of normal tissue development (1-3). The same underlying mechanisms that affect the cell processes needed for normal mammary development contribute to cancer progression. By affecting the distribution of interacting cells and communication among them through nontargeted effects, carcinogens can promote the outgrowth of altered cells with malignant potential. Exposure to environmental agents can affect mammary gland development and alter breast cancer risk. Epidemiologic studies have associated a number of environmental factors with increased breast cancer risk (4). Some of these factors may have low-level effects that are not genotoxic but alter immune responses, vascularity, or the microenvironment or that change susceptibility to carcinogens. A current weakness in models of cancer risk assessment is the lack of consideration of factors that influence the susceptibility of mixed cell populations to transformation. Indeed, ionizing radiation, the prototypical carcinogen, promotes changes in the biochemical properties in cultured mouse and human breast cells, in the stromal environment, and in intact mouse mammary gland (5-7).Physiologically relevant 3D culture models can recapitulate crucial aspects of the dynamic and reciprocal signaling necessary for establishing and maintaining tissue-specific morphogenetic programs. The determination of the molecular mechanisms underlying m...

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Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery

Cited by 220 publications

References 72 publications

Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

Quantitative proteomic analyses of mammary organoids reveals distinct signatures after exposure to environmental chemicals

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