Retinitis pigmentosa (RP) is a hereditary disorder caused by mutations in more than 70 different genes including those that encode proteins important for pre-mRNA splicing. Most RP-associated mutations in splicing factors reduce either their expression, stability or incorporation into functional splicing complexes. However, we have previously shown that two RP mutations in PRPF8 (F2314L and Y2334N) and two in SNRNP200 (S1087L and R1090L) behaved differently, and it was still unclear how these mutations affect the functions of both proteins. To investigate this in the context of functional spliceosomes, we used iCLIP in HeLa and retinal pigment epithelial (RPE) cells. We found that both mutations in the RNA helicase SNRNP200 change its interaction with U4 and U6 snRNAs. The significantly broader binding profile of mutated SNRNP200 within the U4 region upstream of the U4/U6 stem I strongly suggests that its activity to unwind snRNAs is impaired. This was confirmed by FRAP measurements and helicase activity assays comparing mutant and WT protein. The RP variants of PRPF8 did not affect snRNAs, but showed a reduced binding to pre-mRNAs, which resulted in the slower splicing of introns and altered expression of hundreds of genes in RPE cells. This suggests that changes in the expression and splicing of specific genes are the main driver of retinal degeneration in PRPF8-linked RP.

• Klíčová slova
• PRPF8, Pre-mRNA splicing, Retinitis pigmentosa, SNRNP200, iCLIP,
• MeSH
• HeLa buňky MeSH
• lidé MeSH
• malý jaderný ribonukleoprotein U4-U6 metabolismus   genetika   MeSH
• mutace * MeSH
• prekurzory RNA * metabolismus   genetika   MeSH
• proteiny vázající RNA * metabolismus   genetika   MeSH
• retinální pigmentový epitel metabolismus   MeSH
• retinopathia pigmentosa * genetika   metabolismus   patologie   MeSH
• ribonukleoproteiny malé jaderné * metabolismus   genetika   MeSH
• RNA malá jaderná * metabolismus   genetika   MeSH
• sestřih RNA genetika   MeSH
• sestřihové faktory metabolismus   genetika   MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• malý jaderný ribonukleoprotein U4-U6 MeSH
• prekurzory RNA * MeSH
• proteiny vázající RNA * MeSH
• PRPF8 protein, human MeSH Prohlížeč
• ribonukleoproteiny malé jaderné * MeSH
• RNA malá jaderná * MeSH
• sestřihové faktory MeSH
• SNRNP200 protein, human MeSH Prohlížeč

A subset of patients with retinitis pigmentosa (RP) carry mutations in several spliceosomal components including the PRPF8 protein. Here, we established two alleles of murine Prpf8 that genocopy or mimic aberrant PRPF8 found in RP patients-the substitution p.Tyr2334Asn and an extended protein variant p.Glu2331ValfsX15. Homozygous mice expressing the aberrant Prpf8 variants developed within the first 2 mo progressive atrophy of the cerebellum because of extensive granule cell loss, whereas other cerebellar cells remained unaffected. We further show that a subset of circRNAs were deregulated in the cerebellum of both Prpf8-RP mouse strains. To identify potential risk factors that sensitize the cerebellum for Prpf8 mutations, we monitored the expression of several splicing proteins during the first 8 wk. We observed down-regulation of all selected splicing proteins in the WT cerebellum, which coincided with neurodegeneration onset. The decrease in splicing protein expression was further pronounced in mouse strains expressing mutated Prpf8. Collectively, we propose a model where physiological reduction in spliceosomal components during postnatal tissue maturation sensitizes cells to the expression of aberrant Prpf8 and the subsequent deregulation of circRNAs triggers neuronal death.

• MeSH
• kruhová RNA MeSH
• mozeček MeSH
• mutace MeSH
• myši MeSH
• proteiny vázající RNA * genetika   MeSH
• retinopathia pigmentosa * MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kruhová RNA MeSH
• proteiny vázající RNA * MeSH

Retinitis pigmentosa (RP) is a hereditary disease affecting tens of thousands of people world-wide. Here we analyzed the effect of an amino acid substitution in the RNA helicase DHX38 (Prp16) causing RP. DHX38 has been proposed as the helicase important for the 2nd step of splicing. We showed that DHX38 associates with key splicing factors involved in both splicing steps but did not find any evidence that the RP mutations changes DHX38 interaction profile with the spliceosome. We further downregulated DHX38 and monitored changes in splicing. We observed only minor perturbations of general splicing but detected modulation of ~70 alternative splicing events. Next, we probed DHX38 function in splicing of retina specific genes and found that FSCN2 splicing is dependent on DHX38. In addition, RHO splicing was inhibited specifically by expression of DHX38 RP variant. Finally, we showed that overexpression of DHX38 promotes usage of canonical as well as cryptic 5' splice sites in HBB splicing reporter. Together, our data show that DHX38 is a splicing factor that promotes splicing of cryptic splice sites and regulate alternative splicing. We further provide evidence that the RP-linked substitution G332D modulates DHX38 splicing activity.

• MeSH
• DEAD-box RNA-helikasy * genetika   MeSH
• lidé MeSH
• místa sestřihu RNA MeSH
• mutace MeSH
• retinopathia pigmentosa * genetika   MeSH
• sestřih RNA MeSH
• sestřihové faktory * genetika   MeSH
• spliceozomy metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DEAD-box RNA-helikasy * MeSH
• DHX38 protein, human MeSH Prohlížeč
• místa sestřihu RNA MeSH
• sestřihové faktory * MeSH

Spliceosomal small nuclear ribonucleoprotein particles (snRNPs) undergo a complex maturation pathway containing multiple steps in the nucleus and in the cytoplasm. snRNP biogenesis is strictly proofread and several quality control checkpoints are placed along the pathway. Here, we analyzed the fate of small nuclear RNAs (snRNAs) that are unable to acquire a ring of Sm proteins. We showed that snRNAs lacking the Sm ring are unstable and accumulate in P-bodies in an LSm1-dependent manner. We further provide evidence that defective snRNAs without the Sm binding site are uridylated at the 3' end and associate with DIS3L2 3'→5' exoribonuclease and LSm proteins. Finally, inhibition of 5'→3' exoribonuclease XRN1 increases association of ΔSm snRNAs with DIS3L2, which indicates competition and compensation between these two degradation enzymes. Together, we provide evidence that defective snRNAs without the Sm ring are uridylated and degraded by alternative pathways involving either DIS3L2 or LSm proteins and XRN1.

• MeSH
• exoribonukleasy metabolismus   MeSH
• HeLa buňky MeSH
• konformace nukleové kyseliny * MeSH
• lidé MeSH
• organely metabolismus   MeSH
• proteinový komplex SMN metabolismus   MeSH
• proteiny vázající RNA metabolismus   MeSH
• protoonkogenní proteiny metabolismus   MeSH
• RNA malá jaderná chemie   metabolismus   MeSH
• sekvence nukleotidů MeSH
• stabilita RNA MeSH
• transport RNA * MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DIS3L2 protein, human MeSH Prohlížeč
• exoribonukleasy MeSH
• GEMIN5 protein, human MeSH Prohlížeč
• LSM1 protein, human MeSH Prohlížeč
• proteinový komplex SMN MeSH
• proteiny vázající RNA MeSH
• protoonkogenní proteiny MeSH
• RNA malá jaderná MeSH

Cajal bodies (CBs) are nuclear non-membrane bound organelles where small nuclear ribonucleoprotein particles (snRNPs) undergo their final maturation and quality control before they are released to the nucleoplasm. However, the molecular mechanism how immature snRNPs are targeted and retained in CBs has yet to be described. Here, we microinjected and expressed various snRNA deletion mutants as well as chimeric 7SK, Alu or bacterial SRP non-coding RNAs and provide evidence that Sm and SMN binding sites are necessary and sufficient for CB localization of snRNAs. We further show that Sm proteins, and specifically their GR-rich domains, are important for accumulating snRNPs in CBs. Accordingly, core snRNPs containing the Sm proteins, but not naked snRNAs, restore the formation of CBs after their depletion. Finally, we show that immature but not fully assembled snRNPs are able to induce CB formation and that microinjection of an excess of U2 snRNP-specific proteins, which promotes U2 snRNP maturation, chases U2 snRNA from CBs. We propose that the accessibility of the Sm ring represents the molecular basis for the quality control of the final maturation of snRNPs and the sequestration of immature particles in CBs.

• MeSH
• buněčné jádro genetika   MeSH
• Cajalova tělíska genetika   metabolismus   MeSH
• HeLa buňky MeSH
• lidé MeSH
• malý jaderný ribonukleoprotein U2 genetika   MeSH
• regulace genové exprese genetika   MeSH
• RNA malá jaderná genetika   MeSH
• spliceozomy genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• malý jaderný ribonukleoprotein U2 MeSH
• RNA malá jaderná MeSH
• U2 small nuclear RNA MeSH Prohlížeč

Splicing is catalyzed by the spliceosome, a complex of five major small nuclear ribonucleoprotein particles (snRNPs). The pre-mRNA splicing factor PRPF8 is a crucial component of the U5 snRNP, and together with EFTUD2 and SNRNP200, it forms a central module of the spliceosome. Using quantitative proteomics, we identified assembly intermediates containing PRPF8, EFTUD2, and SNRNP200 in association with the HSP90/R2TP complex, its ZNHIT2 cofactor, and additional proteins. HSP90 and R2TP bind unassembled U5 proteins in the cytoplasm, stabilize them, and promote the formation of the U5 snRNP. We further found that PRPF8 mutants causing Retinitis pigmentosa assemble less efficiently with the U5 snRNP and bind more strongly to R2TP, with one mutant retained in the cytoplasm in an R2TP-dependent manner. We propose that the HSP90/R2TP chaperone system promotes the assembly of a key module of U5 snRNP while assuring the quality control of PRPF8. The proteomics data further reveal new interactions between R2TP and the tuberous sclerosis complex (TSC), pointing to a potential link between growth signals and the assembly of key cellular machines.

• MeSH
• elongační faktory genetika   metabolismus   MeSH
• HeLa buňky MeSH
• interakční proteinové domény a motivy MeSH
• lidé MeSH
• malý jaderný ribonukleoprotein U1 metabolismus   MeSH
• malý jaderný ribonukleoprotein U4-U6 metabolismus   MeSH
• malý jaderný ribonukleoprotein U5 genetika   metabolismus   MeSH
• messenger RNA genetika   metabolismus   MeSH
• multiproteinové komplexy MeSH
• mutace MeSH
• prekurzory RNA genetika   metabolismus   MeSH
• proteiny tepelného šoku HSP90 metabolismus   MeSH
• proteiny vázající RNA genetika   metabolismus   MeSH
• proteiny vázající vápník metabolismus   MeSH
• proteomika metody   MeSH
• retinopathia pigmentosa genetika   metabolismus   MeSH
• RNA interference MeSH
• sestřih RNA * MeSH
• stabilita proteinů MeSH
• transfekce MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• EFTUD2 protein, human MeSH Prohlížeč
• elongační faktory MeSH
• malý jaderný ribonukleoprotein U1 MeSH
• malý jaderný ribonukleoprotein U4-U6 MeSH
• malý jaderný ribonukleoprotein U5 MeSH
• messenger RNA MeSH
• multiproteinové komplexy MeSH
• prekurzory RNA MeSH
• proteiny tepelného šoku HSP90 MeSH
• proteiny vázající RNA MeSH
• proteiny vázající vápník MeSH
• PRPF8 protein, human MeSH Prohlížeč
• TESC protein, human MeSH Prohlížeč

A majority of human genes contain non-coding intervening sequences - introns that must be precisely excised from the pre-mRNA molecule. This event requires the coordinated action of five major small nuclear ribonucleoprotein particles (snRNPs) along with additional non-snRNP splicing proteins. Introns must be removed with nucleotidal precision, since even a single nucleotide mistake would result in a reading frame shift and production of a non-functional protein. Numerous human inherited diseases are caused by mutations that affect splicing, including mutations in proteins which are directly involved in splicing catalysis. One of the most common hereditary diseases associated with mutations in core splicing proteins is retinitis pigmentosa (RP). So far, mutations in more than 70 genes have been connected to RP. While the majority of mutated genes are expressed specifically in the retina, eight target genes encode for ubiquitous core snRNP proteins (Prpf3, Prpf4, Prpf6, Prpf8, Prpf31, and SNRNP200/Brr2) and splicing factors (RP9 and DHX38). Why mutations in spliceosomal proteins, which are essential in nearly every cell in the body, causes a disease that displays such a tissue-specific phenotype is currently a mystery. In this review, we recapitulate snRNP functions, summarize the missense mutations which are found in spliceosomal proteins as well as their impact on protein functions and discuss specific models which may explain why the retina is sensitive to these mutations.

• Klíčová slova
• Retinitis pigmentosa, snRNP, splicing,
• MeSH
• introny MeSH
• krysa rodu Rattus MeSH
• lidé MeSH
• missense mutace MeSH
• myši MeSH
• prekurzory RNA genetika   metabolismus   MeSH
• retinopathia pigmentosa genetika   MeSH
• ribonukleoproteiny malé jaderné genetika   metabolismus   MeSH
• sestřih RNA MeSH
• sestřihové faktory genetika   metabolismus   MeSH
• spliceozomy genetika   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• prekurzory RNA MeSH
• ribonukleoproteiny malé jaderné MeSH
• sestřihové faktory MeSH

Histone acetylation modulates alternative splicing of several hundred genes. Here, we tested the role of the histone acetyltransferase p300 in alternative splicing and showed that knockdown of p300 promotes inclusion of the fibronectin (FN1) alternative EDB exon. p300 associates with CRE sites in the promoter via the CREB transcription factor. We created mini-gene reporters driven by an artificial promoter containing CRE sites. Both deletion and mutation of the CRE site affected EDB alternative splicing in the same manner as p300 knockdown. Next we showed that p300 controls histone H4 acetylation along the FN1 gene. Consistently, p300 depletion and CRE deletion/mutation both reduced histone H4 acetylation on mini-gene reporters. Finally, we provide evidence that the effect of CRE inactivation on H4 acetylation and alternative splicing is counteracted by the inhibition of histone deacetylases. Together, these data suggest that histone acetylation could be one of the mechanisms how promoter and promoter binding proteins influence alternative splicing.

• Klíčová slova
• alternative splicing, fibronectin, histone acetylation, p300, promoter,
• MeSH
• acetylace MeSH
• alternativní sestřih * MeSH
• fibronektiny genetika   metabolismus   MeSH
• genový knockdown MeSH
• HeLa buňky MeSH
• histony metabolismus   MeSH
• integrasy genetika   MeSH
• lidé MeSH
• messenger RNA metabolismus   MeSH
• promotorové oblasti (genetika) MeSH
• protein p300 asociovaný s E1A genetika   metabolismus   MeSH
• reportérové geny MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• Cre recombinase MeSH Prohlížeč
• EP300 protein, human MeSH Prohlížeč
• fibronektiny MeSH
• FN1 protein, human MeSH Prohlížeč
• histony MeSH
• integrasy MeSH
• messenger RNA MeSH
• protein p300 asociovaný s E1A MeSH

Processing bodies (P-bodies) are dynamic cytoplasmic structures involved in mRNA degradation, but the mechanism that governs their formation is poorly understood. In this paper, we address a role of Like-Sm (LSm) proteins in formation of P-bodies and provide evidence that depletion of nuclear LSm8 increases the number of P-bodies, while LSm8 overexpression leads to P-body loss. We show that LSm8 knockdown causes relocalization of LSm4 and LSm6 proteins to the cytoplasm and suggest that LSm8 controls nuclear accumulation of all LSm2-7 proteins. We propose a model in which redistribution of LSm2-7 to the cytoplasm creates new binding sites for other P-body components and nucleates new, microscopically visible structures. The model is supported by prolonged residence of two P-body proteins, DDX6 and Ago2, in P-bodies after LSm8 depletion, which indicates stronger interactions between these proteins and P-bodies. Finally, an increased number of P-bodies has negligible effects on microRNA-mediated translation repression and nonsense mediated decay, further supporting the view that the function of proteins localized in P-bodies is independent of visible P-bodies.

• MeSH
• autoantigeny metabolismus   MeSH
• buněčné jádro metabolismus   MeSH
• cytoplazmatická granula metabolismus   MeSH
• DEAD-box RNA-helikasy metabolismus   MeSH
• fluorescenční mikroskopie MeSH
• lidé MeSH
• malý jaderný ribonukleoprotein U4-U6 metabolismus   fyziologie   MeSH
• N-terminální acetyltransferasa C metabolismus   fyziologie   MeSH
• posttranskripční úpravy RNA * MeSH
• proteiny vázající RNA metabolismus   MeSH
• protoonkogenní proteiny metabolismus   MeSH
• rekombinantní fúzní proteiny metabolismus   MeSH
• ribonukleoproteiny malé jaderné metabolismus   MeSH
• transport proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• autoantigeny MeSH
• DDX6 protein, human MeSH Prohlížeč
• DEAD-box RNA-helikasy MeSH
• malý jaderný ribonukleoprotein U4-U6 MeSH
• N-terminální acetyltransferasa C MeSH
• NAA38 protein, human MeSH Prohlížeč
• proteiny vázající RNA MeSH
• protoonkogenní proteiny MeSH
• rekombinantní fúzní proteiny MeSH
• ribonukleoproteiny malé jaderné MeSH
• TNRC6A protein, human MeSH Prohlížeč

There is increasing evidence to suggest that splicing decisions are largely made when the nascent RNA is still associated with chromatin. Here we demonstrate that activity of histone deacetylases (HDACs) influences splice site selection. Using splicing-sensitive microarrays, we identified ∼700 genes whose splicing was altered after HDAC inhibition. We provided evidence that HDAC inhibition induced histone H4 acetylation and increased RNA Polymerase II (Pol II) processivity along an alternatively spliced element. In addition, HDAC inhibition reduced co-transcriptional association of the splicing regulator SRp40 with the target fibronectin exon. We further showed that the depletion of HDAC1 had similar effect on fibronectin alternative splicing as global HDAC inhibition. Importantly, this effect was reversed upon expression of mouse HDAC1 but not a catalytically inactive mutant. These results provide a molecular insight into a complex modulation of splicing by HDACs and chromatin modifications.

• MeSH
• alternativní sestřih účinky léků   genetika   fyziologie   MeSH
• HeLa buňky MeSH
• histondeacetylasa 1 genetika   fyziologie   MeSH
• histondeacetylasy genetika   metabolismus   fyziologie   MeSH
• inhibitory histondeacetylas farmakologie   MeSH
• jaderné proteiny genetika   MeSH
• kultivované buňky MeSH
• lidé MeSH
• mikročipová analýza MeSH
• myši MeSH
• proteiny vázající RNA genetika   MeSH
• regulace genové exprese účinky léků   MeSH
• serin-arginin sestřihové faktory MeSH
• stanovení celkové genové exprese MeSH
• transfekce MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• Hdac1 protein, mouse MeSH Prohlížeč
• histondeacetylasa 1 MeSH
• histondeacetylasy MeSH
• inhibitory histondeacetylas MeSH
• jaderné proteiny MeSH
• proteiny vázající RNA MeSH
• serin-arginin sestřihové faktory MeSH