Nicotinamide adenine dinucleotide (NAD) is a critical component of the cellular metabolism and also serves as an alternative 5' cap on various RNAs. However, the function of the NAD RNA cap is still under investigation. We studied NAD capping of RNAs in HIV-1-infected cells because HIV-1 is responsible for the depletion of the NAD/NADH cellular pool and causing intracellular pellagra. By applying the NAD captureSeq protocol to HIV-1-infected and uninfected cells, we revealed that four snRNAs (e.g., U1) and four snoRNAs lost their NAD cap when infected with HIV-1. Here, we provide evidence that the presence of the NAD cap decreases the stability of the U1/HIV-1 pre-mRNA duplex. Additionally, we demonstrate that reducing the quantity of NAD-capped RNA by overexpressing the NAD RNA decapping enzyme DXO results in an increase in HIV-1 infectivity. This suggests that NAD capping is unfavorable for HIV-1 and plays a role in its infectivity.

• MeSH
• HIV infekce * virologie   metabolismus   MeSH
• HIV-1 * MeSH
• lidé MeSH
• malá jadérková RNA * metabolismus   genetika   MeSH
• NAD * metabolismus   MeSH
• RNA čepičky metabolismus   MeSH
• RNA malá jaderná * metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• dopisy MeSH
• práce podpořená grantem MeSH
• Názvy látek
• malá jadérková RNA * MeSH
• NAD * MeSH
• RNA čepičky MeSH
• RNA malá jaderná * MeSH

BACKGROUND: Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS: We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS: We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.

• Klíčová slova
• Cardiac hypertrophy, Complex disease, Genetic variation, HXB/BXH rat recombinant inbred panel, Ribosome biogenesis, Ribosome profiling, Ribosomopathy, Spontaneously hypertensive rats (SHR), Translational efficiency, trans QTL mapping,
• MeSH
• biogeneze organel MeSH
• genetická variace MeSH
• iniciace translace peptidového řetězce * MeSH
• kardiomegalie genetika   metabolismus   patologie   MeSH
• krysa rodu Rattus MeSH
• lokus kvantitativního znaku * MeSH
• malá jadérková RNA genetika   metabolismus   MeSH
• messenger RNA genetika   metabolismus   MeSH
• myokard metabolismus   patologie   MeSH
• myši inbrední C57BL MeSH
• myši knockoutované MeSH
• myši MeSH
• potkani inbrední SHR MeSH
• potkani transgenní MeSH
• regulace genové exprese MeSH
• ribozomální proteiny genetika   metabolismus   MeSH
• ribozomy genetika   metabolismus   patologie   MeSH
• Saccharomyces cerevisiae genetika   metabolismus   MeSH
• sarkomery metabolismus   patologie   MeSH
• stanovení celkové genové exprese MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• mužské pohlaví MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• malá jadérková RNA MeSH
• messenger RNA MeSH
• ribozomální proteiny MeSH

Genomic regions that encode small RNA genes exhibit characteristic patterns in their sequence, secondary structure, and evolutionary conservation. Convolutional Neural Networks are a family of algorithms that can classify data based on learned patterns. Here we present MuStARD an application of Convolutional Neural Networks that can learn patterns associated with user-defined sets of genomic regions, and scan large genomic areas for novel regions exhibiting similar characteristics. We demonstrate that MuStARD is a generic method that can be trained on different classes of human small RNA genomic loci, without need for domain specific knowledge, due to the automated feature and background selection processes built into the model. We also demonstrate the ability of MuStARD for inter-species identification of functional elements by predicting mouse small RNAs (pre-miRNAs and snoRNAs) using models trained on the human genome. MuStARD can be used to filter small RNA-Seq datasets for identification of novel small RNA loci, intra- and inter- species, as demonstrated in three use cases of human, mouse, and fly pre-miRNA prediction. MuStARD is easy to deploy and extend to a variety of genomic classification questions. Code and trained models are freely available at gitlab.com/RBP_Bioinformatics/mustard.

• MeSH
• algoritmy MeSH
• genomika metody   MeSH
• lidé MeSH
• malá jadérková RNA genetika   MeSH
• mikro RNA genetika   MeSH
• myši MeSH
• nekódující RNA genetika   MeSH
• neuronové sítě MeSH
• software MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• malá jadérková RNA MeSH
• mikro RNA MeSH
• nekódující RNA MeSH

Fibrillarin is a highly conserved nucleolar methyltransferase responsible for ribosomal RNA methylation across evolution from Archaea to humans. It has been reported that fibrillarin is involved in the methylation of histone H2A in nucleoli and other processes, including viral progression, cellular stress, nuclear shape, and cell cycle progression. We show that fibrillarin has an additional activity as a ribonuclease. The activity is affected by phosphoinositides and phosphatidic acid and insensitive to ribonuclease inhibitors. Furthermore, the presence of phosphatidic acid releases the fibrillarin-U3 snoRNA complex. We show that the ribonuclease activity localizes to the GAR (glycine/arginine-rich) domain conserved in a small group of RNA interacting proteins. The introduction of the GAR domain occurred in evolution in the transition from archaea to eukaryotic cells. The interaction of this domain with phospholipids may allow a phase separation of this protein in nucleoli.

• Klíčová slova
• fibrillarin, nucleolus, phosphoinositides, rRNA, ribonucleolar particle, viral progression,
• MeSH
• chromozomální proteiny, nehistonové chemie   genetika   metabolismus   MeSH
• fosfolipidy metabolismus   MeSH
• HeLa buňky MeSH
• lidé MeSH
• malá jadérková RNA metabolismus   MeSH
• mutace genetika   MeSH
• proteinové domény MeSH
• rekombinantní proteiny metabolismus   MeSH
• ribonukleasy chemie   genetika   metabolismus   MeSH
• ribonukleoproteiny metabolismus   MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chromozomální proteiny, nehistonové MeSH
• fibrillarin MeSH Prohlížeč
• fosfolipidy MeSH
• malá jadérková RNA MeSH
• rekombinantní proteiny MeSH
• ribonukleasy MeSH
• ribonukleoproteiny MeSH
• RNA, U3 small nucleolar MeSH Prohlížeč

Ribosome biosynthesis, best studied in opisthokonts, is a highly complex process involving numerous protein and RNA factors. Yet, very little is known about the early stages of pre-18S rRNA processing even in these model organisms, let alone the conservation of this mechanism in other eukaryotes. Here we extend our knowledge of this process by identifying and characterizing the essential protein TbUTP10, a homolog of yeast U3 small nucleolar RNA-associated protein 10 - UTP10 (HEATR1 in human), in the excavate parasitic protist Trypanosoma brucei. We show that TbUTP10 localizes to the nucleolus and that its ablation by RNAi knock-down in two different T. brucei life cycle stages results in similar phenotypes: a disruption of pre-18S rRNA processing, exemplified by the accumulation of rRNA precursors, a reduction of mature 18S rRNA, and also a decrease in the level of U3 snoRNA. Moreover, polysome profiles of the RNAi-induced knock-down cells show a complete disappearance of the 40S ribosomal subunit, and a prominent accumulation of the 60S large ribosomal subunit, reflecting impaired ribosome assembly. Thus, TbUTP10 is an important protein in the processing of 18S rRNA.

• Klíčová slova
• Pre-18S rRNA processing, Ribosomal RNA, Trypanosoma, U3 snoRNA, UTP10,
• MeSH
• esenciální geny * MeSH
• malá jadérková RNA metabolismus   MeSH
• posttranskripční úpravy RNA * MeSH
• proteiny vázající RNA genetika   metabolismus   MeSH
• protozoální proteiny genetika   metabolismus   MeSH
• RNA ribozomální 18S metabolismus   MeSH
• Trypanosoma brucei brucei enzymologie   metabolismus   MeSH
• umlčování genů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• malá jadérková RNA MeSH
• proteiny vázající RNA MeSH
• protozoální proteiny MeSH
• RNA ribozomální 18S MeSH

BACKGROUND: RT-qPCR quantification of miRNAs expression may play an essential role in pancreatic ductal adenocarcinoma (PDAC) diagnostics. RT-qPCR-based experiments require endogenous controls for the result normalization and reliability. However, expression instability of reference genes in tumors may introduce bias when determining miRNA levels. METHODS: We investigated expression of 6 miRNAs, isolated from FFPE samples of pancreatic adenocarcinomas. Four internal controls were utilized for RT-qPCR result normalization: artificial miR-39 from C. elegans, U6 snRNA, miR-16 and snoRNA U91. RESULTS: We found miR-21, miR-155 or miR-217 expression values in tumors may differ up to several times, depending on selected internal controls. Moreover, different internal controls can produce controversial results for miR-96, miR-148a or miR-196a quantification. Also, expression of our endogenous controls varied significantly in tumors. U6 demonstrated variation from -1.03 to 8.12-fold, miR-16 from -2.94 up to 7.38-fold and the U91 from -3.05 to 4.36-fold respectively. On the other hand, the most stable gene, determined by NormFinder algorithm, was U91. Each miRNA normalized relatively to the spike or U91, demonstrated similar expression values. Thus, statistically significant and insignificant differences between tumors and normal tissues for miRNAs were equal for the spike and the U91. Also, the differences between the spike and U91 were statistically insignificant for all of miRs except miR-217. Among three endogenous controls, U91 had the lowest average expression values and standard deviation in cancer tissues. CONCLUSIONS: We recommend U91 as a new normalizer for miRNA quantification in PDACs.

• MeSH
• adenokarcinom genetika   MeSH
• analýza rozptylu MeSH
• dospělí MeSH
• kvantitativní polymerázová řetězová reakce metody   MeSH
• lidé středního věku MeSH
• lidé MeSH
• malá jadérková RNA metabolismus   MeSH
• mikro RNA analýza   metabolismus   MeSH
• nádorové biomarkery genetika   MeSH
• nádory slinivky břišní genetika   MeSH
• regulace genové exprese u nádorů MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• stanovení celkové genové exprese MeSH
• studie případů a kontrol MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• malá jadérková RNA MeSH
• mikro RNA MeSH
• MIRN155 microRNA, human MeSH Prohlížeč
• MIRN21 microRNA, human MeSH Prohlížeč
• MIRN217 microRNA, human MeSH Prohlížeč
• nádorové biomarkery MeSH

Non-coding RNAs (ncRNAs) are important regulatory molecules involved in various physiological and pathological cellular processes. Small nucleolar RNAs (snoRNAs), subclass of small ncRNAs, have been considered important but unglamorous elements in the production of protein synthesis machinery of cells. However, recent evidence has indicated that these non-coding RNAs might have a crucial role also in controlling cell behavior, and snoRNAs dysfunction could significantly contribute to carcinogenesis. Here, we summarize the most important aspects of snoRNAs biology, their functioning in cancer cell, and potential usage in diagnosis or as a new class of therapeutic targets in cancer.

• MeSH
• alternativní sestřih MeSH
• cílená molekulární terapie MeSH
• fyziologický stres MeSH
• lidé MeSH
• malá jadérková RNA fyziologie   MeSH
• nádorové biomarkery fyziologie   MeSH
• nádory genetika   metabolismus   terapie   MeSH
• posttranskripční úpravy RNA MeSH
• regulace genové exprese u nádorů MeSH
• RNA interference MeSH
• sekvence nukleotidů MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• malá jadérková RNA MeSH
• nádorové biomarkery MeSH