Expression of the nascent RNA transcript is regulated by its interaction with a number of proteins. The misregulation of such interactions can often result in impaired cellular functions that can lead to cancer and a number of diseases. Thus, our understanding of RNA-protein interactions within the cellular context is essential for the development of novel diagnostic and therapeutic tools. While there are many in vitro methods that analyze RNA-protein interactions in vivo approaches are scarce. Here we established a method based on fluorescence resonance energy transfer (FRET), which we term RNA-binding mediated FRET (RB-FRET), which determines RNA-protein interaction inside cells and tested it on hnRNP H protein binding to its cognate RNA. Using two different approaches, we provide evidence that RB-FRET is sensitive enough to detect specific RNA-protein interactions in the cell, providing a powerful tool to study spatial and temporal localization of specific RNA-protein complexes.

• MeSH
• Genetic Vectors genetics   MeSH
• HeLa Cells MeSH
• Humans MeSH
• RNA-Binding Proteins genetics   metabolism   MeSH
• Fluorescence Resonance Energy Transfer methods   MeSH
• RNA analysis   metabolism   MeSH
• Base Sequence MeSH
• Substrate Specificity MeSH
• Protein Binding MeSH
• Binding Sites MeSH
• Check Tag
• Humans MeSH
• Publication type
• Evaluation Study MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH

In situ hybridization is a tool for evaluation of gene expression within tissues or single cells. This protocol describes optimized sensitive fluorescence detection of gene transcripts (mRNAs) in semithin sections of Schistosoma mansoni adult worms using specifically designed and labeled RNA probes. Due to improved methodologies in tissue preservation, sectioning, amplification of fluorescent signal, and prehybridization tissue treatment, it is possible to detect transcripts in the fine structures of schistosomes. The protocol is sensitive enough to detect very low abundance targets. This procedure is optimized for tissues derived from S. mansoni adult worms; however, it can be successfully applied to other trematode species.

• MeSH
• Digoxigenin metabolism   MeSH
• In Situ Hybridization, Fluorescence methods   MeSH
• RNA, Messenger genetics   metabolism   MeSH
• RNA Probes metabolism   MeSH
• Schistosoma mansoni cytology   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Východiska: Dlouhé nekódující RNA (long non-coding RNA – lncRNA) jsou RNA molekuly o délce větší než 200 nukleotidů, které ovlivňují řadu fyziologických funkcí a mají významnou regulační roli v buňkách. Jejich hladiny jsou často změněny u různých malignit, a představují tak slibný biomarker pro diagnostiku, prognózu nebo rekurenci nádorových onemocnění. Díky důležitosti těchto molekul výrazně roste i počet publikací na toto téma. Mezi nejčastěji studované lncRNA patří např. HOTAIR, MALAT1 a PCA3. Cíl: V současné době jsou vyvíjeny různé metody pro analýzu či detekci lncRNA, obvykle založené na optických metodách pro detekci mediátorové RNA (mRNA), např. polymerázová řetězová reakce s reverzní transkripcí, fl uorescenční in situ hybridizace nebo sekvenování nové generace. Je však potřeba dbát na rozdíly ve struktuře mRNA a lncRNA. V této práci popisujeme nejenom standardní metody, ale i nové přístupy pro detekci lncRNA zahrnující např. chemiluminescenční a elektrochemické techniky. Závěr: I navzdory pokrokům a velkému množství publikovaných prací existuje pouze jeden schválený diagnostický test založený na detekci lncRNA, a to PCA3 test pro diagnostiku karcinomu prostaty analýzou moči. Ostatní jsou v současnosti pouze ve fázi vývoje a bude potřeba je validovat. Dia gnostika založená na lncRNA i tak skýtá obrovský potenciál, a je proto velmi pravděpodobné, že se v blízké době objeví další diagnostické testy cílící na jiné typy lncRNA.

Background: Long non-coding RNAs (lncRNA) are more than 200-nucleotide-long RNA molecules that affect multiple physiologic phenomena and have important regulatory functions in cells. Their levels are often altered in various malignancies, thus they represent a potential biomarker for the diagnostics, prognosis or recurrence of cancer. Their importance has recently led to an enormous increase in a number of publications on the subject. The most frequently studied lncRNAs are HOTAIR, MALAT1 and PCA3. Aim: Numerous methods are currently being developed for the analysis or detection of lncRNA. They are mostly based on optical methods used for the detection of messenger RNAs, including polymerase chain reaction with reverse transcription, fluorescence in situ hybridisation or next-generation sequencing, but caution must be taken due to their structural differences. Here, we describe not only standard but also novel techniques for lncRNA detection, including chemiluminescent and electrochemical techniques. Conclusion: Despite the great progress and plethora of papers on this topic, there is only one single approved lncRNA-based diagnostic test, a PCA3 test for the diagnosis of prostate cancer from the patient’s urine. All other tests are only in their research phase and need to be validated. Nevertheless, lncRNA diagnostics offer enormous potential and thus it is highly probable that other diagnostic tests on different lncRNA types will soon appear.

• MeSH
• Biosensing Techniques methods   MeSH
• Carcinogenesis MeSH
• Humans MeSH
• Biomarkers, Tumor * MeSH
• RNA, Long Noncoding * analysis   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH

• MeSH
• Polymerase Chain Reaction MeSH
• Ribonucleoproteins MeSH
• RNA isolation & purification   MeSH
• Sequence Analysis, RNA MeSH
• Publication type
• Monograph MeSH

• Conspectus
• Biochemie. Molekulární biologie. Biofyzika
• NML Fields
• biochemie
• molekulární biologie, molekulární medicína

• MeSH
• Influenza, Human diagnosis   microbiology   MeSH
• Fluorescent Antibody Technique MeSH
• Humans MeSH
• Orthomyxoviridae isolation & purification   MeSH
• RNA, Viral analysis   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Comparative Study MeSH

BACKGROUND: The blood flukes of genus Schistosoma are the causative agent of schistosomiasis, a parasitic disease that infects more than 200 million people worldwide. Proteases of schistosomes are involved in critical steps of host-parasite interactions and are promising therapeutic targets. We recently identified and characterized a group of S1 family Schistosoma mansoni serine proteases, including SmSP1 to SmSP5. Expression levels of some SmSPs in S. mansoni are low, and by standard genome sequencing technologies they are marginally detectable at the method threshold levels. Here, we report their spatial gene expression patterns in adult S. mansoni by the high-sensitivity localization assay. METHODOLOGY: Highly sensitive fluorescence in situ RNA hybridization (FISH) was modified and used for the localization of mRNAs encoding individual SmSP proteases (including low-expressed SmSPs) in tissues of adult worms. High sensitivity was obtained due to specifically prepared tissue and probes in combination with the employment of a signal amplification approach. The assay method was validated by detecting the expression patterns of a set of relevant reference genes including SmCB1, SmPOP, SmTSP-2, and Sm29 with localization formerly determined by other techniques. RESULTS: FISH analysis revealed interesting expression patterns of SmSPs distributed in multiple tissues of S. mansoni adults. The expression patterns of individual SmSPs were distinct but in part overlapping and were consistent with existing transcriptome sequencing data. The exception were genes with significantly low expression, which were also localized in tissues where they had not previously been detected by RNA sequencing methods. In general, SmSPs were found in various tissues including reproductive organs, parenchymal cells, esophagus, and the tegumental surface. CONCLUSIONS: The FISH-based assay provided spatial information about the expression of five SmSPs in adult S. mansoni females and males. This highly sensitive method allowed visualization of low-abundantly expressed genes that are below the detection limits of standard in situ hybridization or by RNA sequencing. Thus, this technical approach turned out to be suitable for sensitive localization studies and may also be applicable for other trematodes. The results suggest that SmSPs may play roles in diverse processes of the parasite. Certain SmSPs expressed at the surface may be involved in host-parasite interactions.

• MeSH
• Gene Expression * MeSH
• In Situ Hybridization, Fluorescence methods   standards   MeSH
• Helminth Proteins genetics   MeSH
• RNA metabolism   MeSH
• Schistosoma mansoni enzymology   genetics   MeSH
• Serine Proteases genetics   MeSH
• Gene Expression Profiling MeSH
• Animals MeSH
• Check Tag
• Male MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH

RNA interference by short interfering RNAs (siRNAs) holds promise as a therapeutic strategy, but use of siRNAs in vivo remains limited. Here, we developed a system to target delivery of siRNAs to glomeruli via poly(ethylene glycol)-poly(l-lysine)-based vehicles. The siRNA/nanocarrier complex was approximately 10 to 20 nm in diameter, a size that would allow it to move across the fenestrated endothelium to access to the mesangium. After intraperitoneal injection of fluorescence-labeled siRNA/nanocarrier complexes, we detected siRNAs in the blood circulation for a prolonged time. Repeated intraperitoneal administration of a mitogen-activated protein kinase 1 (MAPK1) siRNA/nanocarrier complex suppressed glomerular MAPK1 mRNA and protein expression in a mouse model of glomerulonephritis; this improved kidney function, reduced proteinuria, and ameliorated glomerular sclerosis. Furthermore, this therapy reduced the expression of the profibrotic markers TGF-beta1, plasminogen activator inhibitor-1, and fibronectin. In conclusion, we successfully silenced intraglomerular genes with siRNA using nanocarriers. This technique could aid the investigation of molecular mechanisms of renal disease and has potential as a molecular therapy of glomerular diseases.

• MeSH
• Financing, Organized MeSH
• Genetic Therapy methods   MeSH
• Glomerulonephritis genetics   therapy   MeSH
• Kidney Glomerulus MeSH
• RNA, Small Interfering MeSH
• Mitogen-Activated Protein Kinase 1 genetics   MeSH
• Mice MeSH
• Animals MeSH
• Check Tag
• Mice MeSH
• Animals MeSH

Many fundamental biological processes depend on intricate networks of interactions between proteins and nucleic acids and a quantitative description of these interactions is important for understanding cellular mechanisms governing DNA replication, transcription, or translation. Here we present a versatile method for rapid and quantitative assessment of protein/nucleic acid (NA) interactions. This method is based on protein induced fluorescence enhancement (PIFE), a phenomenon whereby protein binding increases the fluorescence of Cy3-like dyes. PIFE has mainly been used in single molecule studies to detect protein association with DNA or RNA. Here we applied PIFE for steady state quantification of protein/NA interactions by using microwell plate fluorescence readers (mwPIFE). We demonstrate the general applicability of mwPIFE for examining various aspects of protein/DNA interactions with examples from the restriction enzyme BamHI, and the DNA repair complexes Ku and XPF/ERCC1. These include determination of sequence and structure binding specificities, dissociation constants, detection of weak interactions, and the ability of a protein to translocate along DNA. mwPIFE represents an easy and high throughput method that does not require protein labeling and can be applied to a wide range of applications involving protein/NA interactions.

• MeSH
• Anisotropy MeSH
• Ku Autoantigen chemistry   MeSH
• Deoxyribonuclease BamHI metabolism   MeSH
• DNA chemistry   MeSH
• Fluorescence MeSH
• Fluorescent Dyes chemistry   MeSH
• Microscopy, Fluorescence MeSH
• Spectrometry, Fluorescence * MeSH
• Transcription, Genetic MeSH
• Ions MeSH
• Humans MeSH
• Nucleic Acids chemistry   MeSH
• DNA Repair MeSH
• Proteins chemistry   MeSH
• Protein Biosynthesis MeSH
• DNA Replication MeSH
• RNA chemistry   MeSH
• Protein Binding MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Based on the matrix-addressing sequence of mitochondrial ribosomal 5S-rRNA (termed MAM), which is naturally imported into mitochondria, we have constructed an import system for in vivo targeting of mitochondrial DNA (mtDNA) or mt-mRNA, in order to provide fluorescence hybridization of the desired sequences. Thus DNA oligonucleotides were constructed, containing the 5'-flanked T7 RNA polymerase promoter. After in vitro transcription and fluorescent labeling with Alexa Fluor(®) 488 or 647 dye, we obtained the fluorescent "L-ND5 probe" containing MAM and exemplar cargo, i.e., annealing sequence to a short portion of ND5 mRNA and to the light-strand mtDNA complementary to the heavy strand nd5 mt gene (5'-end 21 base pair sequence). For mitochondrial in vivo fluorescent hybridization, HepG2 cells were treated with dequalinium micelles, containing the fluorescent probes, bringing the probes proximally to the mitochondrial outer membrane and to the natural import system. A verification of import into the mitochondrial matrix of cultured HepG2 cells was provided by confocal microscopy colocalizations. Transfections using lipofectamine or probes without 5S-rRNA addressing MAM sequence or with MAM only were ineffective. Alternatively, the same DNA oligonucleotides with 5'-CACC overhang (substituting T7 promoter) were transcribed from the tetracycline-inducible pENTRH1/TO vector in human embryonic kidney T-REx®-293 cells, while mitochondrial matrix localization after import of the resulting unlabeled RNA was detected by PCR. The MAM-containing probe was then enriched by three-order of magnitude over the natural ND5 mRNA in the mitochondrial matrix. In conclusion, we present a proof-of-principle for mitochondrial in vivo hybridization and mitochondrial nucleic acid import.

• MeSH
• Transcription, Genetic MeSH
• Humans MeSH
• DNA, Mitochondrial chemistry   genetics   MeSH
• Nucleic Acids chemistry   genetics   MeSH
• Oligonucleotides chemistry   genetics   MeSH
• RNA, Ribosomal chemistry   genetics   MeSH
• RNA chemistry   genetics   MeSH
• Sequence Homology, Nucleic Acid MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

A high level of nucleolin (NCL) expression is often associated with a poor prognosis of patients with lung cancer (LC), suggesting that NCL can be used as a possible biomarker. NCL has been shown to display a marked preference for the binding to G-quadruplexes (G4). Here, we investigate the formation of an RNA quadruplex structure in a sequence found in the human precursor pre-MIR150 with the potential to recognize NCL. Circular dichroism (CD) spectra of pre-MIR150 G4-forming sequence (designated by rG4) indicate the formation of a parallel quadruplex structure in KCl or when complexed with the well-known G4 ligand PhenDC3. The thermal stability of rG4 is very high, and further increases in the presence of PhenDC3. The binding affinities of rG4 to PhenDC3 and NCL RBD1,2 are similar with KD values in the nanomolar range. PAGE results suggest the formation of a ternary quadruplex-ligand-protein complex (rG4-PhenDC3-NCL RBD1,2), indicative that PhenDC3 does not prevent the binding of rG4 to NCL RBD1,2. Finally, rG4 can recognize NCL-positive cells and, when fluorescently labeled, can be used as a probe for this protein. ELISA experiments indicate altered NCL expression patterns in liquid biopsies of LC patients in a non-invasive manner, potentially helping the diagnosis, prognosis, and patient response to treatment. Hence, labeled rG4 could be used as a detection probe of LC in liquid biopsies.

• MeSH
• Amino Acid Motifs physiology   MeSH
• Adult MeSH
• Phosphoproteins biosynthesis   genetics   MeSH
• G-Quadruplexes * MeSH
• Gene Targeting methods   MeSH
• Cells, Cultured MeSH
• Leukocytes, Mononuclear metabolism   MeSH
• Humans MeSH
• Lung Neoplasms genetics   metabolism   therapy   MeSH
• RNA-Binding Proteins biosynthesis   genetics   MeSH
• Gene Expression Regulation, Neoplastic MeSH
• Check Tag
• Adult MeSH
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH