Epigenetika se zabývá tím, jak zevní i vnitřní faktory ovlivňují funkci DNA daného organizmu, aniž by se přitom měnila její sekvence. Epigenetické vlivy jsou významné jak v buňkách stávajících, tak dceřiných, a to v rámci jedince i mezigeneračního přenosu získaných znaků. Za nejvýznamnější epigenetické mechanizmy bývají považovány acetylace histonů a metylace DNA, k nim však přistupuje řada dalších molekulárních procesů. Vedle epigenetiky je dalším odvětvím molekulární biologie výzkum nekódující RNA, který se začíná uplatňovat také ve studiu psychických poruch. Nekódující RNA, vznikající především z tzv. nesmyslné DNA, ovlivňuje genovou expresi. I Epigenetické výzkumy doposud byly prováděny jen na tkáních in vitro, pokusných zvířatech a zemřelých nemocných. Chybí epigenetické klinické studie. Do budoucna se jako nadějná jeví epigenetická terapie kognitivních poruch, schizofrenie a poruch nálady. Přitom je možno využívat jak léků stávajících (např. valproát, klozapin, sulpirid, escitalopram, lithium), tak látek nově syntetizovaných. Problémem je, že epigenetické účinky uvedených látek nejsou topicky, tkáňově, enzymaticky či genově specifické. To může vést k závažným nežádoucím účinkům. V budoucnu je zapotřebí vyrábět substrátově specifická farmaka s epigenetickými účinky a začít jejich testování na lidech. Epigenetika nám může napomoci při překonávání farmakorezistence duševních poruch, případně v jejich časné detekci a prevenci.

Epigenetics deals with the influence of external as well as intrinsic factors on the DNA function in a given organism without t he chan- ge of DNA sequence. Epigenetic effects are significant in both currently existing cells and their daughter cells. This holds tr ue for an individual organism as well as intergenerational transmission of acquired signs. Histone acetylation and DNA methylat ion are considered as the most important epigenetic mechanisms. In addition to this, other molecular procedures have already been recognized, including non-coding RNA molecules which influence gene expression. Non-coding RNA is mostly synthesized based on so called nonsense DNA. Epigenetic research has only been performed on in vitro tissues, experimental animals and brain tissue of decea- sed psychiatric patients so far. Clinical epigenetic studies in the treatment of mental disorders are lacking. Epigenetic thera py of cognitive disorders, schizophrenia, and mood disorders seems to be promising for the future. In this effort, both existing medi caments (valproate, clozapine, sulpiride, escitalopram, lithium) and newly synthesized chemical substances can be utilized. The problem is that epigenetic effects of currently known substances are not specific for individual parts of the brain, brain cells, enzymes or ge nes. This may induce serious adverse effects. In the future, it is necessary to produce substrate-specific epigenetic medicaments, and start epigenetic cli- nical studies. Epigenetics can help us to overcome treatment resistance of mental disorders, and possibly detect and prevent th em early.

• Klíčová slova
• léčba, epigenetika, farmakorezistence,
• MeSH
• Alzheimerova nemoc genetika   patologie   terapie   MeSH
• cytosin biosyntéza   MeSH
• DNA modifikační methylasy MeSH
• duševní poruchy * diagnóza   farmakoterapie   prevence a kontrola   MeSH
• epigenomika * metody   trendy   MeSH
• exozómy MeSH
• exprese genu MeSH
• histony biosyntéza   MeSH
• klinické zkoušky jako téma MeSH
• krysa rodu rattus MeSH
• kyselina valproová terapeutické užití   MeSH
• léková rezistence MeSH
• lidé MeSH
• psychofarmakologie trendy   MeSH
• RNA dlouhá nekódující dějiny   genetika   MeSH
• schizofrenie genetika   patologie   terapie   MeSH
• synapse fyziologie   účinky léků   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• lidé MeSH
• zvířata MeSH

Chemical modifications of viral RNA are an integral part of the viral life cycle and are present in most classes of viruses. To date, more than 170 RNA modifications have been discovered in all types of cellular RNA. Only a few, however, have been found in viral RNA, and the function of most of these has yet to be elucidated. Those few we have discovered and whose functions we understand have a varied effect on each virus. They facilitate RNA export from the nucleus, aid in viral protein synthesis, recruit host enzymes, and even interact with the host immune machinery. The most common methods for their study are mass spectrometry and antibody assays linked to next-generation sequencing. However, given that the actual amount of modified RNA can be very small, it is important to pair meticulous scientific methodology with the appropriate detection methods and to interpret the results with a grain of salt. Once discovered, RNA modifications enhance our understanding of viruses and present a potential target in combating them. This review provides a summary of the currently known chemical modifications of viral RNA, the effects they have on viral machinery, and the methods used to detect them.

• MeSH
• buněčné jádro metabolismus   MeSH
• lidé MeSH
• messenger RNA MeSH
• posttranskripční úpravy RNA * MeSH
• replikace viru * MeSH
• RNA virová genetika   metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

The precise and unambiguous detection and quantification of internal RNA modifications represents a critical step for understanding their physiological functions. The methods of direct RNA sequencing are quickly developing allowing for the precise location of internal RNA marks. This detection is, however, not quantitative and still presents detection limits. One of the biggest remaining challenges in the field is still the detection and quantification of m6A, m6Am, inosine, and m1A modifications of adenosine. The second intriguing and timely question remaining to be addressed is the extent to which individual marks are coregulated or potentially can affect each other. Here, we present a methodological approach to detect and quantify several key mRNA modifications in human total RNA and in mRNA, which is difficult to purify away from contaminating tRNA. We show that the adenosine demethylase FTO primarily targets m6Am marks in noncoding RNAs in HEK293T cells. Surprisingly, we observe little effect of FTO or ALKBH5 depletion on the m6A mRNA levels. Interestingly, the upregulation of ALKBH5 is accompanied by an increase in inosine level in overall mRNA.

• MeSH
• adenosin * analogy a deriváty   metabolismus   genetika   analýza   MeSH
• alfa-ketoglutarát-dependentní dioxygenasa, AlkB homolog 5 * metabolismus   genetika   MeSH
• chromatografie kapalinová metody   MeSH
• gen pro FTO * metabolismus   genetika   MeSH
• HEK293 buňky MeSH
• inosin * metabolismus   genetika   MeSH
• kapalinová chromatografie-hmotnostní spektrometrie MeSH
• lidé MeSH
• messenger RNA * genetika   metabolismus   MeSH
• posttranskripční úpravy RNA MeSH
• tandemová hmotnostní spektrometrie * metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Although posttranscriptional modification of mitochondrial (mt) transcripts plays key roles in completion of the coding information and in the expression of mtDNA-encoded genes, there is little experimental evidence on the polyadenylation status and the location of mt gene poly(A) sites for non-human mammals. RESULTS: Poly(A)-enriched RNA-Seq reads collected for two wild-caught bank voles (Clethrionomys glareolus) were mapped to the complete mitochondrial genome of that species. Transcript polyadenylation was detected as unmapped adenine residues at the ends of the mapped reads. Where the tRNA punctuation model applied, there was the expected polyadenylation, except for the nad5 transcript, whose polyadenylated 3' end is at an intergenic sequence/cytochrome b boundary. As in human, two pairs of bank vole genes, nad4l/nad4 and atp8/atp6, are expressed from bicistronic transcripts. TAA stop codons of four bank vole protein-coding genes (nad1, atp6, cox3 and nad4) are incompletely encoded in the DNA and are completed by polyadenylation. This is three genes (nad2, nad3 and cob) less than in human. The bank vole nad2 gene encodes a full stop codon (TAA in one vole and TAG in the other), which is followed by a 2 bp UTR and the gene conforms to the tRNA punctuation model. In contrast, the annotations of the reference mouse and some other rodent mt genomes in GenBank include complete TAG stop codons in both nad1 and nad2, which overlap downstream trnI and trnW, respectively. Thus the RNA-Seq data of bank voles provides a model for stop codons of mt-encoded genes in mammals comparable to humans, but at odds with some of the interpretation based purely on genomic data in mouse and other rodents. CONCLUSIONS: This work demonstrates how RNA-Seq data were useful to recover mtDNA transcriptome data in a non-model rodent and to shed more light on mammalian mtDNA transcriptome and post-transcriptional modification. Even though gene content and organisation of mtDNA are strongly conserved among mammals, annotations that neglect the transcriptome may be prone to errors in relation to the stop codons.

• MeSH
• Arvicolinae genetika   MeSH
• genom mitochondriální genetika   MeSH
• mapování chromozomů MeSH
• mitochondriální DNA genetika   MeSH
• sekvenční analýza RNA MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Our knowledge of the variety and abundances of RNA base modifications is rapidly increasing. Modified bases have critical roles in tRNAs, rRNAs, translation, splicing, RNA interference, and other RNA processes, and are now increasingly detected in all types of transcripts. Can new biological principles associated with this diversity of RNA modifications, particularly in mRNAs and long non-coding RNAs, be identified? This review will explore this question by focusing primarily on adenosine to inosine (A-to-I) RNA editing by the adenine deaminase acting on RNA (ADAR) enzymes that have been intensively studied for the past 20 years and have a wide range of effects. Over 100 million adenosine to inosine editing sites have been identified in the human transcriptome, mostly in embedded Alu sequences that form potentially innate immune-stimulating dsRNA hairpins in transcripts. Recent research has demonstrated that inosine in the epitranscriptome and ADAR1 protein establish innate immune tolerance for host dsRNA formed by endogenous sequences. Innate immune sensors that detect viral nucleic acids are among the readers of epitranscriptome RNA modifications, though this does preclude a wide range of other modification effects.

• MeSH
• adenosin genetika   MeSH
• adenosindeaminasa genetika   MeSH
• aminohydrolasy genetika   MeSH
• editace RNA genetika   MeSH
• inosin genetika   MeSH
• lidé MeSH
• messenger RNA genetika   MeSH
• posttranskripční úpravy RNA genetika   MeSH
• přirozená imunita genetika   MeSH
• proteiny vázající RNA genetika   MeSH
• transkriptom genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Pro správné pochopení fyziologických procesů v buňce a případně jejich odchylek jsou molekulárně‑bio­logické analýzy nezbytným nástrojem využívaným v bio­medicínském výzkumu a také v klinické dia­gnostice. Existuje množství technik, které umožňují určit lokalizaci studovaných proteinů a jejich interakční aktivitu. Tyto přístupy využívají především interakce specificky se vážících molekul s cílovými proteiny (protilátky) nebo synteticky připravené rekombinantní proteiny (GFP fúzní protein; metody fluorescenčního/bio­luminiscenčního rezonančního přenosu energie). „Proximity ligation assay“ (PLA) in situ představuje novou techniku zobrazující proteiny na úrovni jednotlivých buněk a tkání s využitím reportérové molekuly DNA a DNA modifikujících procesů. Tato metoda umožňuje přímou vizualizaci proteinů, jejich hladiny, modifikace a interakce v jednotlivých fixovaných buňkách a tkáních. Sondy jsou tvořeny specifickými protilátkami s navázaným oligonukleotidem, který slouží jako reportérová molekula. Pokud dojde k navázání sond v těsné blízkosti, následuje vznik kružnicové DNA, jež slouží jako templát pro amplifikaci otáčivou kružnicí. Amplifikační reakce umožňuje vizualizaci sledované interakce. Ve srovnání s dostupnými molekulárně‑bio­logickými metodami vycházejícími z genového inženýrství, PLA in situ umožňuje studovat endogenní proteiny v jejich přirozených podmínkách, a může být tudíž použita pro studium klinického materiálu. PLA in situ je využitelná v jakékoliv výzkumné oblasti zaměřené na studium proteinových interakcí, jako je studium buněčných signálních drah, identifikace cílů farmakologicky účinných látek či v onkologické dia­gnostice.

To understand cellular processes and events responsible for their perturbations, proteomic analyses are needed in bio­medical research and clinical dia­gnostics. Several techniques based on specifically binding reagents (antibodies) or recombinant proteins (GFP fusion protein, methods of fluorescence/bio­luminescence resonance energy transfer) are generally used to study protein location and activity resulting from secondary modifications and interactions. The in situ proximity ligation assay represents a novel technique of in situ protein imaging using DNA as a reporter molecule and DNA amplification processes. This method enables direct visualization of single molecules, their levels, modifications and pattern of interactions in individual fixed cells and tissues. Proximity probes consist of specific antibody with attached oligonucleotides that are used as reporter molecules for identification of such events. Proximity probes guide the formation of a circular DNA strand when bound in close proximity. The DNA circle after that serves as a template for rolling‑circle amplification allowing the interaction to be visualized. Compared to available proteomic techniques benefiting from genetic engineering, in situ PLA enables study of endogenous proteins in their natural environment and thus can be used for clinical specimens. The areas of applicability where proximity ligation procedure can be used include any research field where protein interaction measurements are important, such as signal­ing pathway studies, monitoring of pharmacological treatment targets and oncological dia­gnostics. Key words: in situ PLA – protein interaction – protein detection methods – proximity ligation This work was supported by the European Regional Development Fund and the State Budget of the Czech Republic (RECAMO, CZ.1.05/2.1.00/03.0101) and by MH CZ – DRO (MMCI, 00209805) and BBMRI_CZ (LM2010004). The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE “uniform requirements” for biomedical papers. Submitted: 31. 1. 2014 Accepted: 25. 3. 2014

• Klíčová slova
• in situ PLA, metody detekce proteinů, proteinové interakce,
• MeSH
• chemické techniky analytické * MeSH
• fyziologie buňky MeSH
• mapování interakce mezi proteiny * metody   MeSH
• molekulární sondy - techniky * MeSH
• molekulární sondy MeSH
• oligonukleotidové sondy MeSH
• oligonukleotidy metabolismus   MeSH
• proteiny MeSH
• protilátky MeSH
• techniky amplifikace nukleových kyselin MeSH
• Publikační typ
• práce podpořená grantem MeSH
• přehledy MeSH

Cardiac tolerance to ischaemia can be increased by dietary interventions such as fasting, which is associated with significant changes in myocardial gene expression. Among the possible mechanisms of how gene expression may be altered are epigenetic modifications of RNA - epitranscriptomics. N6-methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am) are two of the most prevalent modifications in mRNA. These methylations are reversible and regulated by proteins called writers, erasers, readers, and m6A-repelled proteins. We analysed 33 of these epitranscriptomic regulators in rat hearts after cardioprotective 3-day fasting using RT-qPCR, Western blot, and targeted proteomic analysis. We found that the most of these regulators were changed on mRNA or protein levels in fasting hearts, including up-regulation of both demethylases - FTO and ALKBH5. In accordance, decreased methylation (m6A+m6Am) levels were detected in cardiac total RNA after fasting. We also identified altered methylation levels in Nox4 and Hdac1 transcripts, both of which play a role in the cytoprotective action of ketone bodies produced during fasting. Furthermore, we investigated the impact of inhibiting demethylases ALKBH5 and FTO in adult rat primary cardiomyocytes (AVCMs). Our findings indicate that inhibiting these demethylases reduced the hypoxic tolerance of AVCMs isolated from fasting rats. This study showed that the complex epitranscriptomic machinery around m6A and m6Am modifications is regulated in the fasting hearts and might play an important role in cardiac adaptation to fasting, a well-known cardioprotective intervention.

• MeSH
• adenosin * genetika   metabolismus   MeSH
• krysa rodu rattus MeSH
• messenger RNA genetika   MeSH
• omezení příjmu potravy MeSH
• proteomika * MeSH
• RNA metabolismus   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

MAIN CONCLUSION: In tobacco, three sequence variants of the TERT gene have been described. We revealed unbalanced levels of TERT variant transcripts in vegetative tobacco tissues and enhanced TERT transcription and telomerase activity in reproductive tissues. Telomerase is a ribonucleoprotein complex responsible for the maintenance of telomeres, structures delimiting ends of linear eukaryotic chromosomes. In the Nicotiana tabacum (tobacco) allotetraploid plant, three sequence variants (paralogs) of the gene coding for the telomerase reverse transcriptase subunit (TERT) have been described, two of them derived from the maternal N. sylvestris genome (TERT_Cs, TERT_D) and one originated from the N. tomentosiformis paternal genome (TERT_Ct). In this work, we analyzed the transcription of TERT variants in correlation with telomerase activity in tobacco tissues. High and approximately comparable levels of TERT_Ct and TERT_Cs transcripts were detected in seedlings, roots, flower buds and leaves, while the transcript of the TERT_D variant was markedly underrepresented. Similarly, in N. sylvestris tissues, TERT_Cs transcript significantly predominated. A specific pattern of TERT transcripts was found in samples of tobacco pollen with the TERT_Cs variant clearly dominating particularly at the early stage of pollen development. Detailed analysis of TERT_C variants representation in functionally distinct fractions of pollen transcriptome revealed their prevalence in large ribonucleoprotein particles encompassing translationally silent mRNA; only a minority of TERT_Ct and TERT_Cs transcripts were localized in actively translated polysomes. Histones of the TERT_C chromatin were decorated predominantly with the euchromatin-specific epigenetic modification in both telomerase-positive and telomerase-negative tobacco tissues. We conclude that the existence and transcription pattern of tobacco TERT paralogs represents an interesting phenomenon and our results indicate its functional significance. Nicotiana species have again proved to be appropriate and useful model plants in telomere biology studies.

• MeSH
• buněčné jádro genetika   MeSH
• chromatinová imunoprecipitace MeSH
• euchromatin metabolismus   MeSH
• genetická transkripce MeSH
• genetická variace * MeSH
• histony metabolismus   MeSH
• messenger RNA genetika   metabolismus   MeSH
• orgánová specificita genetika   MeSH
• polyribozomy metabolismus   MeSH
• posttranslační úpravy proteinů MeSH
• pylová láčka růst a vývoj   MeSH
• regulace genové exprese u rostlin * MeSH
• tabák genetika   MeSH
• telomerasa genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH

Current progress in the field of next-generation transcriptome sequencing have contributed significantly to the study of various malignancies including glioblastoma multiforme (GBM). Differential sequencing of transcriptomes of patients and non-tumor controls has a potential to reveal novel transcripts with significant role in GBM. One such candidate group of molecules are long non-coding RNAs (lncRNAs) which have been proved to be involved in processes such as carcinogenesis, epigenetic modifications and resistance to various therapeutic approaches. To maximize the value of transcriptome sequencing, a proper protocol for library preparation from tissue-derived RNA needs to be found which would produce high quality transcriptome sequencing data and increase the number of detected lncRNAs. It is important to mention that success of library preparation is determined by the quality of input RNA, which is in case of real-life tissue specimens very often altered in comparison to high quality RNA commonly used by manufacturers for development of library preparation chemistry. In the present study, we used GBM and non-tumor brain tissue specimens and compared three different commercial library preparation kits, namely NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific), SENSE Total RNA-Seq Library Prep Kit (Lexogen) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Libraries generated using SENSE kit were characterized by the most normal distribution of normalized average GC content, the least amount of over-represented sequences and the percentage of ribosomal RNA reads (0.3-1.5%) and highest numbers of uniquely mapped reads and reads aligning to coding regions. However, NEBNext kit performed better having relatively low duplication rates, even transcript coverage and the highest number of hits in Ensembl database for every biotype of our interest including lncRNAs. Our results indicate that out of three approaches the NEBNext library preparation kit was most suitable for the study of lncRNAs via transcriptome sequencing. This was further confirmed by highly consistent data reached in an independent validation on an expanded cohort.

• MeSH
• genová knihovna MeSH
• glioblastom genetika   MeSH
• lidé MeSH
• nádory mozku genetika   MeSH
• reagenční diagnostické soupravy MeSH
• regulace genové exprese u nádorů MeSH
• RNA dlouhá nekódující genetika   MeSH
• sekvenční analýza RNA MeSH
• stanovení celkové genové exprese metody   MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH

BACKGROUND: ChIP-seq has become a routine method for interrogating the genome-wide distribution of various histone modifications. An important experimental goal is to compare the ChIP-seq profiles between an experimental sample and a reference sample, and to identify regions that show differential enrichment. However, comparative analysis of samples remains challenging for histone modifications with broad domains, such as heterochromatin-associated H3K27me3, as most ChIP-seq algorithms are designed to detect well defined peak-like features. RESULTS: To address this limitation we introduce histoneHMM, a powerful bivariate Hidden Markov Model for the differential analysis of histone modifications with broad genomic footprints. histoneHMM aggregates short-reads over larger regions and takes the resulting bivariate read counts as inputs for an unsupervised classification procedure, requiring no further tuning parameters. histoneHMM outputs probabilistic classifications of genomic regions as being either modified in both samples, unmodified in both samples or differentially modified between samples. We extensively tested histoneHMM in the context of two broad repressive marks, H3K27me3 and H3K9me3, and evaluated region calls with follow up qPCR as well as RNA-seq data. Our results show that histoneHMM outperforms competing methods in detecting functionally relevant differentially modified regions. CONCLUSION: histoneHMM is a fast algorithm written in C++ and compiled as an R package. It runs in the popular R computing environment and thus seamlessly integrates with the extensive bioinformatic tool sets available through Bioconductor. This makeshistoneHMM an attractive choice for the differential analysis of ChIP-seq data. Software is available from http://histonehmm.molgen.mpg.de .

• MeSH
• algoritmy * MeSH
• chromatinová imunoprecipitace MeSH
• genomika metody   MeSH
• histony chemie   genetika   metabolismus   MeSH
• krysa rodu rattus MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• lidé MeSH
• Markovovy řetězce MeSH
• myši MeSH
• posttranslační úpravy proteinů * MeSH
• software * MeSH
• výpočetní biologie metody   MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• lidé MeSH
• mužské pohlaví MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH