It was long time pressumed that only eukaryotes protect their RNA by 5'-RNA cap. Recently, it was shown that also prokaryotes employ some kind of protection of their RNA in the form of 5'-triphosphate or NAD covalently attached to 5'-terminus. This review discusses the state of art of 5'-RNA cap in eukaryotes and prokaryotes.
- Keywords
- modifikace RNA,
- MeSH
- RNA Processing, Post-Transcriptional MeSH
- RNA Caps * MeSH
- Research MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
Biologická terapie, jejímž mechanizmem účinku je použití monoklonálních protilátek proti nějakému proteinu, je používána v klinické praxi již řadu let. V současné době ale vstupují do klinické praxe nové léky ze skupiny biologické terapie, které účinkují na principu RNA-interference. RNA-interference je proces, kterým buňky všech živých organizmů regulují expresi svých genů a při kterém může být zastaven přenos informace o syntéze konkrétního proteinu mezi DNA a ribosomy. Pro terapeutické účely se tohoto efektu dosahuje podáním umělých syntetizovaných oligonukleotidů s přesně danou sekvencí nukleosidů. Jde buď o krátké úseky dvouvláknové RNA, nebo o jednovláknové oligonukleotidy. Pro klinické využití byla nutná pro zvýšení jejich stability a odstranění některých nežádoucích účinků jejich chemická modifikace, a dále pak vazba na další substance, které umožní jejich cílený transport do požadované tkáně. Celá řada těchto léků je již v pokročilých fázích klinických studií a některé z nich vstupují na farmaceutický trh.
Biological therapy, whose mechanism of action is the use of monoclonal antibodies against a protein, has been used in clinical practice for many years. However, new drugs from the group of biological therapies that act on the principle of RNA interference are now entering clinical practice. RNA interference is the process by which cells in all living organisms regulate the expression of their genes, and in which the transfer of information about the synthesis of a particular protein between DNA and ribosomes can be stopped. For therapeutic purposes, this effect is achieved by administering artificially synthesized oligonucleotides – short chains of RNA with a precise nucleoside sequence. These are either short stretches of double- stranded RNA or single-stranded oligonucleotides. For clinical use, their chemical modification was necessary to increase their stability and remove some of their side effects, and then binding to other substances to allow their targeted transport to the desired tissue. A number of these drugs are already in advanced stages of clinical trials, and some are entering the pharmaceutical market.
Epitranscriptomic modifications have recently emerged into the spotlight of researchers due to their vast regulatory effects on gene expression and thereby cellular physiology and pathophysiology. N6,2'-O-dimethyladenosine (m6Am) is one of the most prevalent chemical marks on RNA and is dynamically regulated by writers (PCIF1, METTL4) and erasers (FTO). The presence or absence of m6Am in RNA affects mRNA stability, regulates transcription, and modulates pre-mRNA splicing. Nevertheless, its functions in the heart are poorly known. This review summarizes the current knowledge and gaps about m6Am modification and its regulators in cardiac biology. It also points out technical challenges and lists the currently available techniques to measure m6Am. A better understanding of epitranscriptomic modifications is needed to improve our knowledge of the molecular regulations in the heart which may lead to novel cardioprotective strategies.
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.
- Keywords
- léčba, epigenetika, farmakorezistence,
- MeSH
- Alzheimer Disease genetics pathology therapy MeSH
- Cytosine biosynthesis MeSH
- DNA Modification Methylases MeSH
- Mental Disorders * diagnosis drug therapy prevention & control MeSH
- Epigenomics * methods trends MeSH
- Exosomes MeSH
- Gene Expression MeSH
- Histones biosynthesis MeSH
- Clinical Trials as Topic MeSH
- Rats MeSH
- Valproic Acid therapeutic use MeSH
- Drug Resistance MeSH
- Humans MeSH
- Psychopharmacology trends MeSH
- RNA, Long Noncoding history genetics MeSH
- Schizophrenia genetics pathology therapy MeSH
- Synapses physiology drug effects MeSH
- Animals MeSH
- Check Tag
- Rats MeSH
- Humans MeSH
- Animals MeSH
- MeSH
- Alkaline Phosphatase MeSH
- Electrophoresis MeSH
- RNA, Viral MeSH
- Cattle MeSH
- Animals MeSH
- Check Tag
- Cattle MeSH
- Animals MeSH
Pseudouridine is the most frequently naturally occurring RNA modification, found in all classes of biologically functional RNAs. Compared to uridine, pseudouridine contains an additional hydrogen bond donor group and is therefore widely regarded as a structure stabilizing modification. However, the effects of pseudouridine modifications on the structure and dynamics of RNAs have so far only been investigated in a limited number of different structural contexts. Here, we introduced pseudouridine modifications into the U-turn motif and the adjacent U:U closing base pair of the neomycin-sensing riboswitch (NSR)-an extensively characterized model system for RNA structure, ligand binding, and dynamics. We show that the effects of replacing specific uridines with pseudouridines on RNA dynamics crucially depend on the exact location of the replacement site and can range from destabilizing to locally or even globally stabilizing. By using a combination of NMR spectroscopy, MD simulations and QM calculations, we rationalize the observed effects on a structural and dynamical level. Our results will help to better understand and predict the consequences of pseudouridine modifications on the structure and function of biologically important RNAs.
- MeSH
- Epigenesis, Genetic * MeSH
- RNA genetics metabolism MeSH
- Transcriptome * MeSH
- Publication type
- Journal Article MeSH
RNA polymerase II (RNA pol II) is not only the fundamental enzyme for gene expression but also the central coordinator of co-transcriptional processing. RNA pol II associates with a large number of enzymes and protein/RNA-binding factors through its C-terminal domain (CTD) that consists of tandem repeats of the heptapeptide consensus Y(1)S(2)P(3) T(4)S(5)P(6)S(7). The CTD is posttranslationally modified, yielding specific patterns (often called the CTD code) that are recognized by appropriate factors in coordination with the transcription cycle. Serine phosphorylations are currently the best characterized elements of the CTD code; however, the roles of the proline isomerization and other modifications of the CTD remain poorly understood. The dynamic remodeling of the CTD modifications by kinases, phosphatases, isomerases, and other enzymes introduce changes in the CTD structure and dynamics. These changes serve as structural switches that spatially and temporally regulate the binding of processing factors. Recent structural studies of the CTD bound to various proteins have revealed the basic rules that govern the recognition of these switches and shed light on the roles of these protein factors in the assemblies of the processing machineries.
- MeSH
- Transcription, Genetic MeSH
- Methyltransferases metabolism MeSH
- Peptidylprolyl Isomerase metabolism MeSH
- Protein Processing, Post-Translational * MeSH
- Proline metabolism MeSH
- RNA-Binding Proteins genetics metabolism MeSH
- RNA Polymerase II * chemistry genetics metabolism MeSH
- Saccharomyces cerevisiae enzymology genetics MeSH
- Amino Acid Sequence MeSH
- Protein Structure, Tertiary MeSH
- Carrier Proteins metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
ADAR RNA editing enzymes (adenosine deaminases acting on RNA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster, which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems.
- MeSH
- Adenosine Deaminase chemistry genetics metabolism MeSH
- Drosophila melanogaster genetics metabolism MeSH
- RNA Editing * MeSH
- Gene Expression MeSH
- Protein Interaction Domains and Motifs MeSH
- Isoenzymes MeSH
- Humans MeSH
- RNA, Messenger genetics MeSH
- Evolution, Molecular MeSH
- Nervous System metabolism MeSH
- Vertebrates MeSH
- Drosophila Proteins genetics metabolism MeSH
- RNA-Binding Proteins genetics metabolism MeSH
- RNA Interference MeSH
- Substrate Specificity MeSH
- Protein Binding MeSH
- Structure-Activity Relationship MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review 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.
