Oocyte-to-embryo transition is a process during which an oocyte ovulates, is fertilized, and becomes a developing embryo. It involves the first major genome reprogramming event in life of an organism where gene expression, which gave rise to a differentiated oocyte, is remodeled in order to establish totipotency in blastomeres of an early embryo. This remodeling involves replacement of maternal RNAs with zygotic RNAs through maternal RNA degradation and zygotic genome activation. This review is focused on expression and function of long noncoding RNAs (lncRNAs) and small RNAs during oocyte-to-embryo transition in mammals. LncRNAs are an assorted rapidly evolving collection of RNAs, which have no apparent protein-coding capacity. Their biogenesis is similar to mRNAs including transcriptional control and post-transcriptional processing. Diverse molecular and biological roles were assigned to lncRNAs although most of them probably did not acquire a detectable biological role. Since some lncRNAs serve as precursors for small noncoding regulatory RNAs in RNA silencing pathways, both types of noncoding RNA are reviewed together.

• MeSH
• Blastomeres chemistry   MeSH
• Gastrulation MeSH
• Humans MeSH
• RNA, Small Untranslated genetics   MeSH
• RNA, Long Noncoding genetics   MeSH
• Mammals embryology   genetics   MeSH
• RNA Stability MeSH
• Gene Expression Regulation, Developmental MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH

The first described small non-coding RNA was microRNA lin-4 from Caenorhabditis elegans in 1993. This miRNA has begun a new age of research leading to the discovery of previously unknown, endogenous, single stranded, 22–25 nucleotides long molecules regulating nearly 30 % of genes. Recently, it was demonstrated that a number of organic substances presented in the diet induces the formation of various miRNAs. Besides this, plant and animal miRNA may enter the host organisms as food. In host organism, they can resist degradation and can enter the bloodstream. Although lacking sufficient experimental support, the discussion whether such dietary miRNAs can participate in post-transcriptional regulation of host genes is an actual topic. Either of these mechanisms could also explain some of the biological activities of medicinal plants. Non-coding RNAs have also significance as diagnostic biomarkers of some diseases or as targets for complex disease therapies.

• MeSH
• Biomarkers metabolism   MeSH
• Transcription, Genetic genetics   immunology   MeSH
• Transcription Initiation, Genetic MeSH
• Humans MeSH
• MicroRNAs isolation & purification   metabolism   MeSH
• RNA, Untranslated * genetics   isolation & purification   metabolism   MeSH
• Food MeSH
• Gene Expression Regulation, Neoplastic genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Research Support, Non-U.S. Gov't MeSH

Although the existence of small molecules of RNA that do not encode any amino acid chain has been proven two decades ago, their significance and extensive effect on cellular processes is still amazing. Many new studies fo-cused on finding new non-coding RNAs and the clarifica-tion of their functions in the organism are continuously published. This paper summarizes the current knowledge of small non-coding RNAs and their functions, both in prokaryotic and eukaryotic organisms.

• MeSH
• Humans MeSH
• RNA, Small Untranslated * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Review MeSH

• MeSH
• Bacteria genetics   MeSH
• Escherichia coli genetics   MeSH
• Research Support as Topic MeSH
• RNA, Small Cytoplasmic genetics   MeSH
• RNA, Small Nuclear genetics   MeSH
• RNA, Messenger, Stored genetics   MeSH
• Publication type
• Review MeSH

Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders with large heterogeneity at the clinical and molecular levels. As diagnostic procedures shift from bone marrow biopsies towards less invasive techniques, circulating small noncoding RNAs (sncRNAs) have become of particular interest as potential novel noninvasive biomarkers of the disease. We aimed to characterize the expression profiles of circulating sncRNAs of MDS patients and to search for specific RNAs applicable as potential biomarkers. We performed small RNA-seq in paired samples of total plasma and plasma-derived extracellular vesicles (EVs) obtained from 42 patients and 17 healthy controls and analyzed the data with respect to the stage of the disease, patient survival, response to azacitidine, mutational status, and RNA editing. Significantly higher amounts of RNA material and a striking imbalance in RNA content between plasma and EVs (more than 400 significantly deregulated sncRNAs) were found in MDS patients compared to healthy controls. Moreover, the RNA content of EV cargo was more homogeneous than that of total plasma, and different RNAs were deregulated in these two types of material. Differential expression analyses identified that many hematopoiesis-related miRNAs (e.g., miR-34a, miR-125a, and miR-150) were significantly increased in MDS and that miRNAs clustered on 14q32 were specifically increased in early MDS. Only low numbers of circulating sncRNAs were significantly associated with somatic mutations in the SF3B1 or DNMT3A genes. Survival analysis defined a signature of four sncRNAs (miR-1237-3p, U33, hsa_piR_019420, and miR-548av-5p measured in EVs) as the most significantly associated with overall survival (HR = 5.866, p < 0.001). In total plasma, we identified five circulating miRNAs (miR-423-5p, miR-126-3p, miR-151a-3p, miR-125a-5p, and miR-199a-3p) whose combined expression levels could predict the response to azacitidine treatment. In conclusion, our data demonstrate that circulating sncRNAs show specific patterns in MDS and that their expression changes during disease progression, providing a rationale for the potential clinical usefulness of circulating sncRNAs in MDS prognosis. However, monitoring sncRNA levels in total plasma or in the EV fraction does not reflect one another, instead, they seem to represent distinctive snapshots of the disease and the data should be interpreted circumspectly with respect to the type of material analyzed.

• MeSH
• Azacitidine pharmacology   MeSH
• Biomarkers blood   MeSH
• Models, Biological MeSH
• RNA Editing genetics   MeSH
• Extracellular Vesicles metabolism   MeSH
• Kaplan-Meier Estimate MeSH
• Humans MeSH
• RNA, Small Untranslated blood   genetics   MeSH
• MicroRNAs genetics   metabolism   MeSH
• Multivariate Analysis MeSH
• Mutation genetics   MeSH
• Myelodysplastic Syndromes blood   genetics   pathology   MeSH
• Prognosis MeSH
• Proportional Hazards Models MeSH
• Gene Expression Regulation MeSH
• Reproducibility of Results MeSH
• Signal Transduction genetics   MeSH
• Treatment Outcome MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

• MeSH
• Gastrointestinal Neoplasms diagnosis   MeSH
• Biomarkers, Tumor MeSH
• RNA, Untranslated MeSH
• Gene Expression Profiling MeSH

• Conspectus
• Patologie. Klinická medicína
• NML Fields
• gastroenterologie
• biologie
• NML Publication type
• studie

Osteoarthritis (OA) is a frequent musculoskeletal disorder affecting millions of people worldwide. Despite advances in understanding the pathogenesis of OA, prognostic biomarkers or effective targeted treatment are not currently available. Research on epigenetic factors has yielded some new insights as new technologies for their detection continue to emerge. In this context, non-coding RNAs, including microRNAs, long non-coding RNAs, circular RNAs, piwi-interacting RNAs, and small nucleolar RNAs, regulate intracellular signaling pathways and biological processes that have a crucial role in the development of several diseases. In this review, we present current knowledge on the role of epigenetic factors with a focus on non-coding RNAs in the development, prediction and treatment of OA. This article is categorized under: RNA in Disease and Development > RNA in Disease.

• MeSH
• RNA, Circular MeSH
• Humans MeSH
• MicroRNAs * genetics   MeSH
• Osteoarthritis * genetics   MeSH
• Piwi-Interacting RNA MeSH
• RNA, Long Noncoding * genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH

The increased interest in assisted reproduction through in vitro fertilization (IVF) leads to an urgent need to identify biomarkers that reliably highly predict the success of pregnancy. Despite advances in diagnostics, treatment, and IVF approaches, the 30% success rate of IVF seems insurmountable. Idiopathic infertility does not have any explanation for IVF failure especially when a patient is treated with a healthy competitive embryo capable of implantation and development. Since appropriate intercellular communication is essential after embryo implantation, the emergence of the investigation of embryonic secretome including short non-coding RNA (sncRNA) molecules is crucial. That's why biomarker identification, sncRNAs secreted during the IVF process into the blastocyst's cultivation medium, by the implementation of artificial intelligence opens the door to a better understanding of the bidirectional communication between embryonic cells and the endometrium and so the success of the IVF. This study presents a set of promising new sncRNAs which are revealed to predictively distinguish a high-quality embryo, suitable for an embryo transfer in the IVF process, from a low-quality embryo with 86% accuracy. The identified exact combination of miRNAs/piRNAs as a non-invasively obtained biomarker for quality embryo determination, increasing the likelihood of implantation and the success of pregnancy after an embryo transfer.

• MeSH
• Biomarkers MeSH
• Fertilization in Vitro MeSH
• Humans MeSH
• RNA, Small Untranslated * MeSH
• Embryo Transfer MeSH
• Pregnancy MeSH
• Artificial Intelligence MeSH
• Check Tag
• Humans MeSH
• Pregnancy MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Lidský genom obsahuje asi 22 000 protein kódujících genů, které dávají vznik ještě většímu množství messengerové RNA (mRNA). Výsledky projektu ENCODE z roku 2012 však ukazují, že byť je až 90 % našeho genomu aktivně přepisováno, tak mRNA dávající vznik proteinům tvoří pouze 2–3 % z celkového množství přepsané RNA. Zbývající RNA transkripty nedávají vznik proteinům a nesou proto označení „nekódující RNA“. Dříve se nekódující RNA považovala za „temnou hmotu genomu“, nebo za „odpad“, který se v naší DNA nahromadil v průběhu evoluce. Dnes již víme, že nekódující RNA plní v našem těle celou řadu regulačních funkcí – zasahují do epigenetických procesů od remodelace chromatinu k metylaci histonů, nebo do vlastního procesu transkripce, či do posttranskripčních procesů. Dlouhé nekódující RNA (lncRNA) jsou jednou ze tříd nekódujících RNA s délkou nad 200 nukleotidů (nekódující RNA s délkou pod 200 nukleotidů označujeme jako krátké nekódující RNA). lncRNA představují velice pestrou a rozsáhlou skupinu molekul s rozličnými regulačními funkcemi. Můžeme je identifkovat ve všech myslitelných buněčných typech, či tkáních, nebo dokonce v extracelulárním prostoru, a to včetně krve, potažmo plazmy. Jejich hladiny se mění v průběhu organogeneze, jsou specifické pro jednotlivé tkáně a k jejich změnám dochází i při vzniku různých onemocnění, včetně aterosklerózy. Cílem tohoto souhrnného článku je jednak představit problematiku lncRNA a některé jejich konkrétní zástupce ve vztahu k procesu aterosklerózy (popsat zapojení lncRNA do biologie endotelových buněk, hladkosvalových buněk cévní stěny, či buněk imunitních), a dále poukázat na možný klinický potenciál lncRNA, ať již v diagnostice či terapii aterosklerózy a jejích klinických manifestací.

The human genome contains about 22 000 protein-coding genes that are transcribed to an even larger amount of messenger RNAs (mRNA). Interestingly, the results of the project ENCODE from 2012 show, that despite up to 90 % of our genome being actively transcribed, protein-coding mRNAs make up only 2–3 % of the total amount of the transcribed RNA. The rest of RNA transcripts is not translated to proteins and that is why they are referred to as “non-coding RNAs”. Earlier the non-coding RNA was considered “the dark matter of genome”, or “the junk”, whose genes has accumulated in our DNA during the course of evolution. Today we already know that non-coding RNAs fulfil a variety of regulatory functions in our body – they intervene into epigenetic processes from chromatin remodelling to histone methylation, or into the transcription process itself, or even post-transcription processes. Long non-coding RNAs (lncRNA) are one of the classes of non-coding RNAs that have more than 200 nucleotides in length (non-coding RNAs with less than 200 nucleotides in length are called small non-coding RNAs). lncRNAs represent a widely varied and large group of molecules with diverse regulatory functions. We can identify them in all thinkable cell types or tissues, or even in an extracellular space, which includes blood, specifically plasma. Their levels change during the course of organogenesis, they are specific to different tissues and their changes also occur along with the development of different illnesses, including atherosclerosis. This review article aims to present lncRNAs problematics in general and then focuses on some of their specific representatives in relation to the process of atherosclerosis (i.e. we describe lncRNA involvement in the biology of endothelial cells, vascular smooth muscle cells or immune cells), and we further describe possible clinical potential of lncRNA, whether in diagnostics or therapy of atherosclerosis and its clinical manifestations.

• MeSH
• Atherosclerosis * physiopathology   MeSH
• Endothelium physiology   MeSH
• Gene Expression MeSH
• Humans MeSH
• RNA, Long Noncoding * physiology   classification   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH

Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.

• MeSH
• MicroRNAs * genetics   MeSH
• RNA, Long Noncoding * genetics   MeSH
• Publication type
• Journal Article MeSH
• Review MeSH