N6-Methyladenosine (m6A) is the predominant internal RNA modification in eukaryotic messenger RNAs (mRNAs) and plays a crucial role in mRNA stability. Here, using human cells, we reveal that m6A sites in the coding sequence (CDS) trigger CDS-m6A decay (CMD), a pathway that is distinct from previously reported m6A-dependent degradation mechanisms. Importantly, CDS m6A sites act considerably faster and more efficiently than those in the 3' untranslated region, which to date have been considered the main effectors. Mechanistically, CMD depends on translation, whereby m6A deposition in the CDS triggers ribosome pausing and transcript destabilization. The subsequent decay involves the translocation of the CMD target transcripts to processing bodies (P-bodies) and recruitment of the m6A reader protein YT521-B homology domain family protein 2 (YTHDF2). Our findings highlight CMD as a previously unknown pathway, which is particularly important for controlling the expression of developmental regulators and retrogenes.

• Keywords
• P-bodies, RNA decay, RNA modification, YTHDF2, coding sequence, m6A, ribosomal A site, ribosome pausing, translation,
• MeSH
• 3' Untranslated Regions MeSH
• Adenosine * analogs & derivatives   metabolism   genetics   MeSH
• HEK293 Cells MeSH
• HeLa Cells MeSH
• Humans MeSH
• RNA, Messenger * genetics   metabolism   MeSH
• Open Reading Frames * MeSH
• RNA-Binding Proteins * genetics   metabolism   MeSH
• Protein Biosynthesis * MeSH
• Ribosomes metabolism   genetics   MeSH
• RNA Stability * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• 3' Untranslated Regions MeSH
• Adenosine * MeSH
• RNA, Messenger * MeSH
• N-methyladenosine MeSH Browser
• RNA-Binding Proteins * MeSH
• YTHDF2 protein, human MeSH Browser

Coat protein (CP) coding regions of six Potato mop-top virus (PMTV) isolates from the Czech Republic and Denmark (54-10, 54-11, 54-15, 54-19, Korneta and Pacov) were sequenced. Comparison of the obtained nucleotide sequences as well as alignment of the deduced amino acid sequences were performed. The obtained results showed that the isolates from different parts of Europe seem to have highly conserved coding regions which is unexpected for a viral RNA genome known for its high mutation rate. Thus considerable differences in virulence and significant variation in biological properties of these isolates should not be attributed to CP but to some other part of the genome.

• MeSH
• Cloning, Molecular MeSH
• Molecular Sequence Data MeSH
• Plant Diseases virology   MeSH
• Open Reading Frames genetics   MeSH
• Reverse Transcriptase Polymerase Chain Reaction MeSH
• Plant Viruses genetics   isolation & purification   MeSH
• Amino Acid Sequence MeSH
• Base Sequence MeSH
• Sequence Alignment MeSH
• Solanum tuberosum virology   MeSH
• Capsid Proteins genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Capsid Proteins MeSH

Cytoplasmic male sterility (CMS) is a widespread phenomenon in flowering plants caused by mitochondrial (mt) genes. CMS genes typically encode novel proteins that interfere with mt functions and can be silenced by nuclear fertility-restorer genes. Although the molecular basis of CMS is well established in a number of crop systems, our understanding of it in natural populations is far more limited. To identify CMS genes in a gynodioecious plant, Silene vulgaris, we constructed mt transcriptomes and compared transcript levels and RNA editing patterns in floral bud tissue from female and hermaphrodite full siblings. The transcriptomes from female and hermaphrodite individuals were very similar overall with respect to variation in levels of transcript abundance across the genome, the extent of RNA editing, and the order in which RNA editing and intron splicing events occurred. We found only a single genomic region that was highly overexpressed and differentially edited in females relative to hermaphrodites. This region is not located near any other transcribed elements and lacks an open-reading frame (ORF) of even moderate size. To our knowledge, this transcript would represent the first non-coding mt RNA associated with CMS in plants and is, therefore, an important target for future functional validation studies.

• Keywords
• Cytoplasmic male sterility, Silene vulgaris, editing, mitochondrion, non-coding RNA, splicing, transcriptome.,
• MeSH
• RNA Editing MeSH
• Flowers genetics   growth & development   MeSH
• Genes, Mitochondrial * MeSH
• RNA, Untranslated * MeSH
• Plant Infertility * MeSH
• Plant Proteins genetics   metabolism   MeSH
• Silene genetics   physiology   MeSH
• Transcriptome * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Names of Substances
• RNA, Untranslated * MeSH
• Plant Proteins MeSH

Long terminal repeat (LTR) retrotransposons make up substantial parts of most higher plant genomes where they accumulate due to their replicative mode of transposition. Although the transposition is facilitated by proteins encoded within the gag-pol region which is common to all autonomous elements, some LTR retrotransposons were found to potentially carry an additional protein coding capacity represented by extra open reading frames located upstream or downstream of gag-pol. In this study, we performed a comprehensive in silico survey and comparative analysis of these extra open reading frames (ORFs) in the group of Ty3/gypsy LTR retrotransposons as the first step towards our understanding of their origin and function. We found that extra ORFs occur in all three major lineages of plant Ty3/gypsy elements, being the most frequent in the Tat lineage where most (77 %) of identified elements contained extra ORFs. This lineage was also characterized by the highest diversity of extra ORF arrangement (position and orientation) within the elements. On the other hand, all of these ORFs could be classified into only two broad groups based on their mutual similarities or the presence of short conserved motifs in their inferred protein sequences. In the Athila lineage, the extra ORFs were confined to the element 3' regions but they displayed much higher sequence diversity compared to those found in Tat. In the lineage of Chromoviruses the extra ORFs were relatively rare, occurring only in 5' regions of a group of elements present in a single plant family (Poaceae). In all three lineages, most extra ORFs lacked sequence similarities to characterized gene sequences or functional protein domains, except for two Athila-like elements with similarities to LOGL4 gene and part of the Chromoviruses extra ORFs that displayed partial similarity to histone H3 gene. Thus, in these cases the extra ORFs most likely originated by transduction or recombination of cellular gene sequences. In addition, the protein domain which is otherwise associated with DNA transposons have been detected in part of the Tat-like extra ORFs, pointing to their origin from an insertion event of a mobile element.

• MeSH
• DNA, Plant * MeSH
• Phylogeny MeSH
• Genetic Linkage MeSH
• Ferns classification   genetics   MeSH
• Terminal Repeat Sequences * MeSH
• Molecular Sequence Data MeSH
• Open Reading Frames * MeSH
• Gene Order MeSH
• Retroelements * MeSH
• Plant Viruses genetics   MeSH
• Amino Acid Sequence MeSH
• Sequence Alignment MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA, Plant * MeSH
• Retroelements * MeSH

Nonsense mutations turn a coding (sense) codon into an in-frame stop codon that is assumed to result in a truncated protein product. Thus, nonsense substitutions are the hallmark of pseudogenes and are used to identify them. Here we show that in-frame stop codons within bacterial protein-coding genes are widespread. Their evolutionary conservation suggests that many of them are not pseudogenes, since they maintain dN/dS values (ratios of substitution rates at non-synonymous and synonymous sites) significantly lower than 1 (this is a signature of purifying selection in protein-coding regions). We also found that double substitutions in codons-where an intermediate step is a nonsense substitution-show a higher rate of evolution compared to null models, indicating that a stop codon was introduced and then changed back to sense via positive selection. This further supports the notion that nonsense substitutions in bacteria are relatively common and do not necessarily cause pseudogenization. In-frame stop codons may be an important mechanism of regulation: Such codons are likely to cause a substantial decrease of protein expression levels.

• Keywords
• expression, in-fame stop codon, negative selection, population polymorphism, short-term evolution,
• MeSH
• Bacteria classification   genetics   MeSH
• Bacterial Proteins classification   genetics   MeSH
• Point Mutation MeSH
• Phylogeny MeSH
• Models, Genetic MeSH
• Evolution, Molecular MeSH
• Codon, Nonsense * MeSH
• Open Reading Frames genetics   MeSH
• Prokaryotic Cells metabolism   MeSH
• Pseudogenes genetics   MeSH
• Base Sequence MeSH
• Sequence Homology, Nucleic Acid MeSH
• Selection, Genetic MeSH
• Codon, Terminator genetics   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Bacterial Proteins MeSH
• Codon, Nonsense * MeSH
• Codon, Terminator 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
• Algorithms MeSH
• Genomics methods   MeSH
• Humans MeSH
• RNA, Small Nucleolar genetics   MeSH
• MicroRNAs genetics   MeSH
• Mice MeSH
• RNA, Untranslated genetics   MeSH
• Neural Networks, Computer MeSH
• Software MeSH
• Computational Biology methods   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• RNA, Small Nucleolar MeSH
• MicroRNAs MeSH
• RNA, Untranslated MeSH

Nod-like receptors (NLRs) are important innate pattern recognition receptors and regulators of inflammation or play a role during development. We systematically analysed 41 non-synonymous single nucleotide polymorphisms (SNPs) in 21 NLR genes in a Czech discovery cohort of sporadic colorectal cancer (CRC) (1237 cases, 787 controls) for their association with CRC risk and survival. Five SNPs were found to be associated with CRC risk and eight with survival at 5% significance level. In a replication analysis using data of two large genome-wide association studies (GWASs) from Germany (DACHS: 1798 cases and 1810 controls) and Scotland (2210 cases and 9350 controls) the associations found in the Czech discovery set were not confirmed. However, expression analysis in human gut-related tissues and immune cells revealed that the NLRs associated with CRC risk or survival in the discovery set were expressed in primary human colon or rectum cells, CRC tissue and/or cell lines, providing preliminary evidence for a potential involvement of NLRs in general in CRC development and/or progression. Most interesting was the finding that the enigmatic development-related NLRP5 (also known as MATER) was not expressed in normal colon tissue but in colon cancer tissue and cell lines. Future studies may show whether regulatory variants instead of coding variants might affect the expression of NLRs and contribute to CRC risk and survival.

• MeSH
• Survival Analysis MeSH
• Genetic Predisposition to Disease MeSH
• Genetic Variation * MeSH
• Genetic Association Studies * MeSH
• Hematopoiesis genetics   MeSH
• Polymorphism, Single Nucleotide genetics   MeSH
• Colorectal Neoplasms genetics   MeSH
• Humans MeSH
• NLR Proteins genetics   MeSH
• Open Reading Frames genetics   MeSH
• Gene Expression Regulation, Neoplastic MeSH
• Risk Factors MeSH
• Aged MeSH
• Case-Control Studies MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Geographicals
• Czech Republic MeSH
• Names of Substances
• NLR Proteins MeSH

Recent years have seen a great expansion in our understandings of how silent mutations can drive a disease and that mRNAs are not only mere messengers between the genome and the encoded proteins but also encompass regulatory activities. This review focuses on how silent mutations within open reading frames can affect the functional properties of the encoded protein. We describe how mRNAs exert control of cell biological processes governed by the encoded proteins via translation kinetics, protein folding, mRNA stability, spatio-temporal protein expression and by direct interactions with cellular factors. These examples illustrate how additional levels of information lie within the coding sequences and that the degenerative genetic code is not redundant and have co-evolved with the encoded proteins. Hence, so called synonymous mutations are not always silent but 'whisper'.

• MeSH
• Genetic Code genetics   MeSH
• Codon genetics   MeSH
• Humans MeSH
• RNA, Messenger chemistry   genetics   MeSH
• Models, Genetic MeSH
• Mutation * MeSH
• Open Reading Frames genetics   MeSH
• Proteins chemistry   genetics   metabolism   MeSH
• Protein Biosynthesis genetics   MeSH
• Protein Folding MeSH
• RNA Folding MeSH
• RNA Stability genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• Codon MeSH
• RNA, Messenger MeSH
• Proteins MeSH

Protein p6 from HIV-1 gag open reading frame is reported to affect both the final phase of assembly of the viral particle and the early stage of the gag polyprotein maturation in vitro. Two separate hypotheses have been proposed, on only one of these reported effects. We think that both observations may be eventually explained if p6 protein strongly inhibits the HIV-1 proteinase. Protein p6 was synthesised by solid-phase peptide synthesis. Several methods of folding the p6 protein were tested, each resulting in the random structure according to both CD and 1D proton NMR spectra. A uniformly high exposure of NH protons to the solution was confirmed by temperature-dependent NMR spectra and isotope exchange experiments. Thus the p6 protein does not have any rigid conformation in solution. A rigid structure is not formed after further cleavage by HIV-1 proteinase as neither the protein nor its fragments are cleaved by this proteinase. In addition, the p6 protein itself does not act as inhibitor of HIV-1 proteinase. This excludes a direct role of p6 protein and supports the hypothesis that p6 is involved in forming the appropriate structure of gag polyprotein precursor. The role of slowly cleaved tight gag-proteinase in the final stage of maturation may be to slow down maturation of the precursor polyproteins prior to their transport to final location in the membrane.

• MeSH
• Circular Dichroism MeSH
• DNA-Binding Proteins chemical synthesis   chemistry   metabolism   MeSH
• HIV-1 enzymology   genetics   MeSH
• HIV Protease Inhibitors chemistry   metabolism   MeSH
• Magnetic Resonance Spectroscopy MeSH
• Molecular Sequence Data MeSH
• Open Reading Frames MeSH
• Protein Structure, Secondary MeSH
• Amino Acid Sequence MeSH
• Software MeSH
• Viral Proteins chemical synthesis   chemistry   metabolism   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA-Binding Proteins MeSH
• HIV Protease Inhibitors MeSH
• viral protein p6 MeSH Browser
• Viral Proteins MeSH

Small extracellular vesicles (sEVs) are a type of membranous vesicles that can be released by cells into the extracellular space. The relationship between sEVs and non-coding RNAs (ncRNAs) is highly intricate and interdependent. This symbiotic relationship plays a pivotal role in facilitating intercellular communication and holds profound implications for a myriad of biological processes. The concept of sEVs and their ncRNA cargo as a "Trojan Horse" highlights their remarkable capacity to traverse biological barriers and surreptitiously deliver their cargo to target cells, evading detection by the host-immune system. Accumulating evidence suggests that sEVs may be harnessed as carriers to ferry therapeutic ncRNAs capable of selectively silencing disease-driving genes, particularly in conditions such as cancer. This approach presents several advantages over conventional drug delivery methods, opening up new possibilities for targeted therapy and improved treatment outcomes. However, the utilization of sEVs and ncRNAs as therapeutic agents raises valid concerns regarding the possibility of unforeseen consequences and unintended impacts that may emerge from their application. It is important to consider the fundamental attributes of sEVs and ncRNAs, including by an in-depth analysis of the practical and clinical potentials of exosomes, serving as a representative model for sEVs encapsulating ncRNAs.

• Keywords
• Exosomes, Non-coding RNAs, Small extracellular vesicles, Therapeutic agent, cancer,
• Publication type
• Journal Article MeSH
• Review MeSH