Nonprotein coding RNA (ncRNA) molecules have been recognized recently as major contributors to regulatory networks in controlling gene expression a highly efficient manner. These RNAs either originate from their individual transcription units or are processing products longer precursor RNAs. For example, tRNA-derived fragments (tRFs) identified all domains of life and represent growing, yet functionally poorly understood, class ncRNA candidates. Here we present evidence that tRFs the...

Summary By generating a specialized cDNA library from the archaeon Sulfolobus solfataricus , we have identified 57 novel small non‐coding RNA (ncRNA) candidates and confirmed their expression by Northern blot analysis. The majority was found to belong one of two classes, either antisense or antisense‐box RNAs, where latter only exhibit partial complementarity targets. most prominent group RNAs is transcribed in opposite orientation transposase genes, encoded insertion elements (transposons)....

In the absence of extensive transcription control mechanisms pathogenic parasite Trypanosoma brucei crucially depends on translation regulation to orchestrate gene expression. However, molecular insight into regulating protein biosynthesis is sparse. Here we analyze small non-coding RNA (ncRNA) interactome ribosomes in T. during different growth conditions and life stages. Ribosome-associated ncRNAs have recently been recognized as unprecedented regulators ribosome functions. Our data show...

Malignant gliomas represent the most devastating group of brain tumors in adults, among which glioblastoma multiforme (GBM) exhibits highest malignancy rate. Despite combined modality treatment, GBM recurs and is invariably fatal. A further insight into molecular background gliomagenesis required to improve patient outcomes. The primary aim this study was gain broad information on miRNA expression pattern malignant gliomas, mainly GBM. We investigated global profile glioma tissues with...

The structural and functional repertoire of small non-protein-coding RNAs (ncRNAs) is central for establishing gene regulation networks in cells organisms. Here, we show that an mRNA-derived 18-nucleotide-long ncRNA capable downregulating translation Saccharomyces cerevisiae by targeting the ribosome. This 18-mer binds to polysomes upon salt stress crucial efficient growth under hyperosmotic conditions. Although RNA originates from TRM10 locus, which encodes a tRNA methyltransferase, genetic...

The exploration of the non-protein-coding RNA (ncRNA) transcriptome is currently focused on profiling microRNA expression and detection novel ncRNA transcription units. However, recent studies suggest that processing can be a multi-layer process leading to generation ncRNAs diverse functions from single primary transcript. Up date no methodology has been presented distinguish stable functional species rapidly degraded side products nucleases. Thus correct assessment widespread events one...

Protein-coding genes, guiding differentiation of ES cells into neural cells, have extensively been studied in the past. However, for class ncRNAs only involvement some specific microRNAs (miRNAs) has described. Thus, to characterize entire small non-coding RNA (ncRNA) transcriptome, involved mouse we generated three specialized ribonucleo-protein particle (RNP)-derived cDNA libraries, i.e. from pluripotent progenitors and differentiated respectively. By high-throughput sequencing...

Up to 450 000 non-coding RNAs (ncRNAs) have been predicted be transcribed from the human genome. However, it still has elucidated which of these transcripts represent functional ncRNAs. Since all ncRNAs in Eukarya form ribonucleo-protein particles (RNPs), we generated specialized cDNA libraries size-fractionated RNPs and validated presence selected within by glycerol gradient centrifugation. As a proof concept, applied RNP method Hela cells or total mouse brain, subjected libraries, two...

Nitroxyl (HNO) is the one-electron reduced and protonated congener of nitric oxide (•NO), owning a distinct chemical profile. Based on real-time detection, we demonstrate that HNO endogenously formed in Arabidopsis. Senescence hypoxia induce shifts redox balance, triggering decay or formation mediated by non-enzymatic •NO/HNO interconversion with cellular reductants. The stimuli-dependent generation supports competes •NO signalling, depending local environment.

AtCyp59 is a multidomain cyclophilin containing peptidyl-prolyl cis/trans isomerase (PPIase) domain and an evolutionarily highly conserved RRM domain. Deregulation of this class cyclophilins has been shown to affect transcription influence phosphorylation the C-terminal repeat largest subunit RNA polymerase II. We used genomic SELEX method for identifying targets AtCyp59. Analysis selected RNAs revealed RNA-binding motif (G[U/C]N[G/A]CC[A/G]) we show that it conserved. Binding was verified...

Despite the fact that all 23S rRNA nucleotides build ribosomal peptidyl transferase ribozyme are universally conserved, standard and atomic mutagenesis studies revealed nucleobase identities being non-critical for catalysis. This indicates these active site residues highly conserved functions distinct from To gain insight into potential contributions, we have manipulated nucleobases via an approach utilized chemically engineered ribosomes in vitro translation reactions. We show most of could...

Regulation of gene expression at the translational level allows rapid adaptation cellular proteomes to quickly changing environmental conditions and is thus central for prokaryotic organisms. Small non-coding RNAs (sRNAs) have been reported effectively orchestrate translation control in bacteria archaea mainly by targeting mRNAs partial base complementarity. Here we report an unprecedented mechanism how sRNAs are capable modulating protein biosynthesis halophilic archaeon Haloferax volcanii....

Short RNA s derived from the cleavage of tRNA molecules are observed in most organisms. Their occurrence seems to be induced by stress conditions, but still little is known about their biogenesis and functions. We find that recovery fragments depends on isolation method. Using an optimized extraction protocol northern blot hybridization technique, we show ‐derived yeast widespread 12 different growth conditions. did not observe significant stress‐dependent changes amounts pool. Instead,...

ABSTRACT Glioblastoma (GBM) is the most aggressive and lethal type of glioma, characterized by aberrant expression non-coding RNAs including circular (circRNAs). They might impact cellular processes interacting with other molecules – like microRNAs or RNA-binding proteins (RBPs). The diagnostic value circRNAs circRNAs/RBPs complexes still largely unknown. To explore RBPs transcripts in GBM, we performed further analyzed RNA-seq data from GBM patients’ primary recurrent tumor samples. We...

DsrA RNA is an 87-nucleotide regulatory non-protein-coding of Escherichia coli for which two secondary structure models (I and II) have been proposed. We compared these by the energy calculations, revealed that currently accepted model II should be rejected on basis thermodynamics. Here we provide new results nuclease footprinting analysis application technologies not previously used structural studies, such as hydrolysis with RNase H, DNAzyme, hydroxyl radicals lead. These approaches...

Glyphosate is a systemic, nonselective and most widely used herbicide in the world. The introduction of glyphosate-resistant crops mid-1990s resulted dramatic increase use glyphosate making it average maize yield loss field caused by pests around 20 % but many regions much higher. It now clear that causes broader range physiological alterations than previously assumed some plants gain higher level resistance to without need genetic engineering methods. To understand mechanisms such...

To study genetic variations between genomes of plants that are naturally tolerant and sensitive to glyphosate, we used two Zea mays L. lines traditionally bred in Poland. overcome the complexity maize genome, sequencing technologies were employed: Illumina Single Molecule Real-Time (SMRT) PacBio. Eleven thousand structural variants, 4 million SNPs approximately 800 indels differentiating identified. Detailed analyses allowed identify 20 within EPSPS gene, but all them predicted have moderate...

In eukaryotic cells tRNA synthesis is negatively regulated by the protein Maf1, conserved from yeast to humans. Maf1 Saccharomyces cerevisiae mediates repression of trna transcription when are transferred medium with glucose glycerol, a non-fermentable carbon source. The strain deleted gene encoding (maf1Δ) viable but accumulates precursors. this study precursors were analysed RNA-Seq and Northern hybridization in wild type maf1Δ mutant grown or upon shift repressive conditions. A negative...

Anti-tumor necrosis factor (TNF) therapy is used for the induction and maintenance of remission in Crohn's disease (CD) patients. However, primary nonresponders to initial treatment constitute 20–40% cases. The causes this phenomenon are still unknown. In study, we aimed determine genetic predictors variable reactions CD patients anti-TNF therapy. Using long-range PCR libraries next-generation sequencing (NGS) method, performed broad pharmacogenetic studies including a panel 23 genes...

Phytophthora infestans, a representative of phytopathogenic oomycetes, have been proven to cope with redundant sources internal and host-derived reactive nitrogen species (RNS). To gain insight into its nitrosative stress resistance mechanisms, metabolic sensors activated in response challenge during both vitro growth colonization the host plant were investigated. The conducted analyses gene expression, protein accumulation, enzyme activity reveal for first time that P. infestans (avirulent...