The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter” belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.

Recently, a number of ribosome-associated non-coding RNAs (rancRNAs) have been discovered in all three domains of life. In our previous studies, we have described several types of rancRNAs in Saccharomyces cerevisiae, derived from many cellular RNAs, including mRNAs, rRNAs, tRNAs and snoRNAs. Here, we present the evidence that the tRNA fragments from simple eukaryotic organism S. cerevisiae directly bind to the ribosomes. Interestingly, rancRNA-tRFs in yeast are derived from both, 5′- and 3′-part of the tRNAs and both types of tRFs associate with the ribosomes in vitro. The location of tRFs within the ribosomes is distinct from classical A- and P-tRNA binding sites. Moreover, 3′-tRFs bind to the distinct site than 5′-tRFs. These interactions are stress dependent and as a consequence, provoke regulation of protein biosynthesis. We observe strong correlation between tRF binding to the ribosomes and inhibition of protein biosynthesis in particular environmental conditions. These results implicate the existence of an ancient and conserved mechanism of translation regulation with the involvement of ribosome-associating tRNA-derived fragments.

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 the recovery of tRNA fragments depends on the RNA isolation method. Using an optimized RNA extraction protocol and northern blot hybridization technique, we show that the tRNA ‐derived fragments in yeast are widespread in 12 different growth conditions. We did not observe significant stress‐dependent changes in the amounts of tRNA fragments pool. Instead, we show the differential processing of almost all individual tRNA s. We also provide evidence that 3′‐part‐derived tRNA fragments are as abundant as the 5′‐ one in Saccharomyces cerevisiae . The resulting set of S. cerevisiae tRNA fragments provides a robust basis for further experimental studies on biological functions of tRF s.

The paper presents some basic physical properties (static electric permittivities, refraction indices, density and viscosity) of 2-chloro-4-n’-alkylphenyl esters of 4-n-alkylbicyclo[2,2,2] octane-1-carboxylic acids (n’=7, n = 5 and 7) which are, at room temperature, nematics with a negative dielectric an-isotropy. On the basis of temperature dependence of the principal static permittivities ε‖(T) and e⊥(T) of the nematics, using the Maier-Meier equations, the angle between the dipole moment vector and the long axis of mesogenic molecules, the apparent molecular dipole moment square pl μ2app(T), and the nematic order parameter S(T) were determined.

The aim of the research was to determine the influence of Gd 2 O 3 addition on the thermal stability of glasses from BaF 2 -NaF-Na 2 O-Gd 2 O 3 -Al 2 O 3 -SiO 2 system. Thermal analysis was carried out using DSC method. An impact of Gd 2 O 3 on thermal parameters such as transformation temperature (T g ), onset temperature of crystallization (T x ), peak crystallization temperature (T p ), change of specific heat (DC p ) and enthalpy of crystallization (DH) was determined. On the basis of thermal analysis, controlled crystallization was conducted. The glass-ceramic materials were identified by XRD. Crystallization kinetics of the glasses was made on the basis of two models: Kissinger and Ozawa. Changes of the glass structure were evaluated in FTIR study. It was determined that the addition of Gd 2 O 3 to the aluminosilicate glass increases the transformation temperature, simultaneously with reducing the Dc p and thermal stability DT values. It results in the decrease of DH. As shown, Gd significantly increases the crystallization activation energy of NaAlSi 3 O 8 . Complete substitution of Al 2 O 3 with Gd 2 O 3 leads to forming of Gd 9.33 (SiO 4 ) 6 O 2 . Forming of Na-silicates is not observed. Because of the participation of Gd in forming of fluoride phases (BaGdF 5 , GdF 3 ), crystallization of Gd 9.33 (SiO 4 ) 6 O 2 is impeded.

Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery reveals pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3’-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning are found to contain multiple editing sites. Adar knockdown or overexpression affect gene expression by 12 hpf. Analysis of adar-/- zygotic mutants further reveals that the previously described role of Adar in mammals in regulating the innate immune response is conserved in zebrafish. Our study therefore establishes distinct maternal and zygotic functions of RNA editing by Adar in embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes, and in the regulation of the innate immune response, respectively.

B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.

The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate expression of adjacent genes in a cell type- and developmental stage-specific manner. To date, a comprehensive analysis of direct MYC targets with essential roles in different types of cancer is missing. To enable identification of functional MYC binding sites and corresponding target genes, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. As a proof of principle, using this library we identified several known and novel MYC targets critical for K562 chronic myelogenous leukemia cells and uncovered specific features of essential E-boxes. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in any cancer type.