Decoding the Atlas of RNA Modifications from Epitranscriptome Sequencing Data

[Epigenetic influences and brain development]

In recent years, the amount of scientific data on the involvement of epigenetic processes in the regulation of brain development in postnatal ontogenesis has been rapidly growing. The article provides an overview of scientific research on the mechanisms of epigenetic influences on brain development. Information was searched in the Scopus, Web of Science, MedLine, The Cochrane Library, PubMed, Pedro, Scholar, eLibrary, CyberLeninka and RSCI databases for the period 1940-2022 by keywords: brain development, epigenetics, neuroontogenesis, methylation, histone modifications, chromatin remodeling, non-coding RNAs. Today, the mechanisms of epigenetic influence on the genome include DNA and RNA methylation, covalent modification of histones, chromatin remodeling, and the influence of non-coding RNAs. Epigenetic modifications are often reversible and provide the necessary plasticity for the response of progenitor cells to environmental signals. The influence of each of these factors on the neurodevelopment is considered. The possibility of transsynaptic transmission of hereditary material by means of circular RNA is indicated. The main ways of microRNA influence on brain development are presented and their universality as an «overgenic» regulator of organism adaptation to external conditions is indicated. Data on the relationship of long non-coding RNAs with the regulation of the functional activity of oligodendroglia are presented. Also, the data presented indicate the paths to the pathogenetically determined prevention of congenital brain pathology.

Advances and Trends in Omics Technology Development

The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.

Isolation of Cell-Free miRNA from Biological Fluids: Influencing Factors and Methods

A vast wealth of recent research has seen attempts of using microRNA (miRNA) found in biological fluids in clinical research and medicine. One of the reasons behind this trend is the apparent their high stability of cell-free miRNA conferred by small size and packaging in supramolecular complexes. However, researchers in both basic and clinical settings often face the problem of selecting adequate methods to extract appropriate quality miRNA preparations for use in specific downstream analysis pipelines. This review outlines the variety of different methods of miRNA isolation from biofluids and examines the key determinants of their efficiency, including, but not limited to, the structural properties of miRNA and factors defining their stability in the extracellular environment.

IGF2BP1, a Conserved Regulator of RNA Turnover in Cancer

The oncofetal IGF2 mRNA-binding protein 1 (IGF2BP1) promotes tumor progression in a variety of solid tumors and its expression is associated with adverse prognosis. The main role proposed for IGF2BP1 in cancer cells is the stabilization of mRNAs encoding pro-oncogenic factors. Several IGF2BP1-RNA association studies, however, revealed a plethora of putative IGF2BP1-RNA targets. Thus, at present the main conserved target RNAs and pathways controlled by IGF2BP1 in cancer remain elusive. In this study, we present a set of genes and cancer hallmark pathways showing a conserved pattern of deregulation in dependence of IGF2BP1 expression in cancer cell lines. By the integrative analysis of these findings with publicly available cancer transcriptome and IGF2BP1-RNA association data, we compiled a set of prime candidate target mRNAs. These analyses confirm a pivotal role of IGF2BP1 in controlling cancer cell cycle progression and reveal novel cancer hallmark pathways influenced by IGF2BP1. For three novel target mRNAs identified by these studies, namely AURKA, HDLBP and YWHAZ, we confirm IGF2BP1 mRNA stabilization. In sum our findings confirm and expand previous findings on the pivotal role of IGF2BP1 in promoting oncogenic gene expression by stabilizing target mRNAs in a mainly 3'UTR, m⁶A-, miRNA-, and potentially AU-rich element dependent manner.