Biology subjects

Ryabykh, G.

Publications and source records attributed to Ryabykh, G..

4 recordsLinked to original sources

bioRxiv2025

COMPARATIVE ANALYSIS OF THE RNA-CHROMATIN INTERACTOME DATA

Two types of experiments are used to study RNA-chromatin interactions: a search for the interactome of individual RNAs (< > or OTA) and a genome-wide search for contacts of all RNAs (< > or ATA). The article presents a comparative analysis of these data. The concept of < > is introduced, which shows the overrepresentation of contacts in ATA data compared to the expected value obtained from RNA sequencing data. It is shown that the use of this characteristic allows one to select RNAs that interact with chromatin more specifically. The consistency of the replicas is studied, and data from experiments of different types are compared. As a result of the analysis, estimates of the completeness and specificity of the contacts found are obtained.

bioinformatics↗

bioRxiv2024

HiMoRNA and RNA-Chrom integration: Chromatin-Associated LncRNAs in Genome-Wide Epigenetic Regulation

Long non-coding RNAs (lncRNAs) significantly contribute to genome structure and regulation. Many lncRNAs are known to interact with chromatin and in this way to affect gene expression patterns through epigenetic regulation. Still, experimental protocols for lncRNA-chromatin interactions do not provide any insight into the mechanisms of lncRNA-based genome-wide regulation. Here we present an integration of HiMoRNA - a resource containing correlated lncRNA-epigenetic changes in specific genomic locations genome-wide, - and RNA-Chrom, a resource featuring uniformly processed experimental data on RNA-chromatin interactions. Our integration approach allows generating interpretable and experimentally supported hypotheses on the mechanisms of lncRNA epigenetic regulation of gene expression. For this integration we have tailored the interface of HiMoRNA such that for many lncRNAs experimentally detected RNA-chromatin contacts are available from RNA-Chrom for browsing, analysis and downloading. HiMoRNA peaks supported by RNA-Chrom contacts can be explained by external experimental data. We believe that the integration of HiMoRNA and RNA-Chrom is a convenient and valuable approach that can provide experimental and mechanistic insights and greatly facilitate functional annotation of lncRNAs.

bioinformatics↗

bioRxiv2023

Comparative analysis of the RNA-chromatin interactions data. Completeness and accuracy

Non-coding RNAs play an essential role in a wide variety of biological processes. We have previously developed RNA-Chrom, an analytical database containing uniformly processed RNA-chromatin interactions data. Here, we analyzed the consistency of these data with each other and performed a comparative analysis of human and mouse datasets from "all-to-all" experiments (interactome of all possible RNAs in a cell) and "one-to-all" experiments (individual RNA interactome). We analyzed the dependence of RNA cis-contacts density as a function of distance to the RNA source gene and found that in all experiments, density of cis-contacts decreases with distance. We tested whether the most contacting RNAs of one "all-to-all" experiment ("RNA-leaders") are the same for the other "all-to-all" experiments. Our analysis shows that "all-to-all" experiments are not complete and require substantially deeper sequencing, and conclusions can only be drawn for highly contacting RNAs. We noted that for "all-to-all" experiments, sequencing depth and the type of cell treatment give a significant impact on the contact map, while the cell line does not have as much of an impact.

bioinformatics↗

bioRxiv2022

RNA-Chrom: a manually-curated analytical database of RNA-chromatin interactome

Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organisation of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.), to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system-level of studying non-coding RNAs. Here we present the RNA-Chrom manually-curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https://rnachrom2.bioinf.fbb.msu.ru/), two approaches to the analysis of the RNA-chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome Browser.

bioinformatics↗