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 organization 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. Database URL https://genome.ucsc.edu/.

[RNA-Chromatin Interactome: What? Where? When?]

It was noticed in the early 1960s that a large amount of RNAs is associated with chromatin. What kind of RNAs are they? Where are they located on chromatin? When and in what processes do these RNAs perform their physiologically normal or pathogenic functions? The review describes the modern approaches that help, to some extent, to answer these questions. Consideration is given to the experimental methods that make it possible to obtain the complete RNA-chromatin interactome of a cell or the genome-wide interaction maps of individual RNAs with chromatin, as well as the methods to process the experimental data. Focus is placed on the noncoding RNAs that function in close contact with chromatin and chromatin-associated protein complexes. A variety of biological examples described using the methods makes it clear that RNAs interacting with chromatin play an important role in the functions of cell systems by finely tuning the chromatin architecture and thus changing the level of gene expression.