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

Ryabykh, Grigory; Kuznetsov, S. V.; Korostelev, Yuriy; Sigorskikh, Andrey; Zharikova, Anastasia A.; Mironov, Andrey A.

doi:10.1101/2022.12.10.519346

Cited by 6 publications

(10 citation statements)

References 63 publications

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“…This effect was described in several studies dedicated to RNA-DNA interaction data analysis (10,12). We observed this distance-dependent effect in both OTA and ATA datasets (Figure 1A) with our previously developed RNA-Chrom database (13). Analogous to Hi-C, we will refer to this phenomenon as scaling (14).…”

Section: Introductionsupporting

confidence: 72%

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BaRDIC: robust peak calling for RNA-DNA interaction data

Mylarshchikov,

Nikolskaya,

Bogomaz

et al. 2023

Preprint

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Chromatin-associated non-coding RNAs play important roles in various cellular processes by targeting genomic loci. Two types of genome-wide NGS experiments exist to detect such targets: "one-to-all", which focuses on targets of a single RNA, and "all-to-all", which captures targets of all RNAs in a sample. As with many NGS experiments, they are prone to biases and noise, so it becomes essential to detect "peaks" — specific interactions of an RNA with genomic targets. Here we present BaRDIC — Binomial RNA-DNA Interaction Caller — a tailored method to detect peaks in both types of RNA-DNA interaction data. BaRDIC is the first tool to simultaneously account for the two most prominent biases in the data: chromatin heterogeneity and distance-dependent decay of interaction frequency, or scaling. Since RNAs differ in their interaction preferences, BaRDIC adapts peak sizes according to the abundances and contact patterns of individual RNAs. These features enable BaRDIC to make more robust predictions than currently applied peak-calling algorithms and better handle the characteristic sparsity of all-to-all data. BaRDIC package is freely available at https://github.com/dmitrymyl/BaRDIC.

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Section: Introductionsupporting

confidence: 72%

“…Pre-processed contacts and MACS2 peaks for OTA experiments were extracted from the RNA-Chrom database (17). The data identifiers (Exp.…”

Section: Methodsmentioning

confidence: 99%

BaRDIC: robust peak calling for RNA-DNA interaction data

Mylarshchikov,

Nikolskaya,

Bogomaz

et al. 2023

Preprint

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“…RNA-chromatin interactions data, excluding “singletons”, were taken from RNA-Chrom database [15]: without normalization to background (“raw”), normalized to back-ground (“normalized”), and background-normalized contacts crossing MACS2 peaks. All experimental identification numbers (“Exp.IDs”) referenced in this paper correspond to the identifiers from the RNA-Chrom DB (Suppl.…”

Section: Methodsmentioning

confidence: 99%

“…The RNA-Chrom database [15] has collected a large amount of uniformly processed RNA-chromatin interactions data. The variety of cell lines on the one hand forms a diverse picture of the behavior of ncRNAs in human and mouse cells.…”

Section: Introductionmentioning

confidence: 99%

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

Ryabykh,

Vasilyev,

Garkul

et al. 2023

Preprint

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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.

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“…The all-to-all experiments show that most of the RNA-chromatin contacts detected are those of protein-coding RNAs [14]. The presence of regulatory functions for these RNAs has not been well established and this observation reflects a high level of non-specific interactions.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of RNA-chromatin, RNA- and DNA-protein interactions

Khlebnikov,

Nikolskaya,

Zharikova

et al. 2024

Preprint

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RNA-chromatin interactome data is considered to be one of the noisiest types of data in biology. This is due to protein-coding RNA contacts and non-specific interactions between RNA and chromatin caused by protocol specifics. Therefore, finding regulatory interactions between certain transcripts and genome loci requires a wide range of filtering techniques to obtain significant results. Using data on pairwise interactions between these molecules, we propose a concept of triad interaction involving RNA, protein and a DNA locus. The constructed triads show significantly less noise contacts and are more significant when compared to a background model for generating pairwise interactions. RNA-chromatin contacts data can be used to validate the proposed triad object as positive (Red-ChIP experiment) or negative (RADICL-Seq NPM) controls. Our approach also filters RNA-chromatin contacts in chromatin regions associated with protein functions based on ChromHMM annotation.

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

Cited by 6 publications

References 63 publications

BaRDIC: robust peak calling for RNA-DNA interaction data

BaRDIC: robust peak calling for RNA-DNA interaction data

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

Comprehensive analysis of RNA-chromatin, RNA- and DNA-protein interactions

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