Abstract
Long non-coding RNAs (lncRNAs) play an important role in genome regulation. Specifically, many lncRNAs interact with chromatin, recruit epigenetic complexes and in this way affect large-scale gene expression programs. However, the experimental data about lncRNA-chromatin interactions is still limited. The majority of experimental protocols do not provide any insight into the mechanics of lncRNA-based genome-wide epigenetic regulation. Here we present the HiMoRNA (Histone-Modifying RNA) database, a resource containing correlated lncRNA–epigenetic changes in specific genomic locations genome-wide. HiMoRNA integrates a large amount of multi-omics data to characterize the effects of lncRNA on epigenetic modifications and gene expression. The current release of HiMoRNA includes more than five million associations in humans for ten histone modifications in multiple genomic loci and 4145 lncRNAs. HiMoRNA provides a user-friendly interface to facilitate browsing, searching and retrieving of lncRNAs associated with epigenetic profiles of various chromatin loci. Analysis of the HiMoRNA data suggests that several lncRNA including JPX might be involved not only in regulation of XIST locus but also in direct establishment or maintenance of X-chromosome inactivation. We believe that HiMoRNA is a convenient and valuable resource that can provide valuable biological insights and greatly facilitate functional annotation of lncRNAs.
Highlights
Transcription in higher organisms is pervasive and produces a wide variety of noncoding RNAs [1], with long non-coding RNAs being one of the most populated classes
The user can choose histone modification(s), Long non-coding RNAs (lncRNAs) name(s), gene names, coordinates of the regions, the Spearman correlation coefficient (SCC) sign and value allowing users to perform a customized search for the contents of interest
HiMoRNA provides a comprehensive collection of lncRNA–genomic loci for which lncRNA expression is significantly correlated with the histone modification signal across multiple cell and tissue types
Summary
Transcription in higher organisms is pervasive and produces a wide variety of noncoding RNAs [1], with long non-coding RNAs (lncRNAs) being one of the most populated classes. Many lncRNAs interact with chromatin and are essential for epigenetic control of specific genome loci as well as organization of the chromosomes [10,11,12,13]. Identification of chromatin-interacting lncRNAs and their genome targets could be a critical first step for dissecting lncRNA function in epigenetic regulation. High-throughput methods suffer from a high level of false-positives, since sporadic contacts could be detected in the experiments These methods have issues with detecting contacts for lowly expressed lncRNAs. high-throughput data on lncRNA-chromatin interactions is limited to a specific cell type and does not uncover a mechanism of lncRNA in regulation of histone modifications
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