Tool:The Encyclopedia of RNA Epitranscriptome : decoding the mechanisms and functions of diverse RNA modifications

Question

[lsp03yjh]

ENCORE (The Encyclopedia of RNA Epitranscriptome) for decoding the mechanism and function of diverse RNA modifications in various RNAs, such as mRNAs, tRNAs, lncRNAs. ENCORE is a most comprehensive platform for efficient studying RNA modifications from large amounts of high-throughput epitranscriptome sequencing data. It provides multiple interfaces and web-based tools to integrate 73 types of RNA modifications among 62 species, uncover the relationships between RNA modifications and a series of interacting factors, and reveal the distribution patterns, biochemical mechanisms, evolutionary conservation of RNA modifications and their biological roles in human diseases. ENCORE provides seven powerful web-based tools including modAnnotation, modMetagene, deepAnno, modFunction, modGeneTool, ConservedFunc and modHistoneTool for custom analysis of RNA modification data.

1. Decode the distribution patterns of 73 types of RNA modifications across 62 species in various RNAs, such as mRNAs, tRNAs, lncRNAs.
2. Explore the interactions between pseudouridylation modifications and known and orphan snoRNAs.
3. Discover the clusters of various RNA modifications.
4. Decipher the interactions of RNA modifications with RNA-binding proteins (RBP), miRNA targets, SNPs, and SNVs.
5. Predict novel readers associated with various RNA modifications, such as m6A, m5C, m1A, m7G, 2'-O-Methylation, pseudouridylation, RNA editing.
6. Explore the regulatory roles of histone modifications (e.g. H3K36me3、H3K79me2、H3K9ac、H3K27ac) on RNA modifications.
7. Investigate the biological functions of RNA modifications in diverse cancers.
8. Uncover the motifs of various RNA modifications.
9. Provide more than 10 tools for exploring the functions and mechanisms of various RNA modifications.

**ENCORE platform is freely available at** https://rna.sysu.edu.cn/encore/.

RMBase is the the pilot version of ENCORE, RMBase paper is available at https://academic.oup.com/nar/article/46/D1/D327/4429298 and pubmed ID

RMBase continually be maintained and updated whenever novel high-throughput epitranscriptome sequencing data sets are released in public databases.

Answer 1

[lsp03yjh]

We have added a new module modHistone, to identify the relationship between RNA modifications (e.g. m6A and m5C) and Histone modifications (e.g. H3K36me3、H3K79me2、H3K9ac、H3K27ac) in humans. We found the signicantly positive correlations between H3K79me2, H3K9ac, H3K27ac modification and m6A, as well as known H3K36me3 and m6A.