ENCORE (The Encyclopedia of RNA Epitranscriptome) is an upgraded version of RMBase that mainly focuses on the mechanism and function of diverse RNA modifications. ENCORE is a comprehensive and convenient platform for efficient studying RNA modifications from large amounts of epitranscriptome high-throughput sequencing data. It provides multiple interfaces and web-based tools to integrate 73 types of RNA modification among 62 species, uncover the relationships between RNA modifications with a series of interacting factors, and reveal the distribution patterns, biochemical mechanisms, evolutionary conservation of RNA modifications and their biological roles in human diseases.
By combining ChIP-seq, ENCORE identifies four novel potential m6A readers including SRSF1, EIF4A3, FAM120A and FMR1. Importantly, ENCORE demonstrates an orphan snoRNA, SNORA38 mediate the formation of Ψs in rRNA and mRNA. Surprisingly, after exploring the expression profiles of RMPs in 16 tumors, ENCORE illustrates NOP2, NOP58 and FBL can promoter cell proliferation in RKO and HCT116, while MOCS3 inhibits it. ENCORE also identifies 38 SCNA-driver RMPs and 16 oncogene drivers. In addition, distribution features of histone modification around m6A sites suggested that four histone modifications, including H3K36me3, H3K79me2, H3K9ac and H3K4me3 may affect m6A in some way.
Finally, ENCORE provides seven powerful web-based tools including modAnnotation, modMetagene, deepAnno, modFunction, modGeneTool, ConservedFunc and modHistoneTool for custom analysis of RNA modification data.
The database idetified 1,074,100 RNA modification sites among 73 type of RNA modifications in 62