ENCORE: The encyclopedia of RNA epitranscriptome.

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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 .

Species	Assembly	Gnome Source
Human	hg38	GENCODE Release-30
Mouse	mm10	GENCODE Release-M22
Macaca Mulatta	rheMac8	Ensembl Release-97
Pan Troglodytes	panTro5	Ensembl Release-97
Rattus	rn6	Ensembl Release-97
Sus Scrofa	susScr11	Ensembl Release-97
Danio Rerio	danRer11	Ensembl Release-97
A.thaliana	TAIR10	Ensembl Release-44
S.cerevisiae	sacCer3	Ensembl Release-97
Fly	BDGP6	Ensembl Release-97
P.aeruginosa	ASM676v1	Ensembl Release-44
E.coli	ASM584v2	Ensembl Release-44
S.pombe	ASM294v2	Ensembl Release-44
Bacillus subtilis	ASM69118v1	Ensembl
Bombyx mori	ASM15162v1	Ensembl
Bos taurus	bosTau9	Ensembl
Brassica napus	AST_PRJEB5043v1	Ensembl
Caenorhabditis elegans	WBcel235 (ce11)	Ensembl
Candida albicans	Cand_albi12Cv2	Ensembl
Chlamydomonas reinhardtii	CHLRE3	NCBI
Clostridium acetobutylicum	ASM78585v1	Ensembl
Cucumis sativus	ASM407v2	Ensembl
Enterobacteria phage T4	ViralProj14044	NCBI
Enterobacteria phage T5	ASM292140v1	NCBI
Fusarium graminearum	ASM24013v3	Ensembl
Fusarium verticillioides	ASM14955v1	Ensembl
Gallus gallus	GRCg6a	Ensembl
Geobacillus stearothermophilus	ASM74998v1	Ensembl
Glycine max	glyMax2	Ensembl
Halobacterium salinarum	ASM680v1	Ensembl
Halococcus morrhuae	ASM33669v1	Ensembl
Haloferax volcanii	ASM2568v1	Ensembl
Lactococcus lactis	ASM76111v1	Ensembl
Mesocricetus auratus	MesAur1	Ensembl
Mycobacterium smegmatis	ASM76770v1	Ensembl
Mycoplasma capricolum	ASM83033v1	Ensembl
Mycoplasma mycoides	ASM25307v1	Ensembl
Neurospora crassa	NC12	Ensembl
Nicotiana tabacum	Ntab_TN90	NCBI
Oryctolagus cuniculus	OryCun2	Ensembl
Ovis aries	Oarv3	Ensembl
Phaseolus vulgaris	PhaVulg1	Ensembl
Pichia jadinii	Cybja1	NCBI
Pyrococcus abyssi	ASM19593v2	Ensembl
Rhodospirillum rubrum	ASM1308v1	Ensembl
Salmonella typhimurium	ASM553737v1	NCBI
Solanum tuberosum	SolTub3	Ensembl
Spinacia oleracea	ASM200726v1	NCBI
Spiroplasma citri	ASM188685v1	NCBI
Streptomyces coelicolor A3(2)	ASM20383v1	Ensembl
Streptomyces griseus	ASM93222v1	Ensembl
Sulfolobus acidocaldarius	ASM1228v1	Ensembl
Sulfolobus solfataricus	ASM96839v1	Ensembl
Synechococcus elongatus PCC 6301	ASM1006v1	NCBI
Synechococcus sp. PCC 7002	ASM1948v1	NCBI
Synechocystis sp.	ASM34078v1	NCBI
Tetrahymena thermophila	JCVI_TTA1_2	Ensembl
Thermoplasma acidophilum	ASM19591v1	Ensembl
Thermotoga maritima	ASM97857v1	Ensembl
Thermus thermophilus	ASM812v1	Ensembl
Xenopus laevis	Xenopus_laevisv2	NCBI
Zea mays	RefGenv4	Ensembl

RNA Modifications

Genes

Mechanisms

Interactome

Regulation in Genomic level

Function of RMP

Motifs

Tools

ENCORE Release Note (March 2020):

Species: 9 clades, 62 species.
Samples: 828 wild type datasets.
RNA Modification: 73 types.
Tools for RNA modifications: 7 tools.
Explore the pseudo sites guided by known and orphan snoRNAs. These pseudo sites occur on mRNA, rRNA, snRNA, tRNA, lncRNA and repeatMasker.
Detect the RNA modification clusters in genome wide.
Decipher the associated functions of RNA modifications with RBP, miRNA target, SNP, and SNV.
Identify novel m6A readers.
Explore the regulatory roles of histone modifications on RNA modifications.
Investigate the biological functions of RNA modifications in diverse cancers.

How to cite:

ENCORE: The Encyclopedia of RNA Epitranscriptome.
Xuan JJ, et al. RMBase v2.0: Deciphering the Map of RNA Modifications from Epitranscriptome Sequencing Data. Nucleic Acids Res. 2018 Jan 4;46(D1):D327-34.
Sun WJ, et al. RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data. Nucleic Acids Res. 2016 Jan 4;44(D1):D259-65.

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Welcome to ENCORE!

ENCORE Release Note (March 2020):

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