MoRNiNG

MoRNiNG modification

About the MoRNiNG database

The MoRNiNG The MoRNiNG (Modification of RNAs in Natural rG4) database provides information on RNA modifications located within experimentally confirmed RNA G-quadruplex (rG4) structures or putative G-quadruplex-forming sequences (PQSs). These sequences are derived from mRNA, lncRNA, and miRNA (both pre-miRNA and mature-miRNA) across nine species: human, mouse, rhesus monkey, chimpanzee, pig, rat, zebrafish, HIV-1, and SV40. The database includes details on nine RNA modifications: m6A, m1A, m7G, m5C, m6Am, m5U, A-to-I, 2’-O-Me, and Ψ.

RNA G-quadruplex

RNA G-quadruplexes (rG4s) are non-canonical secondary structures formed by the stacking of two or more G-quartets— planar arrangements held together by Hoogsteen hydrogen bonds among four guanines. Specifically, putative G-quadruplex-forming sequences (PQSs) typically contain four G-tracts separated by three loops, a pattern that enables computational prediction. RNA modifications occurring within or near these PQSs have the potential to influence rG4 thermostability, interactions with rG4-binding proteins, and conformational dynamics. Given that many PQSs are nested within canonical stem-loop structures in the transcriptome, exploring the role of RNA modifications in regulating conformational dynamics is essential for understanding RNA function.

RNA modification

m6A

m1A

m7G

m5C

m5U

m6Am

2'-O-Me

References from Wikipedia

Framework

Data collection & processing

The MoRNING database integrates RNA modification sites from six sources, including GEO, RMbase, RMVar, MiREDiBase, m6A Atlas, and published datasets. Here we used seven software to identify PQSs in the longest transcripts, which include both mRNA and lncRNA, based on transcript biotypes from the Ensembl database (release 109) and miRNAs from miRBase (version 22). The software used includes pqsfinder (score > 1), QGRS (default parameter: score >= 17), G4hunter (-w 25 -s 1.2), G4RNA screener (cGcC >= 4.5, G4H >= 0.9, G4NN >= 0.5), RNAfold, and G4NN score > 0.5 & Quadparser-based (G >= 2N1-12)3G >= 2 sequence motif (G2L12 motif). Additionally, the database also features PQSs with experimental support from techniques including rG4-seq, ultra-low-input rG4-seq, and circular dichroism spectrum.
For each entry in the database, potential stem-loop structures are predicted using RNAfold, with the results displayed in dot-bracket notation. However, rG4/PQS lacking stem-loop structures will not show the dot-bracket illustration.
Furthermore, we collected 801 potential GI-Quadruplex-forming sequences (PIQS) on human transcripts for rG4 introduced by A-I editing, which can be obtained using the "ModType" option on the search page.

Functions

The MoRNING database offers three major functional modules: search, tool, and download. Users can search for rG4 structures featuring various RNA modification sites across different species, customized to their specific needs. Alternatively. Users can manually input genomic loci or intervals, and utilize our tool function to directly find predicted PQS on the tool page. For convenience, we offer 27 datasets from nine different species for users to download.

Manuals

Search-mainpage:
This function enables users to efficiently query PQS with modifications within a specific genome range for a given species.
peaks_analysis_manual

Search:
Users can use multiple filter tags to query PQS with modifications. The above four options are required.
peaks_analysis_manual

Genomic loci:
Users can provide the locus on the exon of a species to find all the intersected PQS.
site_analysis_manual

Genomic interval:
By providing the genomic intervals, users can identify the predicted PQSs.
peaks_analysis_manual

Detection of Modification

Category 	Method	literature	DOI
High	Aza-IP	Nat Biotechnol	10.1038/nbt.2566
	RNA-BisSeq	Nucleic Acids Res	10.1093/nar/gkn954
	BS-seq-with-improved-protocol	Nat Struct Mol Biol	10.1038/s41594-019-0218-x
	DART-seq	Nat Methods	10.1038/s41592-019-0570-0
	DART-seq&Bullseye	Mol Cell	10.1016/j.molcel.2021.12.038
	CeU-Seq	Nat Chem Biol	10.1038/nchembio.1836
	Nm-REP-seq	Sci China Life Sci	10.1007/s11427-022-2210-0
	CIMS_miCLIP	Nat Methods	10.1038/nmeth.3453
	CITS_miCLIP	Nat Methods	10.1038/nmeth.3453
	m6ACE-seq	Nat Commun	10.1038/s41467-019-13561-z
	miCLIP	Nat Methods	10.1038/nmeth.3453
	m6A-REF-seq	Sci Adv	10.1126/sciadv.aax0250
	m6A-SAC-seq	Nat Protoc	10.1038/s41596-022-00765-9
	m6A-seq-with-improved-protocol	Cell Rep	10.1016/j.celrep.2014.05.048
	DM-Ψ-seq	Nat Chem Biol	10.1038/s41589-019-0420-5
	FICC-Seq	Nucleic Acids Res	10.1093/nar/gkz658
	m6A-CLIP/IP	Genes Dev	10.1101/gad.269415.115
	PA-m6A-Seq	Methods Mol Biol	10.1007/978-1-0716-1374-0_8
	m6A-Label-seq	STAR Protoc	10.1016/j.xpro.2021.101096
	GLORI	Nat Biotechnol	10.1038/s41587-022-01487-9
	PRAISE	Nat Chem Biol	10.1038/s41589-023-01304-7
	BACS	Nat Methods	10.1038/s41592-024-02439-8
	m1A-IP-seq	Nat Methods	10.1038/s41592-019-0550-4
	m1A-quant-seq	Nat Methods	10.1038/s41592-019-0550-4
	m1A-MAP	Mol Cell	10.1016/j.molcel.2017.10.019
	UBS-seq	Nat Biotechnol	10.1038/s41587-023-02034-w
	Nm-Mut-seq	Cell Res	10.1038/s41422-023-00836-w
	Nm-seq	Nat Methods	10.1038/nmeth.4294
	RBS-Seq	Proc Natl Acad Sci U S A	10.1073/pnas.1817334116
	RiboMeth-seq	Methods Mol Biol	10.1007/978-1-4939-6807-7_13
	m7G-miCLIP-Seq	Cell Res	10.1038/s41422-019-0230-z
	m7G-seq	Mol Cell	10.1016/j.molcel.2019.03.036
	MAZTER-seq	Cell	10.1016/j.cell.2019.06.013
	meCLIP	RNA	10.1261/rna.078543.120
	miCLIP&m6Aboost	Nucleic Acids Res	10.1093/nar/gkab485
	miCLIP2&m6Aboost	Nucleic Acids Res	10.1093/nar/gkab485
	RNA-Seq	Nat Methods	10.1038/s41592-018-0017-z
	Ψ-seq	Cell	10.1016/j.cell.2014.08.028
	Slic-seq	Nucleic Acids Res	10.1093/nar/gkad604
Medium	m1A-seq	Nature	10.1038/nature16998
	m5C-RIP-seq	Methods Mol Biol	10.1007/978-1-4939-9045-0_24
	m6A-Seal-seq	Nat Chem Biol	10.1038/s41589-020-0525-x
	m6A-seq	Nature	10.1038/nature11112
	miR-mmPCR-seq	Genome Res	10.1101/gr.224386.117
	BoRed-seq&m7G-RIP-seq	Mol Cell	10.1016/j.molcel.2019.03.040

	m6A-CLIP	Nature	10.1038/nature21355
Low	DARNED	Bioinformatics	10.1093/bioinformatics/btq285
	RADAR	Nucleic Acids Res	10.1093/nar/gkt996
	Modomics	Nucleic Acids Res	10.1093/nar/gkab1083
	ELIGOS	Nucleic Acids Res	10.1093/nar/gkaa620
	Prediction by CNN model	Nucleic Acids Res	10.1093/nar/gkaa811
	Protocol for analyzing RNA editing in mature miRNAs using deep sequencing data	Methods Mol Biol	10.1007/978-1-4939-2291-8_14

Detection of rG4

Category	Method	literature	DOI
Experiment	rG4-seq	Nat Methods	10.1038/nmeth.3965
	Ultra-low-input rG4-seq	Under Review at Nature Portfolio	10.21203/rs.3.rs-5687952/v1
	circular dichroism spectrum	NA	NA
Prediction	pqsfinder	Bioinformatics	10.1093/bioinformatics/btx413
	QGRS	Hum Genomics	10.1186/1479-7364-8-8
	G4Hunter	Bioinformatics	10.1093/bioinformatics/btz087
	G4RNA screener	Biochimie	10.1016/j.biochi.2018.06.002
	G4NNscore>0.5&G2L12motif	Chem Commun (Camb)	10.1039/c8cc04635b

Citation

Yicen Zhou^#, Shanxin Lyu^#, Shiau Wei Liew^#, Xi Mou, Ian Hoffecker, Jian Yan, Yu Li, Chun Kit Kwok^*, Jilin Zhang^*, MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics, Genomics, Proteomics & Bioinformatics, 2025;, qzaf106,