A Census and Categorization Method of Epitranscriptomic Marks
Abstract
:1. Introduction
2. A Categorization Method for RNA Modifications
3. Adenosine-Derived Modifications
4. Cytidine-Derived Modifications
5. Guanosine-Derived Modifications
6. Uridine-Derived Modifications
7. Epitranscriptomics Role in Physiology and Disease
8. Epitranscriptomics Web Resources
9. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
A | Adenosine |
A-to-I | Adenosine-to-Inosine |
ac4C | N4-acetylcytidine |
ADAR | Adenosine deaminases acting on mRNA |
ADAT | Adenosine deaminases acting on tRNA |
ALKBH5 | AlkB homolog 5 proteins |
ALKBH8 | AlkB homolog 8, tRNA methyltransferase |
Am | 2-O-methyladenosine |
C | Cytidine |
cDNA | Complementary DNA |
Cm | 2-O-methylcytidine |
CoA | Coenzyme A |
CTU | Cytosolic thiouridylase |
D | Dihydrouridine |
DNMT2 | DNA methyltransferase homologue |
ELP3 | Elongator acetyltransferase complex subunit 3 |
f6A | N6-formyladenosine |
FTO | Fat mass and obesity-associated protein |
G | Guanosine |
Gm | 2-O-methylguanosine |
hm5C | 5-hydroxymethylcytidine |
hm6A | N6-hydroxymethyladenosine |
HPLC | High-performance liquid chromatography |
HTS | High-throughput sequencing |
I | Inosine |
IGF2BP | Insulin like growth factor 2 mRNA binding protein |
Im | 2-O-methylinosine |
LC-MS(MS) | Liquid chromatography-mass spectrometry |
lncRNA | Long non-coding RNA |
m1A | 1-methyladenosine |
m1G | 1-methylguanosine |
m1I | 1-methylinosine |
m1 | 1-methylpseudouridine |
m2G | 2-methylguanosine |
m2,2G | N2’,N2-dimethylguanosine |
m2,7G | N2,7-dimethylguanosine |
m3C | 3-methylcytidine |
m5C | 5-methylcytidine |
m6A | 6-methyladenosine |
m6Am | N6,2-O-dimethyladenosine |
m7G | 7-methylguanosine |
mcm5s2U | 5-methoxycarbonylmethyl-2-thiouridine |
MELAS | Mitochondrial myopathy encephalopathy lactic acidosis and stroke-like episodes |
MERRF | Myoclonus epilepsy associated with with ragged red fibers |
METTL | Methyltransferase-like |
miRNA | MicroRNA |
mRNA | Messenger RNA |
NAD | Nicotinamide adenine dinucleotide |
NGS | Next-generation sequencing |
ncm5U | 5-carbamoylmethyluridine |
Nm | 2-O-methylation |
o2yW | Peroxywybutosine |
OMIM | Online Mendelian Inheritance in Man |
ONT | Oxford Nanopore Technologies |
PacBio | Pacific BioSciences |
Poly-A | A polyadenylated |
piRNA | Piwi-interacting RNA |
Q | Queuosine |
RBPs | RNA binding proteins |
RIP-seq | RNA immunoprecipitation followed by high-throughput sequencing |
rRNA | Ribosomal RNA |
RT | Reverse transcriptase |
s2U | 2-thiouridine |
SMRT | Single-molecule real-time |
SNP | Single Nucleotide Polymorphism |
snoRNAs | Small nucleolar RNAs |
snRNA | Small nuclear RNA |
T | Thymine |
TLC | Thin-layer chromatography |
tRNA | Transfer RNA |
U | Uridine |
Um | 2-O-methyluridine |
UTR | Untranslated region |
Pseudouridine | |
YTHDF | YTH-domain family member |
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Database | Description | Reference |
---|---|---|
DARNED | Database of A-to-I editing sites in humans, mice, and fruit flies | [179] |
FairBase | RNA editing sites in fungi | [186] |
MeT-DB | m6A sites in 7 species | [183] |
MODOMICS | RNA modifications and pathways from multiple species | [8] |
RADAR | Curated A-to-I editing sites in humans, mice, and flies | [180] |
REDIdb | RNA editing sites in plants | [185] |
REDIportal | A-to-I sites across different human tissues and mouse brain | [76] |
RNAMDB | RNA modifications from multiple species | [140] |
RMBase | Multiple RNA modification sites in 13 species | [182] |
snOPY | snoRNAs, snoRNA gene loci, and target RNAs from multiple species | [188] |
tRNAdb | RNA editing sites in tRNA in archaea, bacteria, eukarya, and viruses | [121] |
T-psi-C | Up-to-date collection of tRNA sequences and structures from multiple species | [187] |
WHISTLE | Predicted m6A sites in humans | [184] |
Tool | Description | Reference |
GIREMI | A-to-I sites in humans | [190] |
HAMR | RNA modification sites based on RT-mutation profile | [23] |
iRNA-m2G | m2G sites in humans, yeast, and mice | [103] |
iRNA-PseU | sites in humans, yeast, and mice | [197] |
PACES | ac4C sites in humans | [189] |
PPUS | sites in humans and yeast | [196] |
REDItools | A-to-I sites in humans | [192] |
RNAEditor | A-to-I sites in humans and mice | [191] |
RNAm5Cfinder | m5C sites in humans and mice | [195] |
RNAMethPre | m6A sites in humans and mice | [194] |
snoGPS | Pseudouridylation guide snoRNAs in humans and yeast | [199] |
SnoSCAN | Nm sites in humans, yeast, and archaea | [199] |
SRAMP | m6A sites in humans and mice | [193] |
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Mathlin, J.; Le Pera, L.; Colombo, T. A Census and Categorization Method of Epitranscriptomic Marks. Int. J. Mol. Sci. 2020, 21, 4684. https://doi.org/10.3390/ijms21134684
Mathlin J, Le Pera L, Colombo T. A Census and Categorization Method of Epitranscriptomic Marks. International Journal of Molecular Sciences. 2020; 21(13):4684. https://doi.org/10.3390/ijms21134684
Chicago/Turabian StyleMathlin, Julia, Loredana Le Pera, and Teresa Colombo. 2020. "A Census and Categorization Method of Epitranscriptomic Marks" International Journal of Molecular Sciences 21, no. 13: 4684. https://doi.org/10.3390/ijms21134684