M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers

Abstract

N6-methyladenosine (m6A) is the most abundant posttranscriptional modification in mammalian mRNA molecules and has a crucial function in the regulation of many fundamental biological processes. The m6A modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Different WERs might have different functions, and even the same WER might function differently in different conditions, which are mostly due to different downstream genes being targeted by the WERs. Therefore, identification of the targets of WERs is particularly important for elucidating this dynamic modification. However, there is still no public repository to host the known targets of WERs. Therefore, we developed the m6A WER target gene database (m6A2Target) to provide a comprehensive resource of the targets of m6A WERs. M6A2Target provides a user-friendly interface to present WER targets in two different modules: ‘Validated Targets’, referred to as WER targets identified from low-throughput studies, and ‘Potential Targets’, including WER targets analyzed from high-throughput studies. Compared to other existing m6A-associated databases, m6A2Target is the first specific resource for m6A WER target genes. M6A2Target is freely accessible at http://m6a2target.canceromics.org.

Recent advances in functional annotation and prediction of the epitranscriptome

“…MeT-DB [54] , REPIC [91] , CVm6A [108] , M6A2Target [109] , m6Avar [107] and m6A-Atlas [51] are databases for m 6 A RNA methylation. MeT-DB [54] is the first database for transcriptome m 6 A modification, which collected context-specific m 6 A sites and annotated the target sites of m 6 A readers, writers and erasers as well as RBP, miRNA target and splicing sites.…”

“…M6A2Target [109] has collected the target gene of writers, erasers and readers of m 6 A modification. M6A2Target contains both 'Validated Targets' which were validated by low-throughput experiments of human and mouse and 'Potential Targets' which were evaluated by high-throughput experiments, such as CLIP-Seq, RIP-seq and ChIP-seq.…”

YTH Domain Proteins: A Family of m6A Readers in Cancer Progression

“…m 6 A-Atlas database enables prediction of the biological function of every m 6 A site and inferences of pathogenesis of m 6 A-evoked disease ( 67 ). The M6A2Target database is a specialist database for estimating the prediction target of m 6 A modification ( 68 ). RNAWRE is the first database for finding effectors of RNA modifications ( 69 ).…”

Dynamics of m6A RNA Methylome on the Hallmarks of Hepatocellular Carcinoma

“…In recent years, several bioinformatics tools and databases addressing different purposes have been developed to organize and integrate complex datasets pertaining to m6A RNA modifications and its associated regulators. An interactive analysis of epitranscriptomic sequencing for m6A site identification can be performed by databases such as deepEA ( Zhai et al, 2020 ) and iMRM ( Liu and Chen, 2020 ), while RNAWRE ( Nie et al, 2020 ), and M6A2Target ( Deng et al, 2020 ) deposit m6A regulator datasets. Furthermore, comprehensive information on reliable m6A methylation sites and peaks from MeRIP-seq data are summarized in m6A-Atlas ( Tang et al, 2020 ) and REPIC ( Liu et al, 2020b ), respectively.…”