m6A-Atlas: a comprehensive knowledgebase for unraveling theN6-methyladenosine (m6A) epitranscriptome

Abstract

N 6-Methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. It plays a pivotal role during various biological processes and disease pathogenesis. We present here a comprehensive knowledgebase, m6A-Atlas, for unraveling the m6A epitranscriptome. Compared to existing databases, m6A-Atlas features a high-confidence collection of 442 162 reliable m6A sites identified from seven base-resolution technologies and the quantitative (rather than binary) epitranscriptome profiles estimated from 1363 high-throughput sequencing samples. It also offers novel features, such as; the conservation of m6A sites among seven vertebrate species (including human, mouse and chimp), the m6A epitranscriptomes of 10 virus species (including HIV, KSHV and DENV), the putative biological functions of individual m6A sites predicted from epitranscriptome data, and the potential pathogenesis of m6A sites inferred from disease-associated genetic mutations that can directly destroy m6A directing sequence motifs. A user-friendly graphical user interface was constructed to support the query, visualization and sharing of the m6A epitranscriptomes annotated with sites specifying their interaction with post-transcriptional machinery (RBP-binding, microRNA interaction and splicing sites) and interactively display the landscape of multiple RNA modifications. These resources provide fresh opportunities for unraveling the m6A epitranscriptomes. m6A-Atlas is freely accessible at: www.xjtlu.edu.cn/biologicalsciences/atlas.

Comprehensive profiling analysis of the N6-methyladenosine-modified circular RNA transcriptome in cultured cells infected with Marek’s disease virus

“…Research has also shown that MDV-miR-M4 plays significant roles in tumorigenesis 32 , 33 . In MDV-infected CEF cells, however, we did not identify a correlation between circRNAs and miRNAs, thus indicating that the m 6 A modification on circRNAs may change the regulatory role on miRNAs 34 , 35 . It has also been demonstrated that miRNA can also be regulated by m 6 A modification.…”

Prognostic Significance and Tumor Immune Microenvironment Heterogenicity of m5C RNA Methylation Regulators in Triple-Negative Breast Cancer

“…5-Methylcytosine (m5C), which exists in mRNAs and ncRNAs, is a common RNA modification in humans (Han et al, 2020). Overall, 95,391 m5C sites in the human genome have been reported to date (Tang et al, 2021), identified with different sequencing methods, including bisulfite sequencing, Aza-IP, and miCLIP-Seq. The writers and readers for m5C modification have been well-studied in previous years.…”

“…The writers and readers for m5C modification have been well-studied in previous years. The NOP2/Sun domain family member 2 (NSUN2) is considered an important methyltransferase of m5C modification in tRNA, abundant noncoding RNAs, and a small number of mRNAs (Hussain et al, 2013;Blanco et al, 2014;Tang et al, 2021). A recent study showed that NSUN6 mediates site-specific deposition of m5C in mRNA to control the translation quality (Selmi et al, 2021, 6).…”

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

“…Reliable m 6 A sites and transcriptional profiles were pooled by m 6 A-Atlas. 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 ).…”