Journal
FRONTIERS IN GENETICS
Volume 11, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fgene.2020.00398
Keywords
RNA; N6-methyladenosine; m(6)A; epitranscriptomics; bioinformatics
Categories
Funding
- Wellcome Trust [215593/Z/19/Z, FC010110]
- Cancer Research UK [FC010110]
- United Kingdom Medical Research Council [FC010110]
- MRC eMedLab Medical Bioinformatics Infrastructure Award [MR/L016311/1]
- Okinawa Institute of Science and Technology Graduate University
- Leonard Wolfson Doctoral Training Fellowship in Neurodegeneration
- Wellcome Trust [215593/Z/19/Z] Funding Source: Wellcome Trust
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A flurry of methods has been developed in recent years to identify N6-methyladenosine (m(6)A) sites across transcriptomes at high resolution. This raises the need to understand both the common features and those that are unique to each method. Here, we complement the analyses presented in the original papers by reviewing their various technical aspects and comparing the overlap between m(6)A-methylated messenger RNAs (mRNAs) identified by each. Specifically, we examine eight different methods that identify m(6)A sites in human cells with high resolution: two antibody-based crosslinking and immunoprecipitation (CLIP) approaches, two using endoribonuclease MazF, one based on deamination, two using Nanopore direct RNA sequencing, and finally, one based on computational predictions. We contrast the respective datasets and discuss the challenges in interpreting the overlap between them, including a prominent expression bias in detected genes. This overview will help guide researchers in making informed choices about using the available data and assist with the design of future experiments to expand our understanding of m(6)A and its regulation.
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