Integrative network analysis identifies cell-specific trans regulators of m6A

Abstract

N6-methyladenosine (m6A) is a reversible and dynamic RNA modification in eukaryotes. However, how cells establish cell-specific m6A methylomes is still poorly understood. Here, we developed a computational framework to systematically identify cell-specific trans regulators of m6A through integrating gene expressions, binding targets and binding motifs of large number of RNA binding proteins (RBPs) with a co-methylation network constructed using large-scale m6A methylomes across diverse cell states. We applied the framework and successfully identified 32 high-confidence m6A regulators that modulated the variable m6A sites away from stop codons in a cell-specific manner. To validate them, we knocked down three regulators respectively and found two of them (TRA2A and CAPRIN1) selectively promoted the methylations of the m6A sites co-localized with their binding targets on RNAs through physical interactions with the m6A writers. Knockdown of TRA2A increased the stabilities of the RNAs with TRA2A bound near the m6A sites and decreased the viability of cells. The successful identification of m6A regulators demonstrates a powerful and widely applicable strategy to elucidate the cell-specific m6A regulators. Additionally, our discovery of pervasive trans-acting regulating of m6A provides novel insights into the mechanisms by which spatial and temporal dynamics of m6A methylomes are established.

Roles of N6-Methyladenosine (m6A) in Stem Cell Fate Decisions and Early Embryonic Development in Mammals

“…In mammals, approximately 0.1 to 0.6% of adenines undergo m 6 A modification, with an average of 3 to 5 methylated sites in each mRNA. Notably, m 6 A modifications can be deposited onto the transcripts in tissue-and cell-type-specific manners (An et al, 2020).…”

“…Notably, the m 6 A modification-related methylase can be regulated by various factors involved in transcriptional, posttranscriptional (miRNAs and lncRNAs), and translational (phosphorylation, ubiquitination, or SUMOylation modification) regulation ( Du et al, 2018 ; Schöller et al, 2018 ; Zhu et al, 2018 ). In addition, several m 6 A modification regulators, such as ZFP217, SMAD2/3, CEBPZ, TARBP2, and TRA2A, have been found to regulate m 6 A modification of mRNAs by recruiting or repelling MTC in a cell-type-specific manner ( Aguilo et al, 2015 ; Barbieri et al, 2017 ; Bertero et al, 2018 ; Fish et al, 2019 ; An et al, 2020 ). In addition, a recent study reported that H3K36me3 recruited METTL14 thus guiding m 6 A deposition on nascent transcripts ( Huang et al, 2019 ).…”

Roles of METTL3 in cancer: mechanisms and therapeutic targeting

“…Another transcriptional factor, CAATT-box-binding protein CEBPZ, was demonstrated to directly recruit METTL3 to chromatin [ 68 ]. A large-scale computational screening aimed at identifying RNA-binding proteins as cell-specific trans regulators of m 6 A, and validated experimentally that TRA2A and CAPRIN1 could interact with METTL3 [ 69 ]. Fish et al found that the RNA-binding protein TARBP2 recruits METTL3 and deposits m 6 A on the introns of the target mRNA, regulating RNA splicing and stability [ 70 ].…”

m6A RNA methylation impacts fate choices during skin morphogenesis

“…A number of studies have focused on dissecting m6A’s functions in cell culture systems, where transcriptome-wide m6A profiles and expression patterns of the writers, erasers and readers were found to vary among cell types ( An et al, 2020 ; Delaunay and Frye, 2019 ; Roundtree et al, 2017 ). In recent years, models have been made to conditionally disrupt specific m6A writers, erasers or readers in mouse tissues ( Cheng et al, 2019 ; Geula et al, 2015 ; Hsu et al, 2017 ; Ivanova et al, 2017 ; Lee et al, 2019 ; Li et al, 2017 ; Li et al, 2018 ; Lin et al, 2017 ; Shi et al, 2018 ; Wu et al, 2018 ; Xu et al, 2017 ; Yoon et al, 2017 ; Zhang et al, 2018 ).…”