Endoribonucleolytic Cleavage of m6A-Containing RNAs by RNase P/MRP Complex

Abstract

N 6 -methyladenosine (m 6 A) is the most abundant internal modification in RNAs and plays regulatory roles in a variety of biological and physiological processes. Despite its important roles, the molecular mechanism underlying m 6 A-mediated gene regulation is poorly understood. Here, we show that m 6 A-containing RNAs are subject to endoribonucleolytic cleavage via YTHDF2 (m 6 A reader protein), HRSP12 (adaptor protein), and RNase P/MRP (endoribonucleases). We demonstrate that HRSP12 functions as an adaptor to bridge YTHDF2 and RNase P/MRP, eliciting rapid degradation of YTHDF2-bound RNAs. Transcriptome-wide analyses show that m 6 A RNAs that are preferentially targeted for endoribonucleolytic cleavage have an HRSP12-binding site and a RNase P/MRP-directed cleavage site upstream and downstream of the YTHDF2-binding site, respectively. We also find that a subset of m 6 A-containing circular RNAs associates with YTHDF2 in an HRSP12-dependent manner and is selectively downregulated by RNase P/MRP. Thus, our data expand the known functions of RNase P/MRP to endoribonucleolytic cleavage of m 6 A RNAs.

Occurrence and Functions of m6A and Other Covalent Modifications in Plant mRNA

“…For example, tethering the IDR of YTHDF2 to reporter mRNAs is sufficient to cause their localization to P-bodies in mammalian cells . The IDR of YTHDF2 also interacts with the deadenylase complex CCR4-NOT and, via the adaptor protein HRSP12, with the endoribonuclease RNase P/MRP (Park et al, 2019). However, since the affinity of isolated YTH domains for m 6 A-modified RNA is modest (0.1-5 mM; Li et al, 2014b;Luo and Tong, 2014;Theler et al, 2014;Xu et al, 2014Xu et al, , 2015Zhu et al, 2014), it is possible that the IDR participates in RNA binding in vivo, as suggested by the loss of mRNA binding in vivo of a mutant in human YTHDF3 containing a deletion in the IDR (Zhang et al, 2019c).…”

“…Herzog et al [2017] or Ke et al [2017] for animals, Bushkin et al [2019] for yeast, or Zaccara et al [2019] for the most recent review), as proposed in early studies (Sommer et al, 1978). Accelerated mRNA decay in mammals involves YTHDF proteins, perhaps in particular YTHDF2 Ivanova et al, 2017;Zhang et al, 2017;Zhao et al, 2017;Paris et al, 2019), but whether the mechanism relies mostly on CCR4-NOT deadenylase recruitment , perhaps concurrent with sorting to P-bodies , enhanced endonucleolysis (Park et al, 2019), or a combination remains unclear. m 6 A may also stimulate translation, in this case via other YTHDF proteins Li et al, 2017a;Shi et al, 2017).…”

N6-Methyladenosine: A Novel RNA Imprint in Human Cancer

“…Recently, the molecular mechanism underpinning YTHDF2-directed RNA decay has been expounded. m 6 A-containing linear and circular RNAs undergo endoribonucleolytic cleavage through YTHDF2-HRSP12-RNase P/MRP axis, coupled to CCR4-NOT complex-mediated deadenylating pathway (38) (Figure 1). In addition, a recent study reported that multivalent m 6 A-modified RNAs could promote the phase separation of YTHDFs and that phase separation of m 6 A and YTHDF2 might participate in cellular response to stresses, despite the uncertainty of its specific role (39).…”

YTHDF2 promotes mitotic entry and is regulated by cell cycle mediators

“…YTH N 6 -methyladenosine RNA binding protein 2 (YTHDF2) was the first functionally verified m 6 A reader to promote the degradation of m 6 A-modified mRNAs in humans [10]. It accelerates the decay of m 6 A-marked transcripts by directly recruiting the Carbon Catabolite Repressor 4-Negative on TATA (CCR4-NOT) deadenylase complex [16] or the endoribonucleolytic RNase P/Mitochondrial RNA Processing (MRP) complex [17]. In zebrafish, Ythdf2 promotes the clearance of the maternal transcripts during maternal to zygotic transition (MZT) [18].…”