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.

N 6 -Methyladenosine (m 6 A), the most prevalent internal modification associated with eukaryotic mRNAs, influences many steps of mRNA metabolism, including splicing, export, and translation, as well as stability. Recent studies have revealed that m 6 A-containing mRNAs undergo one of two distinct pathways of rapid degradation: deadenylation via the YT521-B homology (YTH) domain-containing family protein 2 (YTHDF2; an m 6 A reader protein)-CCR4/NOT (deadenylase) complex or endoribonucleolytic cleavage by the YTHDF2-HRSP12-ribonuclease (RNase) P/mitochondrial RNA-processing (MRP) (endoribonuclease) complex. Some m 6 A-containing circular RNAs (circRNAs) are also subject to endoribonucleolytic cleavage by YTHDF2-HRSP12-RNase P/MRP. Here, we highlight recent progress on the molecular mechanisms underlying rapid mRNA degradation via m 6 A and describe our current understanding of the dynamic regulation of m 6 A-mediated mRNA decay through the crosstalk between m 6 A (or YTHDF2) and other cellular factors. RNA Modification: An Emerging Layer of Post-Transcriptional Gene RegulationMany recent studies point to the role of RNA modification as a mode of post-transcriptional gene regulation and this field has been termed 'epitranscriptomics' [1-4]. To date, approximately 150 post-transcriptional modifications have been associated with various RNA species, including mRNAs, tRNAs, rRNAs, noncoding RNAs (ncRNAs), and viral RNA genomes [5][6][7]. In this review, we summarize recent reports on m 6 A deposition and function. In particular, we discuss recent findings regarding how m 6 A contributes to mRNA stability at the molecular level. HighlightsN 6 -Methyladenosine (m 6 A) as an mRNA modification plays multiple roles in various steps/characteristics of mRNA processing and metabolism, such as splicing, export, translation, and stability.YTHDF2 preferentially recognizes m 6 A and recruits RNA-degrading enzymes or adaptor proteins to trigger rapid degradation of the m 6 A-containing mRNA.Depending on the presence of HRSP12binding sites in m 6 A-containing mRNAs, YTHDF2 elicits one of two RNA decay pathways: deadenylation by the YTHDF2-CCR4/NOT deadenylase complex or endoribonucleolytic cleavage via the YTHDF2-HRSP12-RNase P/MRP complex.The stability of m 6 A-containing mRNAs is regulated by the dynamic crosstalk between m 6 A and other cellular factors, such as RNA-binding proteins, RNA structures, and/or other types of modification.

Glucocorticoid receptor (GR), which was originally known to function as a nuclear receptor, plays a role in rapid mRNA degradation by acting as an RNA-binding protein. The mechanism by which this process occurs remains unknown. Here, we demonstrate that GR, preloaded onto the 5′UTR of a target mRNA, recruits UPF1 through proline-rich nuclear receptor coregulatory protein 2 (PNRC2) in a ligand-dependent manner, so as to elicit rapid mRNA degradation. We call this process GR-mediated mRNA decay (GMD). Although GMD, nonsense-mediated mRNA decay (NMD), and staufen-mediated mRNA decay (SMD) share upstream frameshift 1 (UPF1) and PNRC2, we find that GMD is mechanistically distinct from NMD and SMD. We also identify de novo cellular GMD substrates using microarray analysis. Intriguingly, GMD functions in the chemotaxis of human monocytes by targeting chemokine (C-C motif) ligand 2 (CCL2) mRNA. Thus, our data provide molecular evidence of a posttranscriptional role of the well-studied nuclear hormone receptor, GR, which is traditionally considered a transcription factor. glucocorticoid receptor | PNRC2 | UPF1 | glucocorticoid receptor-mediated mRNA decay | Nonsense-mediated mRNA decay A t the cellular level, glucocorticoid receptor (GR), which belongs to the nuclear receptor superfamily, functions as a transcription factor regulating various physiological processes (1-3). In the presence of a glucocorticoid, which diffuses through the plasma membrane into the cytoplasm, cytosolic GR binds to the glucocorticoid. The resulting glucocorticoid-GR complex is activated and then enters the nucleus. Once in the nucleus, GR dimerizes, binds to specific cis-acting elements, and recruits coregulatory proteins for transcriptional activation or repression (4, 5).The majority of the coregulatory proteins commonly contain a nuclear receptor box (NR box, also called an LXXLL motif), which is important for interactions between coregulatory proteins and nuclear receptors (4-6). The proline-rich nuclear receptor coregulatory protein (PNRC), however, is an exception because it interacts with nuclear receptors through an SH3-binding motif [SD(E)PPSPS] rather than an NR box (7,8). Two PNRC paralogs, PNRC1 and PNRC2, have been identified in mammalian cells (7,8). PNRC1 and PNRC2 are believed to play similar roles in nuclear receptor-mediated signaling because they interact with similar groups of nuclear receptors.Although PNRC2 is known to function as a coregulatory protein for nuclear receptors, it has a distinct function in mRNA decay pathways including nonsense-mediated mRNA decay (NMD), staufen (STAU)-mediated mRNA decay (SMD), and replication-dependent histone mRNA degradation (HMD) (9-13). NMD serves as a mechanism of both mRNA quality control and posttranscriptional regulation by selectively recognizing and degrading cellular transcripts that are abnormal or that contain a premature translation termination codon (PTC), as reviewed elsewhere (14-16). A key NMD factor, UPF1, is recruited to a terminating ribosome at a PTC. UPF1 then recr...

p62/SQSTM1 is the key autophagy adapter protein and the hub of multi-cellular signaling. It was recently reported that autophagy and N-end rule pathways are linked via p62. However, the exact recognition mode of degrading substrates and regulation of p62 in the autophagic pathway remain unknown. Here, we present the complex structures between the ZZ-domain of p62 and various type-1 and type-2 N-degrons. The binding mode employed in the interaction of the ZZ-domain with N-degrons differs from that employed by classic N-recognins. It was also determined that oligomerization via the PB1 domain can control functional affinity to the R-BiP substrate. Unexpectedly, we found that self-oligomerization and disassembly of p62 are pH-dependent. These findings broaden our understanding of the functional repertoire of the N-end rule pathway and provide an insight into the regulation of p62 during the autophagic pathway.

Glucocorticoid (GC) receptor (GR) has been shown recently to bind a subset of mRNAs and elicit rapid mRNA degradation. However, the molecular details of GR-mediated mRNA decay (GMD) remain unclear. Here, we demonstrate that GMD triggers rapid degradation of target mRNAs in a translation-independent and exon junction complexindependent manner, confirming that GMD is mechanistically distinct from nonsense-mediated mRNA decay (NMD). Efficient GMD requires PNRC2 (proline-rich nuclear receptor coregulatory protein 2) binding, helicase ability, and ATM-mediated phosphorylation of UPF1 (upstream frameshift 1). We also identify two GMD-specific factors: an RNA-binding protein, YBX1 (Y-box-binding protein 1), and an endoribonuclease, HRSP12 (heat-responsive protein 12). In particular, using HRSP12 variants, which are known to disrupt trimerization of HRSP12, we show that HRSP12 plays an essential role in the formation of a functionally active GMD complex. Moreover, we determine the hierarchical recruitment of GMD factors to target mRNAs. Finally, our genome-wide analysis shows that GMD targets a variety of transcripts, implicating roles in a wide range of cellular processes, including immune responses.

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It has long been thought that glucocorticoid receptor (GR) functions as a DNA-binding transcription factor in response to its ligand (a glucocorticoid) and thus regulates various cellular and physiological processes. It is also known that GR can bind not only to DNA but also to mRNA; this observation points to the possible role of GR in mRNA metabolism. Recent data revealed a molecular mechanism by which binding of GR to target mRNA elicits rapid mRNA degradation. GR binds to specific RNA sequences regardless of the presence of a ligand. In the presence of a ligand, however, the mRNA-associated GR can recruit PNRC2 and UPF1, both of which are specific factors involved in nonsense-mediated mRNA decay (NMD). PNRC2 then recruits the decapping complex, consequently promoting mRNA degradation. This mode of mRNA decay is termed “GR-mediated mRNA decay” (GMD). Further research demonstrated that GMD plays a critical role in chemotaxis of immune cells by targeting CCL2 mRNA. All these observations provide molecular insights into a previously unappreciated function of GR in posttranscriptional regulation of gene expression. [BMB Reports 2015; 48(7): 367-368]

All metazoan mRNAs have a poly(A) tail at the 3′ end with the exception of replication‐dependent histone (RDH) mRNAs, which end in a highly conserved stem‐loop (SL) structure. However, a subset of RDH mRNAs are reported to be polyadenylated under physiologic conditions. The molecular details of the biogenesis of polyadenylated RDH [poly(A)+ RDH] mRNAs remain unknown. In this study, our genome‐wide analyses reveal that puromycin treatment or UVC irradiation stabilizes poly(A)+ RDH mRNAs, relative to canonical RDH mRNAs, which end in an SL structure. We demonstrate that the stabilization of poly(A)+ RDH mRNAs occurs in a translation‐independent manner and is regulated via human antigen R (HuR) binding to the extended 3′ UTR under stress conditions. Our data suggest that HuR regulates the expression of poly(A)+ RDH mRNAs.—Ryu, I., Park, Y., Seo, J.‐W., Park, O. H., Ha, H., Nam, J.‐W., Kim, Y. K. HuR stabilizes a polyadenylated form of replication‐dependent histone mRNAs under stress conditions. FASEB J. 33, 2680–2693 (2019). http://www.fasebj.org