The m⁶A reader protein YTHDC2 interacts with the small ribosomal subunit and the 5′–3′ exoribonuclease XRN1

Abstract

-methyladenosine (mA) modifications in RNAs play important roles in regulating many different aspects of gene expression. While mAs can have direct effects on the structure, maturation, or translation of mRNAs, such modifications can also influence the fate of RNAs via proteins termed "readers" that specifically recognize and bind modified nucleotides. Several YTH domain-containing proteins have been identified as mA readers that regulate the splicing, translation, or stability of specific mRNAs. In contrast to the other YTH domain-containing proteins, YTHDC2 has several defined domains and here, we have analyzed the contribution of these domains to the RNA and protein interactions of YTHDC2. The YTH domain of YTHDC2 preferentially binds mA-containing RNAs via a conserved hydrophobic pocket, whereas the ankyrin repeats mediate an RNA-independent interaction with the 5'-3' exoribonuclease XRN1. We show that the YTH and R3H domains contribute to the binding of YTHDC2 to cellular RNAs, and using crosslinking and analysis of cDNA (CRAC), we reveal that YTHDC2 interacts with the small ribosomal subunit in close proximity to the mRNA entry/exit sites. YTHDC2 was recently found to promote a "fast-track" expression program for specific mRNAs, and our data suggest that YTHDC2 accomplishes this by recruitment of the RNA degradation machinery to regulate the stability of mA-containing mRNAs and by utilizing its distinct RNA-binding domains to bridge interactions between mA-containing mRNAs and the ribosomes to facilitate their efficient translation.

m6A-dependent glycolysis enhances colorectal cancer progression

“…Insulin-like growth factor 2 mRNA binding proteins (IGF2BP1, IGF2BP2 and IGF2BP3) are three well-established m 6 A readers in mammalian cells [33], and responsible for stabilizing mRNA. m 6 A readers YTHDF2, YTHDF3 and YTHDC2 are responsible for mRNA decay [34][35][36]. Real-time PCR data showed that knockdown of IGF2BP2, but not IGF2BP1/3 significantly reduced the mRNA level of HK2 in HCT116 and SW480 cells ( Figure S5i).…”

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

“…In addition to knockout, knockdown, and overexpression lines, transgenic plants expressing point mutants of ECT2 (12-14), ECT3 (12), ECT4 (12), and CPSF30 (15) with impaired ability to bind m 6 A, or a catalytically inactive ALKBH10b (9), are also described in the indicated references and behave like null mutants for the phenotypes described in all cases. References are as follows: 1, Zhong et al, 2008;2, Bodi et al, 2012;3, R u zička et al, 2017;4, Shen et al, 2016;5, Vespa et al, 2004;6, Parker et al, 2019;7, Schomburg et al, 2001;8, Kim et al, 2008;9, Duan et al, 2017;10, Martínez-Pérez et al, 2017;11, Mielecki et al, 2012;12, Arribas-Hernández et al, 2018;13, Scutenaire et al, 2018;14, Wei et al, 2018b;15, Pontier et al, 2019;16, Li et al, 2014a. two very different proteins in mammals: YTHDC1 is nuclear and binds to some sites in mRNAs and nuclear non-coding RNAs, whereas YTHDC2 is enriched in perinuclear regions of the cytoplasm and its mRNAbinding profile shows little overlap with m 6 A sites (Patil et al, 2016;Hsu et al, 2017;Kretschmer et al, 2018;Zaccara et al, 2019). YTHDC2 is specific to mammals and contains several other folded domains in addition to the YTHDC domain (Bailey et al, 2017;Wojtas et al, 2017;Kretschmer et al, 2018), while YTHDC1 has long N-and C-terminal IDRs (Patil et al, 2016).…”

“…References are as follows: 1, Zhong et al, 2008;2, Bodi et al, 2012;3, R u zička et al, 2017;4, Shen et al, 2016;5, Vespa et al, 2004;6, Parker et al, 2019;7, Schomburg et al, 2001;8, Kim et al, 2008;9, Duan et al, 2017;10, Martínez-Pérez et al, 2017;11, Mielecki et al, 2012;12, Arribas-Hernández et al, 2018;13, Scutenaire et al, 2018;14, Wei et al, 2018b;15, Pontier et al, 2019;16, Li et al, 2014a. two very different proteins in mammals: YTHDC1 is nuclear and binds to some sites in mRNAs and nuclear non-coding RNAs, whereas YTHDC2 is enriched in perinuclear regions of the cytoplasm and its mRNAbinding profile shows little overlap with m 6 A sites (Patil et al, 2016;Hsu et al, 2017;Kretschmer et al, 2018;Zaccara et al, 2019). YTHDC2 is specific to mammals and contains several other folded domains in addition to the YTHDC domain (Bailey et al, 2017;Wojtas et al, 2017;Kretschmer et al, 2018), while YTHDC1 has long N-and C-terminal IDRs (Patil et al, 2016). YTHDF-and YTHDC1-type proteins are found in many eukaryotes (Balacco and Soller, 2019), including plants, whose genomes encode more YTH domain proteins than other organisms (Li et al, 2014a;Scutenaire et al, 2018).…”

m6A-binding proteins: the emerging crucial performers in epigenetics

“…Furthermore, YTHDC1 plays a promoting role in the X chromosome genes transcriptional silencing mediated by XIST [12]. YTHDC2, a putative RNA helicase, contains YTH domain, helicase domain, R3H domain, and ankyrin repeats [37], which is of great significance to increase the translation efficiency of mRNAs [25,26].…”