Context-dependent functional compensation between Ythdf m6A readers

Abstract

15The N6-methyladenosine (m 6 A) modification is the most prevalent post-transcriptional mRNA 16 modification, regulating mRNA decay, translation and splicing. It plays a major role during normal 17 development, differentiation, and disease progression. The modification is dynamically regulated 18 by a set of writer, eraser and reader proteins. The YTH-domain family of proteins: Ythdf1, Ythdf2, 19and Ythdf3, are three homologous m 6 A binding proteins, which have different cellular functions. 20However, their sequence similarity and their tendency to bind the same targets suggest that they 21 may have overlapping roles. We systematically knocked out (KO) the Mettl3 writer for each of 22 E7.5, and to embryonic lethality. By using systematic genotyping of viable offspring, we found 81 that in early development there is compensation between the readers, which is dosage-82 dependent, i.e. Ythdf2-hetrozygouse mice need to have at least one functional copy of another 83Ythdf reader to escape mortality. Furthermore, we used mESCs to analyze the function of each 84Ythdf reader separately, and together. We found that only triple-KO mESCs are not able to 85 differentiate properly, and present a prolonged mRNA degradation rate, similar to the effect 86shown in Mettl3-KO, while no significant effect is seen in the single-KOs. This suggests that just 87 like in early development, in mouse ESCs, a system in which all the readers are expressed in the 88 same cells and compartment, there is a redundancy between Ythdf readers, which enables 89 compensation in the absence of the other. 90 91Results 92 93Mettl3 writer plays an essential role in oogenesis and spermatogenesis 94 95We started by systematically testing the three readers in a specific system in-vivo, focusing on 96 spermatogenesis and oogenesis. m 6 A writers Mettl3 and Mettl14 and m 6 A erasers FTO and 97ALKBH5 were found to be essential for proper gametogenesis in mouse. Their KO typically leads 98to defective maturation of sperm or ova, and hypofertility (Xu et al.

m 6 A RNA methylation: from mechanisms to therapeutic potential

“…Further highlighting the complexity of these multifaceted regulatory mechanisms and underlining the need for future studies to fully unravel the molecular details, is the fact that two recent studies have proposed that YTHDF proteins function more similarly in the regulation of gene expression than previously described (Lasman et al , 2020; Zaccara & Jaffrey, 2020). Zaccara and Jaffrey report that in HeLa cells, YTHDF proteins all promote RNA decay, share common binding sites on mRNAs, and share similar protein interaction partners and subcellular localizations.…”

Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-low Induction of Therapy Resistance

“…Recent work has demonstrated that the majority of the effects of m 6 A is mediated through a reduction in transcript stability 16,45 . Given this, one would expect that we would see an increase in expression of the highly methylated AR pathways genes ( Figure 2D), and therefore AR signaling, with METTL3 knockdown.…”

Mechanisms of epitranscriptomic gene regulation

“…[ 61 ] YTHDF3, which has been less well studied than YTHDF1 and YTHDF2, appears to have dual roles in promoting degradation and translation in concert with YTHDF1 and YTHDF2. [ 38,39 ] While the aforementioned work has established a model whereby YTHDF proteins have distinct biological roles, two recent studies from Jaffrey [ 62 ] and Hanna [ 63 ] have called this model into question by proposing that YTHDF1/2/3 proteins are functionally redundant and all mediate mRNA decay but have no role in mRNA translation. The recent work, which includes both independent experiments and re‐analysis of previously published data, stands in sharp contrast to previous studies, particularly regarding the finding that YTHDF1/3 do not promote mRNA translation.…”

“…[38,39] While the aforementioned work has established a model whereby YTHDF proteins have distinct biological roles, two F I G U R E 2 Protein readers of epitranscriptomic modifications. Different reader proteins bind to m 6 A, m 5 C, and m 1 A and regulate cellular fate of modified RNAs recent studies from Jaffrey [62] and Hanna [63] have called this model into question by proposing that YTHDF1/2/3 proteins are functionally redundant and all mediate mRNA decay but have no role in mRNA translation. The recent work, which includes both independent experiments and re-analysis of previously published data, stands in sharp contrast to previous studies, particularly regarding the finding that YTHDF1/3 do not promote mRNA translation.…”