Cross-Species Analysis of YTH Domain Proteins from H. sapiens and A. ricinus

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2024

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Abstract

RNAs are known to undergo a large number of post-synthesis chemical modifications that can alter their function and structure. Current studies are uncovering the significance of modified RNAs by delineating their associations with RNA-binding proteins, known as “readers.” One such family of protein readers contains a YTH RNA-binding domain, which is widely conserved and involved in recognizing N6-Methyladenosine (m6A) modifications found in eukaryotic mRNA. More recently, the YTH domain proteins have been found to recognize other RNA modifications, such as N1‐Methyladenosine (m1A) and 5-Methylcytosine (m5C). However, the “rules” that govern the YTH domain protein interactions with other modifications still remain unclear. In this study, we explored the biochemical characteristics of the YTH domain identified in Acarus ricinus via sequence and structural alignment. This particular YTH domain contains a sequence insertion akin to that observed in YTHDC1, which we hypothesize will impact the affinity and specificity for RNA modifications like m1A and m5C when compared to the human YTHDF1. In addition to sequence-based analysis, we validated protein expression of these domain proteins with SDS-PAGE. We also performed microscale thermophoresis binding assays to compare the binding affinities of YTHDF1 with m6A-containing RNA and unmodified RNA. These experiments lay the groundwork for future comparison of the YTHDF1 YTH domain with the A. ricinus YTH domain.

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