Quantitative analysis of protein-RNA interactions in fission yeast

Characterizing the interactions between RNAs and proteins in vivo is key to better understand how organisms regulate gene expression. Here, we describe a robust and quantitative protocol to measure specific RNA-protein interactions in a native context using RNA immunoprecipitation (RIP). We provide a comprehensive experimental framework to detect cotranslational interactions and detail the quantitative analysis of purified RNAs by PCR and high-throughput sequencing. Although we developed the protocol in fission yeast, it can be readily implemented in other yeast species.

For complete details on the use and execution of this protocol, please refer to Toullec et al. (2021).

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Simple and robust detection of RNA-protein interactions in a native context

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Ribonucleoprotein complex isolated by immunoprecipitation

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Quantitative analysis of purified RNA by PCR or high-throughput sequencing

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Detailed experimental pipeline to demonstrate cotranslational interactions

Drosophila MOV10 regulates the termination of midgut regeneration

The molecular mechanisms by which stem cell proliferation is precisely controlled during the course of regeneration are poorly understood. Namely, how a damaged tissue senses when to terminate the regeneration process, inactivates stem cell mitotic activity, and organizes ECM integrity remain fundamental unanswered questions. The Drosophila midgut intestinal stem cell (ISC) offers an excellent model system to study the molecular basis for stem cell inactivation. Here, we show that a novel gene, CG6967 or dMOV10, is induced at the termination stage of midgut regeneration, and shows an inhibitory effect on ISC proliferation. dMOV10 encodes a putative component of the microRNA (miRNA) gene silencing complex (miRISC). Our data, along with previous studies on the mammalian MOV10, suggest that dMOV10 is not a core member of miRISC, but modulates miRISC activity as an additional component. Further analyses identified direct target mRNAs of dMOV10-containing miRISC, including Daughter against Dpp (Dad), a known inhibitor of BMP/TGF-β signaling. We show that RNAi knockdown of Dad significantly impaired ISC division during regeneration. We also identified six miRNAs that are induced at the termination stage and their potential target transcripts. One of these miRNAs, mir-1, is required for proper termination of ISC division at the end of regeneration. We propose that miRNA-mediated gene regulation contributes to the precise control of Drosophila midgut regeneration.

m6A Reader YTHDC2 Promotes Radiotherapy Resistance of Nasopharyngeal Carcinoma via Activating IGF1R/AKT/S6 Signaling Axis

N6-methyladenosine (m⁶A) modification has been reported as a critical regulator of gene transcript expression. Although m⁶A modification plays important roles in tumor development, its role in therapeutic resistance remains unknown. In this study, we aimed to examine the expression level of m⁶A-modification related proteins and elucidate the effect of m⁶A-related proteins on radiation response in nasopharyngeal carcinoma (NPC). Among the genes that participated in m⁶A modification, YTHDC2, a m⁶A reader, was found to be consistently highly expressed in radioresistant NPC cells. Knocking down of YTHDC2 expression in radioresistant NPC cells improved the therapeutic effect of radiotherapy in vitro and in vivo, whereas overexpression of YTHDC2 in radiosensitive NPC cells exerted an opposite effect. Bioinformatics and mechanistic studies revealed that YTHDC2 could physically bound to insulin-like growth factor 1 receptor (IGF1R) messenger RNA and promoted translation initiation of IGF1R mRNA, which in turn activated the IGF1R-AKT/S6 signaling pathway. Thus, the present study suggests that YTHDC2 promotes radiotherapy resistance of NPC cells by activating the IGF1R/ATK/S6 signaling axis and may serve as a potential therapeutic target in radiosensitization of NPC cells.

Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila

Paip2 (Poly(A)-binding protein - interacting protein 2) is a conserved metazoan-specific protein that has been implicated in regulating the translation and stability of mRNAs. However, we have found that Paip2 is not restricted to the cytoplasm but is also found in the nucleus in Drosophila embryos, salivary glands, testes, and tissue culture cells. Nuclear Paip2 is associated with chromatin, and in chromatin immunoprecipitation experiments it maps to the promoter regions of active genes. However, this chromatin association is indirect, as it is RNA-dependent. Thus, Paip2 is one more item in the growing list of translation factors that are recruited to mRNAs co-transcriptionally.