YTHDF2 promotes mitotic entry and is regulated by cell cycle mediators.

Qili Fei,Ian A Roundtree,Zhongyu Zou,Chuan He,Hui-Lung Sun,Wendy V Gilbert

doi:10.1371/journal.pbio.3000664

Abstract

The N6-methyladenosine (m6A) modification regulates mRNA stability and translation. Here, we show that transcriptomic m6A modification can be dynamic and the m6A reader protein YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) promotes mRNA decay during cell cycle. Depletion of YTHDF2 in HeLa cells leads to the delay of mitotic entry due to overaccumulation of negative regulators of cell cycle such as Wee1-like protein kinase (WEE1). We demonstrate that WEE1 transcripts contain m6A modification, which promotes their decay through YTHDF2. Moreover, we found that YTHDF2 protein stability is dependent on cyclin-dependent kinase 1 (CDK1) activity. Thus, CDK1, YTHDF2, and WEE1 form a feedforward regulatory loop to promote mitotic entry. We further identified Cullin 1 (CUL1), Cullin 4A (CUL4A), damaged DNA-binding protein 1 (DDB1), and S-phase kinase-associated protein 2 (SKP2) as components of E3 ubiquitin ligase complexes that mediate YTHDF2 proteolysis. Our study provides insights into how cell cycle mediators modulate transcriptomic m6A modification, which in turn regulates the cell cycle.

Highlights

Gene ontology (GO) enrichment analysis of the m6A-marked common genes at 3 phases identified a number of GO terms, including “cell cycle” (S1B Fig), suggesting that the m6A pathway regulates genes involved in cell cycle control, consistent with a previous study in mouse embryonic stem cells (mESC) [24]
From the m6A MeRIP-seq and PAR-CLIP data, we found that Wee1-like protein kinase (WEE1) transcripts contain m6A modification mainly at the 30 untranslated region (UTR) region (Fig 3C), suggesting that WEE1 is regulated at the epitranscriptomic level through YTH N6-methyladenosine RNA binding protein 2 (YTHDF2)
YTHDF2 promotes mitotic entry and is regulated by cell cycle mediators whether transcriptomic m6A is impacted by cell cycle regulation and found that m6A-modified transcripts, especially the ones with phase-specific expression patterns, display dynamic changes during cell cycle

Summary

Introduction

Methyltransferase Like 3 (METTL3) and METTL14 [1]—together with several key components, such as Wilms tumor 1-associated protein (WTAP) [2], Vir Like m6A MethyltransferaseAssociated (VIRMA) [3], and Zinc Finger CCCH-Type Containing 13 (ZC3H13) [4]—form a methyltransferase complex to mediate N6-methyladenosine (m6A) modification on mRNAs in a co-transcriptional manner [5,6]. m6A, the most abundant modification on mRNAs, plays multifaceted roles in regulating pre-mRNA processing [7,8], nuclear export [9], stability [10], translation [11], and other biochemical properties [12,13] of mRNA in eukaryotes. YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) was the first functionally verified m6A reader to promote the degradation of m6A-modified mRNAs in humans [10]. It accelerates the decay of m6A-marked transcripts by directly recruiting the Carbon Catabolite Repressor 4-Negative on TATA (CCR4-NOT) deadenylase complex [16] or the endoribonucleolytic RNase P/Mitochondrial RNA Processing (MRP) complex [17]. The significant role of YTHDF2 in cell differentiation was further shown with depletion of YTHDF2-blocking differentiation and driving self-renewal of both mouse and human hematopoietic stem cells [21,22] This protein is critical to acute myeloid leukemia (AML) [23]

Methods

Results

Conclusion