The RNA m 6 A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence

Ivanova, Ivayla; Much, Christian; Giacomo, Monica Di; Azzi, Chiara; Morgan, Marcos; Moreira, Pedro Ventura De Oliveira; Monahan, Jack; Carrieri, Claudia; Enright, Anton J.; O’Carroll, Dónal

doi:10.1016/j.molcel.2017.08.003

Cited by 303 publications

(322 citation statements)

References 49 publications

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“…Eventually, these 309 maternal messages will be eliminated later on in the zygote and in the embryo at the time of 310 zygote genome activation in two successive waves of degradation. Recently, mRNA methylation 311 has emerged as a key regulator of mRNA stability during oocyte development, and the m6A 312 reader YTHDF2 has been implicated in message destabilization 22,39 . However, we found minimal 313 overlap between mRNAs destabilized in MI and those stabilized by YTHDF2 ablation.…”

Section: Activation Of Translation During Meiotic Maturation Is Depenmentioning

confidence: 99%

Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

Luong

Daldello

Rajkovic³

et al. 2019

Preprint

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Cell development relies on elaborate changes in gene expression in order to transition 38 through different phenotypic and functional stages that ultimately lead to terminal differentiation. 39Changes in gene expression are achieved through transcriptional and post-transcriptional 40 regulations. Although transcriptional regulation is understood in considerable detail 1, 2 , much less 41 is known about the molecular machinery involved in translation regulation. 42Large oligomeric complexes involving proteins and non-coding RNAs are assembled on 43 the mRNA 3 to regulate its interaction with ribosomes, its translation rate, and its stability 4, 5 . In 44 somatic cells, numerous observations indicate that translation is intimately coupled with 45 degradation of mRNAs 5, 6 . Proteins recruited on the mRNA interact with elements located 46 throughout the length of the transcript 3, 7 . However, complexes nucleated around the 5' and 3' 47 polyadenylation element-binding protein (CPEB) is considered a master regulator of 63 polyadenylation and translation 18,19 . Much less is known about the role of CPEB in mammalian 64 oocytes. Here, we have used a genome-wide approach to investigate the role of this RNA-binding 65 protein (RBP) during the transition from quiescence to re-entry into the meiosis. Through a 66 detailed time course, we have investigated the temporal association between maternal mRNA 67 translation and the different steps involved in oocyte re-entry into and progression through the 68 meiosis. Using a RiboTag/RNA-Seq strategy, we describe a genome-wide switch in the 69 translation program of maternal mRNAs, and define new, critical functions of CPEB in the control 70 of this switch. 71 4 Results 72 Re-entry into meiosis coincides with rapid translational changes of stable mRNAs 73We have used a RiboTag/RNA-Seq strategy to characterize mRNA translation in oocytes 74 arrested at prophase I (GV) and in those undergoing meiotic maturation. (Fig. 1a). This strategy 75 has been previously validated 20, 21 and additional quality controls are reported (Supplementary 76 Fig. 1a-d). Upon meiotic resumption, there were both progressive increases and decreases in 77 ribosome loading of maternal mRNAs (Fig. 1b). By late metaphase I (MI), mRNAs were either 78 constitutively translated (n = 5580, CONSTITUTIVE), translationally repressed (n = 1092, 79 DOWN), or translationally activated (n = 871, UP) (FDR ≤ 0.05 and -1 ≥ log2(FC) (LFC) ≥ 1, 80 Supplementary Fig. 1e). Total mRNA levels remained stable up to MI and significant 81 destabilization was only detectable for 3% of maternal mRNAs at late MI ( Fig. 1b and 82 Supplementary Fig. 1f). Comparison of changes in total mRNA levels (transcriptome) to changes 83 in ribosome-associated mRNA levels (translatome) confirms this late MI destabilization (Fig. 1c), 84 which became prominent later during MII arrest, with a subset of mRNAs remaining stable even 85 if their translation was repressed. Changes in translation that initiate during MI were extended into 86 and amplified ...

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Section: Activation Of Translation During Meiotic Maturation Is Depenmentioning

confidence: 99%

Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

Luong

Daldello

Rajkovic³

et al. 2019

Preprint

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“…First, there is an abundance of phenotypes in settings involving cell state transitions, such as the maternal-to-zygotic transition (Ivanova et al, 2017;Zhao et al, 2017b), or between stem cell renewal and differentiation states (Bertero et al, 2018;Vu et al, 2017;Zhang et al, 2017). This may reflect intense interest particularly in stem cell research, but on the other hand, may reflect frequent roles for RNA methylation in facilitating turnover of transcriptome programs between state or identity changes .…”

Section: Introductionmentioning

confidence: 99%

A neural m⁶A/YTHDF pathway is required for learning and memory inDrosophila

Kan

Ott

Joseph

et al. 2020

Preprint

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The roles of epitranscriptomic modifications in mRNA regulation have recently received substantial attention, with appreciation growing for their phenotypically selective impacts within the animal. We adopted Drosophila melanogaster as a model system to study m 6 A, the most abundant internal modification of mRNA. Here, we report proteomic and functional analyses of fly m 6 A-binding proteins, confirming nuclear (YTHDC) and cytoplasmic (YTHDF) YTH domain proteins as the major m 6 A binders. Since all core m 6 A pathway mutants are viable, we assessed in vivo requirements of the m 6 A pathway in cognitive processes. Assays of short term memory revealed an age-dependent requirement of m 6 A writers working via YTHDF, but not YTHDC, comprising the first phenotypes assigned to Drosophila mutants of the cytoplasmic m 6 A reader.These factors promote memory via neural-autonomous activities, and are required in the mushroom body, the center for associative learning. To inform their basis, we mapped m 6 A from wild-type and mettl3 null mutant heads, allowing robust discrimination of Mettl3-dependent m 6 A sites. In contrast to mammalian m 6 A, which is predominant in 3' UTRs, Drosophila m 6 A is highly enriched in 5' UTRs and occurs in an adenosine-rich context. Genomic analyses demonstrate that Drosophila m 6 A does not directionally affect RNA stability, but is preferentially deposited on genes with low translational efficiency. However, functional tests indicate a role for m 6 A in translational activation, since we observe reduced nascent protein synthesis in mettl3-KO cells.Finally, we show that ectopic YTHDF can increase m 6 A target reporter output in an m 6 A-binding dependent manner, and that this activity is required for in vivo neural function of YTHDF in memory. Altogether, we provide the first tissue-specific m 6 A maps in this model organism and reveal selective behavioral and translational defects for m 6 A/YTHDF mutants.

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“…It is possible that the somewhat reduced proportion of the variability explained by our model in mESCs compared to yeast (35% vs. 50%) could be due to the fact that in yeast only a single YTH containing m6A reader is present (Schwartz et al, 2013) and no m6A demethylases have been documented to date. This contrasts with human, which express five different YTH containing readers (Bailey et al, 2017;Dominissini et al, 2012;Ivanova et al, 2017;Shi et al, 2017;Wang et al, 2014Wang et al, , 2015Zhu et al, 2014) , in addition to a growing number of proteins that have been implicated with an ability to read m6A (Edupuganti et al, 2017) , and two putative m6A demethylases (Jia et al, 2011;Mauer et al, 2016;Zheng et al, 2013) . MASTER-seq provides a fresh, quantitative lens for exploring the sources of variability in methylation levels within cells, and between conditions.…”

Section: Discussionmentioning

confidence: 88%

Deciphering the ‘m⁶A code’ via quantitative profiling of m⁶A at single-nucleotide resolution

Edelheit

Toth

et al. 2019

Preprint

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N6-methyladenosine (m 6 A) is the most abundant modification on mRNA, and is implicated in critical roles in development, physiology and disease. The ability to map m 6 A using immunoprecipitation-based approaches has played a critical role in dissecting m 6 A functions and mechanisms of action. Yet, these approaches are of limited specificity, unknown sensitivity, and unable to quantify m6A stoichiometry. These limitations have severely hampered our ability to unravel the factors determining where m6A will be deposited, to which levels (the 'm6A code'), and to quantitatively profile m6A dynamics across biological systems. Here, we used the RNase MazF, which cleaves specifically at unmethylated RNA sites, to develop MASTER-seq for systematic quantitative profiling of m6A sites at 16-25% of all m6A sites at single nucleotide resolution. We established MASTER-seq for orthogonal validation and de novo detection of m6A sites, and for tracking of m6A dynamics in yeast gametogenesis and in early mammalian differentiation. We discover that antibody-based approaches severely underestimate the number of m6A sites, and that both the presence of m6A and its stoichiometry are 'hard-coded' via a simple and predictable code within the extended sequence composition at the methylation sites. This code accounts for~50% of the variability in methylation levels across sites, allows excellent de novo prediction of methylation sites, and predicts methylation acquisition and loss across evolution. We anticipate that MASTER-seq will pave the path towards a more quantitative investigation of m6A biogenesis and regulation in a wide variety of systems, including diverse cell types, stimuli, subcellular components, and disease states.

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The RNA m 6 A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence

Cited by 303 publications

References 49 publications

Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

A neural m⁶A/YTHDF pathway is required for learning and memory inDrosophila

Deciphering the ‘m⁶A code’ via quantitative profiling of m⁶A at single-nucleotide resolution

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The RNA m 6 A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence

Cited by 303 publications

References 49 publications

Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

A neural m6A/YTHDF pathway is required for learning and memory inDrosophila

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution

Contact Info

Product

Resources

About

A neural m⁶A/YTHDF pathway is required for learning and memory inDrosophila

Deciphering the ‘m⁶A code’ via quantitative profiling of m⁶A at single-nucleotide resolution