N6-methyladenosine regulates maternal RNA maintenance in oocytes and timely RNA decay during mouse maternal-to-zygotic transition

Expression pattern of RNA demethylase ALKBH5 in fetal and adult human testis

N6-methyladenosine (m6A) is a common post-transcriptional modification of RNAs in eukaryotic cells, which is involved in various biological processes. ALKBH5 is one of the m6A demethylases and has been reported to play important roles in mouse testis. But the function of ALKBH5 in human testis remained undiscovered. Here we aimed to analyze the expression and location of ALKBH5 in fetal and adult human testis. We found that fetal human testis is characterized by the formation of testis cords filled with pre-spermatogonia and pre-Sertoli cells, which is significantly distinct from the convoluted seminiferous epithelium in adult testis. ALKBH5 is not only widely expressed in adult human testis, but also expressed in VASA positive pre-spermatogonia, SOX9 positive pre-Sertoli cells, and CYP11A positive pre-Leydig cells in fetal human testis. Moreover, bioinformatics analysis of published RNA-sequencing data (GSE63392) revealed the expression of ALKBH5 in human fetal germ cells is upregulated with the increase of gestational weeks. Thus, our results indicate the potential role of ALKBH5 in fetal human testis development and function.

RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation

BACKGROUND

Omics technologies are widely applied in assisted reproductive technology (ART), such as embryo selection, investigation of infertility causes, and mechanisms underlying reproductive cell development. While RNAomics has shown great potential in investigating the physiology and pathology in female reproductive system, its applications are still not fully developed. More studies on epitranscriptomic regulation mechanisms and novel sequencing methods are needed to advance the field.

RESULTS

Here, we developed a method named Cap to Tail sequencing application (C2T-APP) and simultaneously characterized the m7G cap, poly(A) tail structure, and gene expression level for the intact RNA molecules in single cells. C2T-APP distinguished the N6, 2'-O-dimethyladenosine modification (m6Am) from N6-methyladenosine (m6A) modification with our published single-cell m6A sequencing (scm6A-seq) data. During oocyte maturation, we found a positive correlation of m7G and m6Am with translation efficiency and finely dissected the step-wised maternal RNA de-capping and de-tailing of different types of genes. Strikingly, we uncovered a subtle structural mechanism regulating poly(A) tails in oocytes: maternal RNA translation is temporarily suppressed by removing the poly(A) tails without complete degradation, while the poly(A)-tail regulators themselves depend strictly on translation initiated after meiotic resumption. Furthermore, we profiled single-cell RNA-multi-omic features of human oocytes with different qualities during in vitro culture maturation (IVM). Defects of epi-transcriptome features, including m6A, m6Am, m7G, and poly(A) structure of maternal RNA in the oocytes with poor quality, were detected.

CONCLUSIONS

Our results provided a valuable tool for RNAomics research and data resources provided novel insights into human oocyte maturation, which is helpful for IVM and oocyte selection for ART.

ZAR1 and ZAR2 orchestrate the dynamics of maternal mRNA polyadenylation during mouse oocyte development

BACKGROUND

During meiosis, the oocyte genome keeps dormant for a long time until zygotic genome activation. The dynamics and homeostasis of the maternal transcriptome are essential for maternal-to-zygotic transition. Zygotic arrest 1 (ZAR1) and its homolog, ZAR2, are RNA-binding proteins that are important for the regulation of maternal mRNA stability.

RESULTS

Smart-seq2 analysis reveals drastically downregulated maternal transcripts. However, the detection of transcript levels by Smart-seq2 may be biased by the polyadenylated tail length of the mRNAs. Similarly, differential expression of maternal transcripts in oocytes with or without Zar1/2 differs when analyzed using total RNA-seq and Smart-seq2, suggesting an influence of polyadenylation. Combined analyses using total RNA-seq, LACE-seq, PAIso-seq2, and immunoprecipitation-mass spectrometry reveals that ZAR1 may target the 3'-untranslated regions of maternal transcripts, regulates their stability in germinal vesicle stage oocytes, and interacts with other proteins to control the polyadenylation of mRNAs.

CONCLUSIONS

The jointly analyzed multi-omics data highlight the limitations of Smart-seq2 in oocytes, clarify the dynamics of the maternal transcriptome, and uncover new roles of ZAR1 in regulating the maternal transcriptome.

YTHDF2 suppresses the 2C-like state in mouse embryonic stem cells via the DUX-ZSCAN4 molecular circuit

Mouse embryonic stem cells (ESCs) consist of a rare population of heterogeneous 2-cell-like cells (2CLCs). These cells transiently recapitulate the transcriptional and epigenetic features of the 2-cell embryos, serving as a unique model for studying totipotency acquisition and embryonic development. Accumulating evidence has demonstrated that transcription factors and epigenetic modifications exert crucial functions in the transition of ESCs to 2CLCs. However, the roles of RNA modification in the regulation of the 2C-like state remain elusive. Using a DUX-induced 2CLCs system, we examine N6-methyladenosine (m6A) modification landscape transcriptome-wide and observe dynamic regulation of m6A during DUX-driven 2C-like reprogramming. Notably, many core 2C transcripts like Dux and Zscan4 are highly methylated. We identify the m6A reader protein YTHDF2 as a critical regulator of 2C-like state. Depletion of YTHDF2 facilitates robust expression of 2C-signature genes and ESCs-to-2CLCs transition. Intriguingly, YTHDF2 binds to a subset of m6A-modified 2C transcripts and promotes their decay. We further demonstrate that YTHDF2 suppresses the 2C-like program in a manner that is dependent on both m6A and the DUX-ZSCAN4 molecular circuit. Mechanistically, YTHDF2 interacts with CNOT1, a key component of the RNA deadenylase complex. Consistently, silencing of CNOT1 upregulates the 2C program and promotes ESCs-to-2CLCs transition. Collectively, our findings reveal novel insights into the epitranscriptomic regulation of the 2C-like state in mouse ESCs.

Histone lactylation regulates early embryonic development through m6A methyltransferase METTL3 in goats

Histone lysine lactylation (Kla) is a novel epigenetic modification that plays a crucial role in cellular processes driven by glycolysis and lactate production. However, the mechanisms of histone lactylation and its interaction with m6A RNA methylation during early embryonic development remain underexplored. This study systematically investigated the effects of oxygen levels-atmospheric oxygen (atmosO2; 20% O2) and physiological oxygen (physO2; 5% O2)-on hallmark events during early embryonic development, revealing that lactylation modification regulates early goat embryonic development through the m6A methyltransferase-like 3 (METTL3). We observed that physO2 conditions significantly promote embryonic development, with higher expression levels of METTL3, global histone lactylation, and histone H3 lysine 18 lactylation (H3K18la) compared to atmosO2 exposure. Furthermore, the addition of lactate dehydrogenase inhibitors led to a decrease in global lactylation, which was accompanied by a significant reduction in METTL3 expression. Sequencing analysis of the METTL3 knockdown embryo revealed that the differentially expressed genes (DEGs) were primarily enriched in the ribosome, oxidative phosphorylation, thermogenesis, RNA degradation, and RNA polymerase pathways. These findings provide novel insights into the epigenetic regulatory mechanisms of histone lactylation during early embryonic development in livestock, highlighting potential molecular targets and strategies to enhance mammalian in vitro embryo production techniques.

Super RNA Pol II domains enhance minor ZGA through 3D interaction to ensure the integrity of major transcriptional waves in late-ZGA mammals

Zygotic genome activation (ZGA) occurs at distinct stages across mammals, with mice initiating ZGA at the 2-cell stage and bovines and humans activating the process in the 4- to 8-cell stages. RNA polymerase II (RNA Pol II) gradually initiates ZGA in mice, but regulation in late-ZGA species remains unclear. Here, RNA Pol II profiling in bovine embryos identified strong intergenic clusters that boost minor ZGA gene expression via chromatin interactions and are named super RNA Pol II domains (SPDs). CRISPRi perturbation of SPDs in bovine embryos decreases the expression of minor ZGA genes, whereas the knockdown of these genes disrupts major ZGA and embryogenesis. Rapid enhancement of minor ZGA genes also occurs in human embryos. Alternatively, mouse and porcine oocytes precociously express these minor ZGA genes without SPDs. Thus, SPDs appear to be an adaptation in bovine embryos, promoting minor ZGA gene expression to comparable levels as early-ZGA species, illuminating species-specific regulation of ZGA timing.

Epigenetic regulation in oogenesis and fetal development: insights into m6A modifications

The unique physiological structure of women has led to a variety of diseases that have attracted the attention of many people in recent years. Disturbances in the reproductive system microenvironment lead to the progression of various female tumours and pregnancy disorders. Numerous studies have shown that epigenetic modifications crucially influence both oogenesis and foetal development. m6A, a modification at the mRNA level, consists of three parts, namely, writers, erasers, and readers, which are involved in several biological functions, such as the nucleation and stabilisation of mRNAs, thereby regulating the development of reproductive system diseases. In this manuscript, we delineate the constituents of m6A, their biological roles, and advancements in understanding m6A within the maternal-foetal immunological context. In addition, we summarise the mechanism of m6A in gynaecological diseases and provide a new perspective for targeting m6A to delay the progression of reproductive system diseases in clinical practice.

METTL14-Induced M6A Methylation Increases G6pc Biosynthesis, Hepatic Glucose Production and Metabolic Disorders in Obesity

METTL14 dimerizes with METTL3 to install N6-methyladenosine (m6A) on mRNA (m6A writers). Subsequently, m6A readers bind to m6A-marked RNA to influence its metabolism. RNA m6A emerges to critically regulate multiple intracellular processes; however, there is a gap in our understanding of m6A in liver metabolism. Glucose-6-phosphatase catalytic subunit (G6pc) mediates hepatic glucose production (HGP) and serves as the gatekeeper for glycogenolysis and gluconeogenesis; however, G6pc regulation is not fully understood. Here, METTL14 is identified as a posttranscriptional regulator of G6pc. Liver METTL14, METTL3, and m6A-methylated G6pc mRNA are upregulated in mice with diet-induced obesity. Deletion of Mettl14 decreases, whereas overexpression of METTL14 increases, G6pc mRNA m6A in hepatocytes in vitro and in vivo. Five m6A sites are identified, and disruption of them (G6pcΔ 5A) blocks METTL14-induced m6A methylation of G6pcΔ 5A mRNA. METTL14 increases both stability and translation of G6pc but not G6pcΔ 5A mRNA. YTHDF1 and YTHDF3 but not YTHDF2 (m6A readers) bind to m6A-marked G6pc mRNA to increase its synthesis. Deletion of hepatic Mettl14 decreases gluconeogenesis in primary hepatocytes, liver slices, and mice. Hepatocyte-specific restoration of G6pc reverses defective HGP in Mettl14 knockout mice. These results unveil a METTL14/G6pc mRNA m6A/G6pc biosynthesis/HGP axis governing glucose metabolism in health and metabolic disease.

RNA G-quadruplex removal promotes a translational switch after meiosis resumption

Oocyte maturation-coupled mRNA post-transcriptional regulation is essential for the establishment of developmental potential. Previously, oocyte mRNA translation efficiencies focused on the trans-regulation of key RNA-binding protein (RBPs), rarely related to RNA structure. RNA G-quadruplexes (rG4s) are four-stranded RNA secondary structures involved in many different aspects of RNA metabolism. In this study, we have developed a low-input technique for rG4 detection (G4-LACE-seq) in mouse oocytes and found that rG4s were widely distributed in maternal transcripts, with enrichment in untranslated regions, and they underwent transcriptome-wide removal during meiotic maturation. The rG4-selective small-molecule ligand BYBX stabilized rG4s in the oocyte transcriptome and impaired spindle assembly and meiotic cell cycle progression. The proteomic spectrum results revealed that rG4 accumulation weakened the binding of a large number of RBPs to mRNAs, especially those associated with translational initiation. Ribosomal immunoprecipitation and translational reporter assays further proved that rG4s in the untranslated regions negatively affected the translational efficiency of key maternal mRNAs. Overexpression DEAH/RHA family helicase-36 partially reverses BYBX-induced oocyte developmental defects, suggesting its importance in rG4 regulation. Collectively, this study describes the distribution, dynamic changes, and regulation of rG4s in the mouse maternal transcriptome. Before meiosis resumption, a large number of rG4s in oocytes are necessary to maintain the translatome at a low level, and DHX36-mediated rG4 removal promotes a translational switch and is required for successful maternal-to-zygotic transition.

METTL3-dependent m6A RNA methylation regulates transposable elements and represses human naïve pluripotency through transposable element-derived enhancers

N 6-methyladenosine (m6A) is the most prevalent messenger RNA modification with diverse regulatory roles in mammalian cells. While its functions are well-documented in mouse embryonic stem cells (mESCs), its role in human pluripotent stem cells (hPSCs) remains to be fully explored. METTL3 is the main enzyme responsible for m6A deposition. Here, using a METTL3 inducible knockout (iKO) system, we uncovered that, unlike in mESCs, METTL3 was indispensable for hPSC maintenance. Importantly, loss of METTL3 caused significant upregulation of pluripotency factors including naïve pluripotency genes and failure to exit pluripotency, thus impairing stem cell differentiation towards both embryonic and extraembryonic cell lineages. Mechanistically, METTL3 iKO in hPSCs promoted expression and enhancer activities of two primate-specific transposable elements (TEs), SVA_D and HERVK/LTR5_Hs. At SVA_D elements, loss of METTL3 leads to reduced H3K9me3 deposition. On the other hand, the activation of LTR5_Hs in the METTL3 iKO cells is accompanied by increased chromatin accessibility and binding pluripotency factors. The activated SVA_D and LTR5_Hs elements can act as enhancers and promote nearby naïve gene expression by directly interacting with their promoters. Together these findings reveal that METTL3-dependent m6A RNA methylation plays critical roles in suppressing TE expression and in regulating the human pluripotency network.

Human oocyte quality and reproductive health

Declining female fertility is a health issue that has received broad global attention. Oocyte quality is the key limiting factor of female fertility, and key processes affecting oocyte quality involve the secretion of and response to hormones, ovarian function, oogenesis, oocyte maturation, and meiosis. However, compared with other species, the research and understanding of human oocyte quality and human reproductive health is limited. This review highlights our current understanding of the physiological factors and pathological factors related to human oocyte quality and discusses potential treatments. In terms of physiology, we discuss the regulation of the hypothalamic-pituitary-gonadal axis, granulosa cells, key subcellular structures, maternal mRNA homeostasis, the extracellular matrix, the maternal microenvironment, and multi-omics resources related to human oocyte quality. In terms of pathology, we review hypothalamic-pituitary-gonadal defects, ovarian dysfunction (including premature ovarian insufficiency and polycystic ovary syndrome), human oocyte development defects, and aging. In terms of the pathological aspects of human oocyte development and quality defects, nearly half of the reported pathogenic genes are involved in meiosis, while the remainder are involved in maternal mRNA regulation, the subcortical maternal complex, zona pellucida formation, ion channels, protein transport, and mitochondrial function. Furthermore, we outline the emerging scientific prospects and challenges for future explorations of the biological mechanisms behind infertility and the development of clinical treatments. This review seeks to deepen our understanding of the mechanisms regulating human oocyte quality and to provide novel insights into clinical female infertility characterized by defects in oocyte quality and oocyte development.

Epigenome dynamics in early mammalian embryogenesis

During early embryonic development in mammals, the totipotency of the zygote - which is reprogrammed from the differentiated gametes - transitions to pluripotency by the blastocyst stage, coincident with the first cell fate decision. These changes in cellular potency are accompanied by large-scale alterations in the nucleus, including major transcriptional, epigenetic and architectural remodelling, and the establishment of the DNA replication programme. Advances in low-input genomics and loss-of-function methodologies tailored to the pre-implantation embryo now enable these processes to be studied at an unprecedented level of molecular detail in vivo. Such studies have provided new insights into the genome-wide landscape of epigenetic reprogramming and chromatin dynamics during this fundamental period of pre-implantation development.

Lethal toxicity of metformin on zebrafish during early embryonic development by multi-omics analysis

Metformin is an antidiabetic drug used in type 2 diabetes as well as indicators in polycystic ovary syndrome (PCOS) and cancer. Due to their increase in popularity, high amounts of metformin are being released into aquatic environments. However, the toxic effect of metformin on embryonic development in aquatic organisms remains limited. Therefore, this study aimed to elucidate the lethal embryotoxicity of metformin and determine the underlying molecular pathways influencing embryonic development using a zebrafish model through multi-omics analysis. Metformin was microinjected into zebrafish embryos at the 1-cell stage with varying concentrations (50 mM, 100 mM, 200 mM, 400 mM, and 800 mM). From the results, hatching rates decreased in a dose dependent manner. Fetal malformation and mortality (LC50 = 339.8 mM) increased in a dose dependent manner. In situ hybridization of whole-embryo assays demonstrated that metformin exerts a significant impact on the initial stages of embryonic development, leading to aberrant differentiation of the germ layers, perturbed organogenesis, and delayed development. Furthermore, transcriptomics, metabolomics, and lipidomics were used to study the molecular mechanisms of embryonic toxicity. The results showed that the cell cycle, dorsoventral axis formation, and collecting duct acid secretion pathways were significantly altered in treated embryos. In brief, these results provide useful information on the lethal toxicity mechanism of metformin overdose and provide clues for further studies in humans.

N6-methyladenosine modification of host Hsc70 attenuates nucleopolyhedrovirus infection in the lepidopteran model insect Bombyx mori

N6-methyladenosine (m6A) is the most prevalent internal modification on mRNA and plays critical roles in various biological processes including virus infection. It has been shown that m6A methylation is able to regulate virus proliferation and host innate immunity in mammals and plants, however, this antiviral defense in insects is largely unknown. Here we investigated function of m6A and its associated methyltransferases in nucleopolyhedrovirus (BmNPV) infection in silkworm. We reported significant changes of m6A methyltransferases METTL3 and METTL14 upon BmNPV treatment. Knockdown of METTL3 and METTL14 enhanced BmNPV infection and promoted viral proliferation, whereas overexpression of these enzymes could prevent viral replication. Further study revealed that host heat shock cognate 70 (Hsc70) as a target gene of m6A would contribute to BmNPV proliferation. CRISPR-dCas9-targeted methylation of Hsc70 by METTL3/METTL14 decreased its expression and further attenuated BmNPV infection. Consistently, knockout of METTL3 in silkworm individuals by CRISPR-Cas9 reduced overall m6A levels, which led to rapid death of silkworms and increase of BmNPV upon virus infection likely due to upregulated expression of Hsc70. Collectively, these findings provided a novel insight into antiviral activity of m6A and demonstrated a distinct immune response via attenuating host Hsc70 expression to counteract BmNPV replication in lepidopteran silkworm.

Decoding N6-methyladenosine's dynamic role in stem cell fate and early embryo development: insights into RNA-chromatin interactions

N6-methyladenosine (m6A), a reversible and dynamic RNA modification, plays pivotal roles in regulating stem cell pluripotency and early embryogenesis. Disruptions in m6A homeostasis lead to profound developmental defects, impairing processes such as stem cell self-renewal, lineage specification, oocyte maturation, zygotic genome activation, and maternal RNA degradation after fertilization. Beyond its well-recognized roles in mRNA transport, stability, and translation, recent studies have highlighted m6A's critical role in transcriptional regulation through intricate RNA-chromatin interactions, notably involving chromatin-associated regulatory RNAs (carRNAs) and retrotransposon RNAs. This review delves into the dynamic regulatory landscape of m6A, highlighting its critical interplay with chromatin modifications, and explores its broader implications in stem cell biology and early embryonic development.

The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus

A fertilized egg is initially transcriptionally silent and relies on maternally provided factors to initiate development. For embryonic development to proceed, the oocyte-inherited cytoplasm and the nuclear chromatin need to be reprogrammed to create a permissive environment for zygotic genome activation (ZGA). During this maternal-to-zygotic transition (MZT), which is conserved in metazoans, transient totipotency is induced and zygotic transcription is initiated to form the blueprint for future development. Recent technological advances have enhanced our understanding of MZT regulation, revealing common themes across species and leading to new fundamental insights about transcription, mRNA decay and translation.

NAT10 regulates zygotic genome activation and the morula-to-blastocyst transition

As the first acetylated nucleoside to be discovered, N-acetyltransferase 10 (NAT10)-catalyzed RNA N4-acetylcytidine (ac4C) modification is involved in the occurrence of various diseases. However, the roles of RNA ac4C in preimplantation embryo development still need more detailed studies. Here, we analyzed the role of RNA ac4C in preimplanted embryonic development in mice through Nat10 siRNA microinjection and growing oocyte stage-specific Nat10 knockout (Zp3-Nat10lox/lox). We found that NAT10 was indispensable for both the morula-to-blastocyst transition and zygotic genome activation (ZGA). Nat10 knockdown by Nat10 siRNA microinjection caused most embryos to arrest at the morula stage, and the expression levels of NANOG and CDX2 were significantly decreased. Moreover, the mRNA stability of Nanog was also significantly decreased in morulae after Nat10 knockdown. Zp3-Nat10lox/lox female mice were completely sterile, and the embryos from Zp3-Nat10lox/lox females were arrested at the 2-cell stage. Both the degradation of maternal mRNA and ZGA were deficient in 2-cell embryos from Zp3-Nat10lox/lox females. In conclusion, our findings demonstrate that NAT10 is crucial for both ZGA and the morula-to-blastocyst transition processes during mouse preimplantation embryonic development.

Totipotent-like reprogramming: Molecular machineries and chemical manipulations

Embryonic stem cells (ESCs) exhibit remarkable pluripotency, possessing the dual abilities of self-renewal and differentiation into any cell type within the embryonic lineage. Among cultivated mouse ESCs, a subpopulation known as 2-cell-like cells (2CLCs) displays a transcriptomic signature reminiscent of the 2-cell embryonic stage, with the capacity to differentiate into both embryonic and extraembryonic tissues. These 2CLCs have served as an invaluable totipotent-like cell model for deciphering the cellular and molecular mechanisms underlying the establishment of totipotency. Accumulating evidence has indicated that a multitude of regulators including transcription factors, epigenetic modifications, and RNA regulators, exert crucial functions in the reprogramming of ESCs towards 2CLCs. In addition to 2CLCs, alternative totipotent-like cell types can be induced and maintained through the administration of single or combined chemical supplements, offering promising cell resources for regenerative medicine. In this review, we summarize the current advancements in the molecular regulations of 2CLCs and chemical manipulations of totipotent-like cells in mice, providing a foundation for understanding the regulatory networks underlying cell totipotency.

METTL3-mediated m6A modification regulates muscle development by promoting TM4SF1 mRNA degradation in P-body via YTHDF2

N6-methyladenosine (m6A), a well-known post-transcriptional modification, is implicated in diverse cellular and physiological processes. However, much remains unknown regarding the precise role and mechanism of m6A modification on muscle development. In this study, we make observation that the levels of m6A and METTL3 are markedly elevated during the differentiation phase (DM) compared to the growth phase (GM) in both C2C12 and bovine myoblasts. Notably, deletion of METTL3 decreased m6A levels, and promoted myoblast proliferation, inhibited myoblast differentiation in vitro. By performing m6A sequencing in both GM and DM myoblast, we further identified that TM4SF1 is involved in m6A -regulated muscle development. Mechanistically, METTL3 increases m6A-modified TM4SF1 transcripts, and subsequently YTHDF2 promotes TM4SF1 mRNA degradation in P-body through liquid-liquid phase separation (LLPS). Additionally, the rescue experiments in vivo showed that overexpressing METTL3 could rescue the attenuated myogenesis induced by TM4SF1 overexpression during muscle regeneration in mice. Collectively, our findings shed light on a regulatory mechanism by which m6A modulates muscle development and raise a new model for m6A-mediated mRNA degradation within P-bodies.

Lysosomal catabolic activity promotes the exit of murine totipotent 2-cell state by silencing early-embryonic retrotransposons

During mouse preimplantation development, a subset of retrotransposons/genes are transiently expressed in the totipotent 2-cell (2C) embryos. These 2C transcripts rapidly shut down their expression beyond the 2C stage of embryos, promoting the embryo to exit from the 2C stage. However, the mechanisms regulating this shutdown remain unclear. Here, we identified that lysosomal catabolism played a role in the exit of the totipotent 2C state. Our results showed that the activation of embryonic lysosomal catabolism promoted the embryo to exit from the 2C stage and suppressed 2C transcript expression. Mechanistically, our results indicated that lysosomal catabolism suppressed 2C transcripts through replenishing cellular amino-acid levels, thereby inactivating transcriptional factors TFE3/TFEB and abolishing their transcriptional activation of 2C retrotransposons, MERVL (murine endogenous retrovirus-L)/MT2_Mm. Collectively, our study identified that lysosomal activity modulated the transcriptomic landscape and development in mouse embryos and identified an unanticipated layer of transcriptional control on early-embryonic retrotransposons from lysosomal signaling.

Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation

The marking of DNA, histones, and RNA is central to gene expression regulation in development and disease. Recent evidence links N6-methyladenosine (m6A), installed on RNA by the METTL3-METTL14 methyltransferase complex, to histone modifications, but the link between m6A and DNA methylation remains scarcely explored. This study shows that METTL3-METTL14 recruits the DNA methyltransferase DNMT1 to chromatin for gene-body methylation. We identify a set of genes whose expression is fine-tuned by both gene-body 5mC, which promotes transcription, and m6A, which destabilizes transcripts. We demonstrate that METTL3-METTL14-dependent 5mC and m6A are both essential for the differentiation of embryonic stem cells into embryoid bodies and that the upregulation of key differentiation genes during early differentiation depends on the dynamic balance between increased 5mC and decreased m6A. Our findings add a surprising dimension to our understanding of how epigenetics and epitranscriptomics combine to regulate gene expression and impact development and likely other biological processes.

Epigenetic regulation in female reproduction: the impact of m6A on maternal-fetal health

With the development of public health, female diseases have become the focus of current concern. The unique reproductive anatomy of women leads to the development of gynecological diseases gradually become an important part of the socio-economic burden. Epigenetics plays an irreplaceable role in gynecologic diseases. As an important mRNA modification, m6A is involved in the maturation of ovum cells and maternal-fetal microenvironment. At present, researchers have found that m6A is involved in the regulation of gestational diabetes and other reproductive system diseases, but the specific mechanism is not clear. In this manuscript, we summarize the components of m6A, the biological function of m6A, the progression of m6A in the maternal-fetal microenvironment and a variety of gynecological diseases as well as the progression of targeted m6A treatment-related diseases, providing a new perspective for clinical treatment-related diseases.

METTL3 improves the development of somatic cell nuclear transfer embryos through AURKB and H3S10ph in goats

Developmental abnormalities are more common in somatic cell nuclear transfer (SCNT) embryos due to epigenetic barriers that occur during the maternal-to-zygotic transition (MZT). N6-methyladenosine (m6A) is an RNA epigenetic modification that plays a significant role in numerous biological processes. However, the relationship between m6A and SCNT embryonic development is largely unexplored. In the present study, we found that the low expression of m6A methyltransferase-like 3 (METTL3) was associated with developmental arrest before zygotic genome activation (ZGA) in goat SCNT embryos and that karyokinesis defects were evident during their development. Notably, we demonstrated that METTL3 overexpression rescued the karyokinesis abnormalities, enhanced embryonic development and elevated the blastocyst formation rate. Further experiments revealed that METTL3 could mitigate the defects of maternal mRNA degradation, enhance the translation of Aurora kinase B (AURKB) and increase the phosphorylation of serine 10 on histone H3 (H3S10ph) to ensure the normal karyokinesis in SCNT embryos before ZGA in goats. Overall, our study highlights the essential role of METTL3 in enhancing the development of goat SCNT embryos. These findings indicate that METTL3 is critical for optimal SCNT efficiency and advance our understanding of m6A's role in embryonic development.

Embryonic Genome Activation (EGA) Occurred at 1-Cell Stage of Embryonic Development in the Mud Crab, Scylla paramamosain, Revealed by RNA-Seq

As a prerequisite for the success of embryo development, embryonic genome activation (EGA) is an important biological event in which zygotic gene products in the embryo are activated to replace maternal-derived transcripts. Although EGA has been extensively studied in a large number of vertebrates and invertebrates, there is a lack of information regarding this event in crustacean crab. In this study, the timing of EGA was confirmed by examining a transcriptomic dataset of early embryonic development, including mature oocytes and embryos through six early developmental stages, and signaling pathways associated with EGA were identified in the mud crab, S. paramamosain. The comprehensive transcriptomic data identified a total of 53,915 transcripts from these sequencing samples. Notable transcriptomic change was evident at the 1-cell stage, indicated by a 36% transcript number shift and a reduction in transcript fragment length, compared to those present in the mature oocytes. Concurrently, a substantial increase in the expression of newly transcribed transcripts was observed, with gene counts reaching 3485 at the 1-cell stage, indicative of the onset of EGA. GO functional enrichment revealed key biological processes initiated at the 1-cell stage, such as protein complex formation, protein metabolism, and various biosynthetic processes. KEGG analysis identified several critical signaling pathways activated during EGA, including the "cell cycle," "spliceosome," "RNA degradation", and "RNA polymerase", pathways. Furthermore, transcription factor families, including zinc finger, T-box, Nrf1, and Tub were predominantly enriched at the 1-cell stage, suggesting their pivotal roles in regulating embryonic development through the targeting of specific DNA sequences during the EGA process. This groundbreaking study not only addresses a significant knowledge gap regarding the developmental biology of S. paramamosain, especially for the understanding of the mechanism underlying EGA, but also provides scientific data crucial for the research on the individual synchronization of seed breeding within S. paramamosain aquaculture. Additionally, it serves as a reference basis for the study of early embryonic development in other crustacean species.

m6A demethylase OsALKBH5 is required for double-strand break formation and repair by affecting mRNA stability in rice meiosis

N6-methyladenosine (m6A) RNA modification is the most prevalent messenger RNA (mRNA) modification in eukaryotes and plays critical roles in the regulation of gene expression. m6A is a reversible RNA modification that is deposited by methyltransferases (writers) and removed by demethylases (erasers). The function of m6A erasers in plants is highly diversified and their roles in cereal crops, especially in reproductive development essential for crop yield, are largely unknown. Here, we demonstrate that rice OsALKBH5 acts as an m6A demethylase required for the normal progression of male meiosis. OsALKBH5 is a nucleo-cytoplasmic protein, highly enriched in rice anthers during meiosis, that associates with P-bodies and exon junction complexes, suggesting that it is involved in regulating mRNA processing and abundance. Mutations of OsALKBH5 cause reduced double-strand break (DSB) formation, severe defects in DSB repair, and delayed meiotic progression, leading to complete male sterility. Transcriptome analysis and m6A profiling indicate that OsALKBH5-mediated m6A demethylation stabilizes the mRNA level of multiple meiotic genes directly or indirectly, including several genes that regulate DSB formation and repair. Our study reveals the indispensable role of m6A metabolism in post-transcriptional regulation of meiotic progression in rice.

RNA modifications: emerging players in the regulation of reproduction and development

The intricate world of RNA modifications, collectively termed the epitranscriptome, covers over 170 identified modifications and impacts RNA metabolism and, consequently, almost all biological processes. In this review, we focus on the regulatory roles and biological functions of a panel of dominant RNA modifications (including m 6A, m 5C, Ψ, ac 4C, m 1A, and m 7G) on three RNA types-mRNA, tRNA, and rRNA-in mammalian development, particularly in the context of reproduction as well as embryonic development. We discuss in detail how those modifications, along with their regulatory proteins, affect RNA processing, structure, localization, stability, and translation efficiency. We also highlight the associations among dysfunctions in RNA modification-related proteins, abnormal modification deposition and various diseases, emphasizing the roles of RNA modifications in critical developmental processes such as stem cell self-renewal and cell fate transition. Elucidating the molecular mechanisms by which RNA modifications influence diverse developmental processes holds promise for developing innovative strategies to manage developmental disorders. Finally, we outline several unexplored areas in the field of RNA modification that warrant further investigation.

METTL3 prevents granulosa cells mitophagy by regulating YTHDF2-mediated BNIP3 mRNA degradation due to arsenic exposure

The ovary is an important reproductive and endocrine organ for the continuation of the species and the homeostasis of the body's internal environment. Arsenic exposure is a global public health problem. However, the damage to the ovaries caused by exposure to arsenic-contaminated drinking water from neonatal mice period remains unclear. Here, we showed that arsenic exposure resulted in reduced granulosa cell proliferation, diminished ovarian reserve, decreased oogenesis, and endocrine disruption in mice. Mechanistically, arsenic exposure decreased the protein level of METTL3 in granulosa cells. The m6A modification levels of mitophagy regulated gene BNIP3 in 3'UTR region was decreased in arsenic exposed granulosa cells. Meanwhile, YTHDF2, which decays mRNA, bound to the 3'UTR region of BNIP3 was also decreased in arsenic exposed ovarian granulosa cells. Thus, BNIP3 mRNA becames more stable, and mitophagy was increased. The excessive mitophagy in granulosa cells led to endocrine disruption, follicular atresia and diminished ovarian reserve. In summary, our study reveals that METTL3-dependent m6A modification regulates granulosa cell mitophagy and follicular atresia by targeting BNIP3 which are induced by arsenic exposure.

ALKBH5 Reduces BMP15 mRNA Stability and Regulates Bovine Puberty Initiation Through an m6A-Dependent Pathway

The timing of puberty significantly influences subsequent reproductive performance in cattle. N6-methyladenosine (m6A) is a key epigenetic modification involved in the regulation of pubertal onset. However, limited research has investigated alterations in m6A methylation within the hypothalamic-pituitary-ovarian (HPO) axis during the onset of puberty. In this study, combined analysis of methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-seq) is used to describe the overall modification pattern of m6A in the HPO axis, while GSEA, KEGG, and GO analyses are used to describe the enrichment pathways of differentially expressed genes and differentially methylated genes. The m6A modifications of the differential genes KL, IGSF10, PAPPA2, and BMP15 and the pathways of cell adhesion molecules (CAMs), TGF-β, cell cycle, and steroid hormone synthesis may play roles in regulating the function of the HPO axis tissue during pubertal transition. Notably, BMP15's m6A modification depends on the action of the demethylase ALKBH5, which is recognized by the reader protein YTHDF2, promoting bovine granulosa cell proliferation, steroid production, and estrogen secretion. This study reveals for the first time the modification mechanism of BMP15 m6A during the initiation of bovine puberty, which will provide useful information for improving the reproductive efficiency of Chinese beef cattle.

The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility

The most common epigenetic modification of messenger RNAs (mRNAs) is N6-methyladenosine (m6A), which is mainly located near the 3' untranslated region of mRNAs, near the stop codons, and within internal exons. The biological effect of m6A is dynamically modulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). By controlling post-transcriptional gene expression, m6A has a significant impact on numerous biological functions, including RNA transcription, translation, splicing, transport, and degradation. Hence, m6A influences various physiological and pathological processes, such as spermatogenesis, oogenesis, embryogenesis, placental function, and human reproductive system diseases. During gametogenesis and embryogenesis, genetic material undergoes significant changes, including epigenomic modifications such as m6A. From spermatogenesis and oogenesis to the formation of an oosperm and early embryogenesis, m6A changes occur at every step. m6A abnormalities can lead to gamete abnormalities, developmental delays, impaired fertilization, and maternal-to-zygotic transition blockage. Both mice and humans with abnormal m6A modifications exhibit impaired fertility. In this review, we discuss the dynamic biological effects of m6A and its regulators on gamete and embryonic development and review the possible mechanisms of infertility caused by m6A changes. We also discuss the drugs currently used to manipulate m6A and provide prospects for the prevention and treatment of infertility at the epigenetic level.

Advanced paternal age exacerbates neuroinflammation in offspring via m6A modification-mediated intergenerational inheritance

BACKGROUND

The trend of postponing childbearing age is prevalent worldwide. Advanced paternal age (APA) is associated with adverse pregnancy outcomes and offspring health. However, the underlying mechanism by which paternal aging affects the risk of offspring neuropsychiatric disorders is unclear. Our study aims to explore the behavioral phenotypes and the pathologic epigenetic alterations of APA offspring inherited from aging sperm.

METHODS

Behavioral tests, ELISA assay, immunofluorescence and western blotting were performed on offspring mice. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA immunoprecipitation sequencing (RIP-seq) were used to investigate the modified N6-methyladenosine (m6A) profiles of paternal sperm and offspring hippocampus. Intervention of gene expression by lentivirus and adeno-associated virus in both vivo and vitro examined the potential therapeutic targets of intergenerational inherited neuroinflammation.

RESULTS

In our study, APA offspring exhibit cognitive impairment and autism-like behavior. An increase in neuroinflammation in APA offspring is associated with microglial overactivation, which manifests as abnormal morphology and augmented engulfment. MeRIP-seq of F0 sperm and F1 hippocampus reveal that Nr4a2 is hypermethylated with decreased expression in APA offspring involving in synaptic plasticity and microglial function. In addition, Ythdc1, an m6A reader protein, is markedly elevated in aging sperm and remains elevated in adult hippocampus of APA group. Enhanced Ythdc1 recognizes and suppresses the hypermethylated Nr4a2, thereby contributing to the abnormal phenotype in offspring. The overexpression of Ythdc1 triggers microglial activation in vitro and its suppression in the hippocampus of APA progeny alleviates behavioral aberrations and attenuates neuroinflammation.

CONCLUSION

Our study provides additional evidence of the abnormal behavioral phenotypes of APA offspring and reveals potential epigenetic inheritance signatures and targeted genes for future research.

N6-methyladenosine modification-tuned lipid metabolism controls skin immune homeostasis via regulating neutrophil chemotaxis

Disrupted N6-methyladenosine (m6A) modification modulates various inflammatory disorders. However, the role of m6A in regulating cutaneous inflammation remains elusive. Here, we reveal that the m6A and its methyltransferase METTL3 are down-regulated in keratinocytes in inflammatory skin diseases. Inducible deletion of Mettl3 in murine keratinocytes results in spontaneous skin inflammation and increases susceptibility to cutaneous inflammation with activation of neutrophil recruitment. Therapeutically, restoration of m6A alleviates the disease phenotypes in mice and suppresses inflammation in human biopsy specimens. We support a model in which m6A modification stabilizes the mRNA of the lipid-metabolizing enzyme ELOVL6 via the m6A reader IGF2BP3, leading to a rewiring of fatty acid metabolism with a reduction in palmitic acid accumulation and, consequently, suppressing neutrophil chemotaxis in cutaneous inflammation. Our findings highlight a previously unrecognized epithelial-intrinsic m6A modification-lipid metabolism pathway that is essential for maintaining epidermal and immune homeostasis and lay the basis for potential therapeutic targeting of m6A modulators to attenuate inflammatory skin diseases.

N6-methyladenosine dynamics in placental development and trophoblast functions, and its potential role in placental diseases

N6-methyladenosine (m6A) is the most abundant modification controlling RNA metabolism and cellular functions, but its roles in placental development are still poorly understood. Here, we characterized the synchronization of m6A modifications and placental functions by mapping the m6A methylome in human placentas (n = 3, each trimester), revealing that the dynamic patterns of m6A were associated with gene expression homeostasis and different biological pathways in placental development. Then, we generated trophoblast-specific knockout mice of Wtap, a critical component of methyltransferase complex, and demonstrated that Wtap was essential for trophoblast proliferation, placentation and perinatal growth. Further in vitro experiments which includes cell viability assays and series molecular binding assays demonstrated that WTAP-m6A-IGF2BP3 axis regulated the RNA stability and translation of Anillin (ANLN) and VEGFA, promoting trophoblast proliferation and secretion. Dysregulation of this regulatory axis was observed in placentas from pregnancies with fetal growth restriction (FGR) or preeclampsia, revealing the pathogenic effects of imbalanced m6A modifications. Therefore, our findings provide novel insights into the functions and regulatory mechanisms of m6A modifications in placental development and placental-related gestational diseases.

The regulatory role of m6A modification in the maintenance and differentiation of embryonic stem cells

As the most prevalent and reversible internal epigenetic modification in eukaryotic mRNAs, N 6-methyladenosine (m6A) post-transcriptionally regulates the processing and metabolism of mRNAs involved in diverse biological processes. m6A modification is regulated by m6A writers, erasers, and readers. Emerging evidence suggests that m6A modification plays essential roles in modulating the cell-fate transition of embryonic stem cells. Mechanistic investigation of embryonic stem cell maintenance and differentiation is critical for understanding early embryonic development, which is also the premise for the application of embryonic stem cells in regenerative medicine. This review highlights the current knowledge of m6A modification and its essential regulatory contribution to the cell fate transition of mouse and human embryonic stem cells.

Epigenetic modifications during embryonic development: Gene reprogramming and regulatory networks

The maintenance of normal pregnancy requires appropriate maturation and transformation of various cells, which constitute the microenvironmental regulatory network at the maternal-fetal interface. Interestingly, changes in the cellular components of the maternal-fetal immune microenvironment and the regulation of epigenetic modifications of the genome have attracted much attention. With the development of epigenetics (DNA and RNA methylation, histone modifications, etc.), new insights have been gained into early embryonic developmental stages (e.g., maternal-to-zygotic transition, MZT). Understanding the various appropriate modes of transcriptional regulation required for the early embryonic developmental process from the perspective of epigenetic modifications will help us to provide new targets and insights into the pathogenesis of embryonic failure during further natural fertilization. This review focuses on the loci of action of epigenetic modifications from the perspectives of female germ cell development and embryo development to provide new insights for personalized diagnosis and treatment of abortion.

RNA m6A modification regulates cell fate transition between pluripotent stem cells and 2-cell-like cells

N6-methyladenosine (m6A) exerts essential roles in early embryos, especially in the maternal-to-zygotic transition stage. However, the landscape and roles of RNA m6A modification during the transition between pluripotent stem cells and 2-cell-like (2C-like) cells remain elusive. Here, we utilised ultralow-input RNA m6A immunoprecipitation to depict the dynamic picture of transcriptome-wide m6A modifications during 2C-like transitions. We found that RNA m6A modification was preferentially enriched in zygotic genome activation (ZGA) transcripts and MERVL with high expression levels in 2C-like cells. During the exit of the 2C-like state, m6A facilitated the silencing of ZGA genes and MERVL. Notably, inhibition of m6A methyltransferase METTL3 and m6A reader protein IGF2BP2 is capable of significantly delaying 2C-like state exit and expanding 2C-like cells population. Together, our study reveals the critical roles of RNA m6A modification in the transition between 2C-like and pluripotent states, facilitating the study of totipotency and cell fate decision in the future.

Roles of N6-methyladenosine writers, readers and erasers in the mammalian germline

N6-methyladenosine (m6A) is the most abundant internal modification of mRNAs in eukaryotes. Numerous studies have shown that m6A plays key roles in many biological and pathophysiological processes, including fertility. The factors involved in m6A-dependent mRNA regulation include writers, which deposit the m6A mark, erasers, which remove it, and readers, which bind to m6A-modified transcripts and mediate the regulation of mRNA fate. Many of these proteins are highly expressed in the germ cells of mammals, and some have been linked to fertility disorders in human patients. In this review, we summarise recent findings on the important roles played by proteins involved in m6A biology in mammalian gametogenesis and fertility. Continued study of the m6A pathway in the mammalian germline will shed further light on the importance of epitranscriptomics in reproduction and may lead to effective treatment of human fertility disorders.

Size-Optimized Layered Double Hydroxide Nanoparticles Promote Neural Progenitor Cells Differentiation of Embryonic Stem Cells Through the Regulation of M6A Methylation

Purpose

The committed differentiation fate regulation has been a difficult problem in the fields of stem cell research, evidence showed that nanomaterials could promote the differentiation of stem cells into specific cell types. Layered double hydroxide (LDH) nanoparticles possess the regulation function of stem cell fate, while the underlying mechanism needs to be investigated. In this study, the process of embryonic stem cells (ESCs) differentiate to neural progenitor cells (NPCs) by magnesium aluminum LDH (MgAl-LDH) was investigated.

Methods

MgAl-LDH with diameters of 30, 50, and 100 nm were synthesized and characterized, and their effects on the cytotoxicity and differentiation of NPCs were detected in vitro. Dot blot and MeRIP-qPCR were performed to detect the level of m6A RNA methylation in nanoparticles-treated cells.

Results

Our work displayed that LDH nanoparticles of three different sizes were biocompatible with NPCs, and the addition of MgAl-LDH could significantly promote the process of ESCs differentiate to NPCs. 100 nm LDH has a stronger effect on promoting NPCs differentiation compared to 30 nm and 50 nm LDH. In addition, dot blot results indicated that the enhanced NPCs differentiation by MgAl-LDH was closely related to m6A RNA methylation process, and the major modification enzyme in LDH controlled NPCs differentiation may be the m6A RNA methyltransferase METTL3. The upregulated METTL3 by LDH increased the m6A level of Sox1 mRNA, enhancing its stability.

Conclusion

This work reveals that MgAl-LDH nanoparticles can regulate the differentiation of ESCs into NPCs by increasing m6A RNA methylation modification of Sox1.

DNA methylation regulates RNA m6A modification through transcription factor SP1 during the development of porcine somatic cell nuclear transfer embryos

Epigenetic modifications play critical roles during somatic cell nuclear transfer (SCNT) embryo development. Whether RNA N6-methyladenosine (m6A) affects the developmental competency of SCNT embryos remains unclear. Here, we showed that porcine bone marrow mesenchymal stem cells (pBMSCs) presented higher RNA m6A levels than those of porcine embryonic fibroblasts (pEFs). SCNT embryos derived from pBMSCs had higher RNA m6A levels, cleavage, and blastocyst rates than those from pEFs. Compared with pEFs, the promoter region of METTL14 presented a hypomethylation status in pBMSCs. Mechanistically, DNA methylation regulated METTL14 expression by affecting the accessibility of transcription factor SP1 binding, highlighting the role of the DNA methylation/SP1/METTL14 pathway in donor cells. Inhibiting the DNA methylation level in donor cells increased the RNA m6A level and improved the development efficiency of SCNT embryos. Overexpression of METTL14 significantly increased the RNA m6A level in donor cells and the development efficiency of SCNT embryos, whereas knockdown of METTL14 suggested the opposite result. Moreover, we revealed that RNA m6A-regulated TOP2B mRNA stability, translation level, and DNA damage during SCNT embryo development. Collectively, our results highlight the crosstalk between RNA m6A and DNA methylation, and the crucial role of RNA m6A during nuclear reprogramming in SCNT embryo development.

RNA m6A modification, signals for degradation or stabilisation?

The RNA modification N6-methyladenosine (m6A) is conserved across eukaryotes, and profoundly influences RNA metabolism, including regulating RNA stability. METTL3 and METTL14, together with several accessory components, form a 'writer' complex catalysing m6A modification. Conversely, FTO and ALKBH5 function as demethylases, rendering m6A dynamic. Key to understanding the functional significance of m6A is its 'reader' proteins, exemplified by YTH-domain-containing proteins (YTHDFs) canonical reader and insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) non-canonical reader. These proteins play a crucial role in determining RNA stability: YTHDFs mainly promote mRNA degradation through different cytoplasmic pathways, whereas IGF2BPs function to maintain mRNA stability. Additionally, YTHDC1 functions within the nucleus to degrade or protect certain m6A-containing RNAs, and other non-canonical readers also contribute to RNA stability regulation. Notably, m6A regulates retrotransposon LINE1 RNA stability and/or transcription via multiple mechanisms. However, conflicting observations underscore the complexities underlying m6A's regulation of RNA stability depending upon the RNA sequence/structure context, developmental stage, and/or cellular environment. Understanding the interplay between m6A and other RNA regulatory elements is pivotal in deciphering the multifaceted roles m6A plays in RNA stability regulation and broader cellular biology.

Single-cell m6A mapping in vivo using picoMeRIP-seq

Current N6-methyladenosine (m6A) mapping methods need large amounts of RNA or are limited to cultured cells. Through optimized sample recovery and signal-to-noise ratio, we developed picogram-scale m6A RNA immunoprecipitation and sequencing (picoMeRIP-seq) for studying m6A in vivo in single cells and scarce cell types using standard laboratory equipment. We benchmark m6A mapping on titrations of poly(A) RNA and embryonic stem cells and in single zebrafish zygotes, mouse oocytes and embryos.

Mycobacterium tuberculosis inhibits METTL14-mediated m6A methylation of Nox2 mRNA and suppresses anti-TB immunity

Internal N6-methyladenosine (m6A) modifications are among the most abundant modifications of messenger RNA, playing a critical role in diverse biological and pathological processes. However, the functional role and regulatory mechanism of m6A modifications in the immune response to Mycobacterium tuberculosis infection remains unknown. Here, we report that methyltransferase-like 14 (METTL14)-dependent m6A methylation of NAPDH oxidase 2 (Nox2) mRNA was crucial for the host immune defense against M. tuberculosis infection and that M. tuberculosis-secreted antigen EsxB (Rv3874) inhibited METTL14-dependent m6A methylation of Nox2 mRNA. Mechanistically, EsxB interacted with p38 MAP kinase and disrupted the association of TAB1 with p38, thus inhibiting the TAB1-mediated autophosphorylation of p38. Interaction of EsxB with p38 also impeded the binding of p38 with METTL14, thereby inhibiting the p38-mediated phosphorylation of METTL14 at Thr72. Inhibition of p38 by EsxB restrained liquid-liquid phase separation (LLPS) of METTL14 and its subsequent interaction with METTL3, preventing the m6A modification of Nox2 mRNA and its association with the m6A-binding protein IGF2BP1 to destabilize Nox2 mRNA, reduce ROS levels, and increase intracellular survival of M. tuberculosis. Moreover, deletion or mutation of the phosphorylation site on METTL14 impaired the inhibition of ROS level by EsxB and increased bacterial burden or histological damage in the lungs during infection in mice. These findings identify a previously unknown mechanism that M. tuberculosis employs to suppress host immunity, providing insights that may empower the development of effective immunomodulators that target M. tuberculosis.

METTL3 and METTL14-mediated N6-methyladenosine modification of SREBF2-AS1 facilitates hepatocellular carcinoma progression and sorafenib resistance through DNA demethylation of SREBF2

As the most prevalent epitranscriptomic modification, N6-methyladenosine (m6A) shows important roles in a variety of diseases through regulating the processing, stability and translation of target RNAs. However, the potential contributions of m6A to RNA functions are unclear. Here, we identified a functional and prognosis-related m6A-modified RNA SREBF2-AS1 in hepatocellular carcinoma (HCC). The expression of SREBF2-AS1 and SREBF2 in HCC tissues and cells was measured by RT-qPCR. m6A modification level of SREBF2-AS1 was measured by methylated RNA immunoprecipitation assay. The roles of SREBF2-AS1 in HCC progression and sorafenib resistance were investigated by proliferation, apoptosis, migration, and cell viability assays. The regulatory mechanisms of SREBF2-AS1 on SREBF2 were investigated by Chromatin isolation by RNA purification, RNA immunoprecipitation, CUT&RUN, and bisulfite DNA sequencing assays. Our findings showed that the expression of SREBF2-AS1 was increased in HCC tissues and cells, and positively correlated with poor survival of HCC patients. m6A modification level of SREBF2-AS1 was also increased in HCC and positively correlated with poor prognosis of HCC patients. METTL3 and METTL14-induced m6A modification upregulated SREBF2-AS1 expression through increasing SREBF2-AS1 transcript stability. Functional assays showed that only m6A-modified, but not non-modified SREBF2-AS1 promoted HCC progression and sorafenib resistance. Mechanistic investigations revealed that m6A-modified SREBF2-AS1 bound and recruited m6A reader FXR1 and DNA 5-methylcytosine dioxygenase TET1 to SREBF2 promoter, leading to DNA demethylation at SREBF2 promoter and the upregulation of SREBF2 transcription. Functional rescue assays showed that SREBF2 was the critical mediator of the oncogenic roles of SREBF2-AS1 in HCC. Together, this study showed that m6A-modified SREBF2-AS1 exerted oncogenic roles in HCC through inducing DNA demethylation and transcriptional activation of SREBF2, and suggested m6A-modified SREBF2-AS1 as a prognostic biomarker and therapeutic target for HCC.

Transition from totipotency to pluripotency in mice: insights into molecular mechanisms

Totipotency is the ability of a single cell to develop into a full organism and, in mammals, is strictly associated with the early stages of development following fertilization. This unlimited developmental potential becomes quickly restricted as embryonic cells transition into a pluripotent state. The loss of totipotency seems a consequence of the zygotic genome activation (ZGA), a process that determines the switch from maternal to embryonic transcription, which in mice takes place following the first cleavage. ZGA confers to the totipotent cell a transient transcriptional profile characterized by the expression of stage-specific genes and a set of transposable elements that prepares the embryo for subsequent development. The timely silencing of this transcriptional program during the exit from totipotency is required to ensure proper development. Importantly, the molecular mechanisms regulating the transition from totipotency to pluripotency have remained elusive due to the scarcity of embryonic material. However, the development of new in vitro totipotent-like models together with advances in low-input genome-wide technologies, are providing a better mechanistic understanding of how this important transition is achieved. This review summarizes the current knowledge on the molecular determinants that regulate the exit from totipotency.

Oocyte Aging: A Multifactorial Phenomenon in A Unique Cell

The oocyte is considered to be the largest cell in mammalian species. Women hoping to become pregnant face a ticking biological clock. This is becoming increasingly challenging as an increase in life expectancy is accompanied by the tendency to conceive at older ages. With advancing maternal age, the fertilized egg will exhibit lower quality and developmental competence, which contributes to increased chances of miscarriage due to several causes such as aneuploidy, oxidative stress, epigenetics, or metabolic disorders. In particular, heterochromatin in oocytes and with it, the DNA methylation landscape undergoes changes. Further, obesity is a well-known and ever-increasing global problem as it is associated with several metabolic disorders. More importantly, both obesity and aging negatively affect female reproduction. However, among women, there is immense variability in age-related decline of oocytes' quantity, developmental competence, or quality. Herein, the relevance of obesity and DNA-methylation will be discussed as these aspects have a tremendous effect on female fertility, and it is a topic of continuous and widespread interest that has yet to be fully addressed for the mammalian oocyte.

Regulation of endogenous retroviruses in murine embryonic stem cells and early embryos

Endogenous retroviruses (ERVs) are important components of transposable elements that constitute ∼40% of the mouse genome. ERVs exhibit dynamic expression patterns during early embryonic development and are engaged in numerous biological processes. Therefore, ERV expression must be closely monitored in cells. Most studies have focused on the regulation of ERV expression in mouse embryonic stem cells (ESCs) and during early embryonic development. This review touches on the classification, expression, and functions of ERVs in mouse ESCs and early embryos and mainly discusses ERV modulation strategies from the perspectives of transcription, epigenetic modification, nucleosome/chromatin assembly, and post-transcriptional control.

A review on the role of RNA methylation in aging-related diseases

Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.

Emerging Roles of RNA Methylation in Development

ConspectusMore than 170 different types of chemical modifications have been identified on diverse types of RNA, collectively known as the epitranscriptome. Among them, N6-methyladenine (m6A), 5-methylcytosine (m5C), N1-methyladenine (m1A), and N7-methylguanosine (m7G) as the ubiquitous post-transcriptional modification are widely involved in regulating the metabolic processes such as RNA degradation, translation, stability, and export, mediating important physiological and pathological processes such as stress regulation, immune response, development, and tumorigenesis. Recently, the regulatory role of RNA modification during developmental processes is getting more attention. Therefore, the development of low-input even single-cell and high-resolution sequencing technologies is crucial for the exploration of the regulatory roles of RNA modifications in these important biological events of trace samples.This account focuses on the roles of RNA modifications in various developmental processes. We describe the distribution characteristics of various RNA modifications, catalytic enzymes, binding proteins, and the development of sequencing technologies. RNA modification is dynamically reversible, which can be catalyzed by methyltransferases and eliminated by demethylases. RNA m6A is the most abundant post-transcriptional modification on eukaryote mRNA, which is mainly concentrated near the stop codon, and involves in RNA metabolism regulation. RNA m5C, another most studied RNA modification, has been identified in a various of organisms and RNA species, mainly enriched in the regions downstream of translation initiation sites and broadly distributes across the whole coding sequence (CDS) in mammalian mRNAs. RNA m1A, with a lower abundance than m6A, is widely distributed in various RNA types, mainly locates in the 5' untranslated region (5'UTR) of mRNA and regulates translation. RNA m7G, one of the most common RNA modifications in eukaryotes, has been identified at cap regions and internal positions of RNAs and recently gained considerable attention.Thanks to the development of sequencing technology, m6A has been found to regulate the tumorigenic process, including tumor proliferation, invasion, and metastasis by modulating oncogenes and tumor suppressor genes, and affect oocyte maturation and embryonic development through regulating maternal and zygotic genes. m5C related proteins have been identified to participate in embryonic development, plant growth, and neural stem cell differentiation in a m5C dependent manner. m1A also has been revealed to be involved in these developmental processes. m7G dysregulation mainly involves in neurodevelopmental disorders and neurodegenerative diseases.Collectively, we summarized the gradually exhibited roles of RNA methylation during development, and discussed the possibility of RNA modifications as candidate biomarkers and potential therapeutic targets. The technological development is anticipated as the major driving force to expand our knowledge in this field.