Mechanisms Of Gene Regulation Research Articles

Changes in RNA Splicing: A New Paradigm of Transcriptional Responses to Probiotic Action in the Mammalian Brain

Elucidating the gene regulatory mechanisms underlying the gut–brain axis is critical for uncovering novel gut–brain interaction pathways and developing therapeutic strategies for gut bacteria-associated neurological disorders. Most studies have primarily investigated how gut bacteria modulate host epigenetics and gene expression; their impact on host alternative splicing, particularly in the brain, remains largely unexplored. Here, we investigated the effects of the gut-associated probiotic Lacidofil® on alternative splicing across 10 regions of the rat brain using published RNA-sequencing data. The Lacidofil® altogether altered 2941 differential splicing events, predominantly, skipped exon (SE) and mutually exclusive exon (MXE) events. Protein–protein interactions and a KEGG analysis of differentially spliced genes (DSGs) revealed consistent enrichment in the spliceosome and vesicle transport complexes, as well as in pathways related to neurodegenerative diseases, synaptic function and plasticity, and substance addiction across brain regions. Using the PsyGeNET platform, we found that DSGs from the locus coeruleus (LConly), medial preoptic area (mPOA), and ventral dentate gyrus (venDG) were enriched in depression-associated or schizophrenia-associated genes. Notably, we highlight the App gene, where Lacidofil® precisely regulated the splicing of two exons causally involved in amyloid β protein-based neurodegenerative diseases. Although the splicing factors exhibited both splicing plasticity and expression plasticity in response to Lacidofil®, the overlap between DSGs and differentially expressed genes (DEGs) in most brain regions was rather low. Our study provides novel mechanistic insight into how gut probiotics might influence brain function through the modulation of RNA splicing.

A cardiac transcriptional enhancer is repurposed during regeneration to activate an anti-proliferative program.

Zebrafish have a high capacity to regenerate their hearts. Several studies have surveyed transcriptional enhancers to understand how gene expression is controlled during heart regeneration. We have identified REN or the runx1 enhancer that during regeneration regulates the expression of the nearby runx1 gene. We show that runx1 mRNA is reduced with deletion of REN (ΔREN) and cardiomyocyte proliferation is enhanced ΔREN mutants only during regeneration. Interestingly, in uninjured hearts, ΔREN mutants have reduced expression of adamts1, a nearby gene that encodes a Collagen protease. This results in excess Collagen within cardiac valves of uninjured hearts. The ΔREN Collagen phenotype is rescued by an allele with Δrunx1 mutations, suggesting that in uninjured hearts REN regulates adamts1 independently of runx1. Taken together, this suggests that REN is rewired from adamts1 in uninjured hearts to stimulate runx1 transcription during regeneration. Our data point to a previously unappreciated mechanism for gene regulation during zebrafish heart regeneration. We report that an enhancer is rewired from expression in a distal cardiac domain to activate a different gene in regenerating tissue.

An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast.

Tissue development relies on the coordinated differentiation of stem cells in dynamically changing environments. The formation of the vertebrate neural tube from stem cells in the caudal lateral epiblast (CLE) is a well characterized example. Despite an understanding of the signalling pathways involved, the gene regulatory mechanisms remain poorly defined. To address this, we developed a multiplexed in vivo CRISPR screening approach in chick embryos targeting genes expressed in the caudal epiblast and neural tube. This revealed a role for MLLT3, a component of the super elongation complex, in the specification of neural fate. Perturbation of MLLT3 disrupted neural tube morphology and reduced neural fate acquisition. Mutant forms of Retinoic Acid Receptor A lacking the MLLT3 binding domain similarly reduced neural fate acquisition. Together, these findings validate an in vivo CRISPR screen strategy in chick embryos and identify a previously unreported role for MLLT3 in caudal neural tissue specification.

Nuclear Argonaute protein NRDE-3 switches small RNA partners during embryogenesis to mediate temporal-specific gene regulatory activity.

RNA interference (RNAi) is a conserved gene regulation mechanism that utilizes the Argonaute protein and their associated small RNAs to exert regulatory function on complementary transcripts. While the majority of germline-expressed RNAi pathway components reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here we find that the small RNA biogenesis machinery is spatially and temporally organized during embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. We also observe that many other RNAi factors form foci in embryonic cells distinct from "SIMR granules", including the Argonaute protein CSR-1, underscoring a potential role for cytoplasmic concentrates of RNAi factors to promote gene regulation in embryos. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. Prior work has shown that NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.

Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging.

Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.

Maternal obesity alters histone modifications mediated by the interaction between Ezh2 and Ampk, impairing neural differentiation in the developing embryonic brain cortex.

Neurodevelopmental disorders have complex origins that manifest early during embryonic growth and are associated with intricate gene regulation dynamics. A perturbed metabolic environment such as hyperglycemia or dyslipidemia, particularly due to maternal obesity, poses a threat to the optimal development of the embryonic central nervous system. Accumulating evidence suggests that these metabolic irregularities during pregnancy may alter neurogenesis pathways, thereby predisposing the developing fetus to neurodevelopmental disorders. One primary mechanism through which such disruptions may occur involves changes in histone modifications resulting from fluctuations in the expression of histone-modifying enzymes or the availability of their substrates. Herein, we have used a rat model of maternal obesity induced by a high-fat diet (HFD) before and during gestation to investigate the cellular and molecular repercussions of maternal obesity on embryonic cortical neurogenesis. Maternal obesity impairs neurogenesis by reducing cell proliferation, increasing neuronal marker expression, and shifting development toward astrogliogenesis. Differentially expressed genes (DEGs) revealed disruptions in key developmental signaling pathways and reduced Akt phosphorylation, particularly at E14.5. These changes were associated with epigenetic alterations, mainly the differential expression and phosphorylation of Ezh2 and subsequent changes in global histone modifications. ChIP-seq revealed reduced H3K27me3 at genes upregulated due to maternal obesity, which could have resulted from reduced expression and increased phosphorylation of Ezh2 at Thr311. Interestingly, Ezh2 also showed increased O-GlcNAcylation in HFD embryos along with increased association with Ampk-Thr172 in accordance with previous studies showing that Ampk catalyzes Ezh2-Thr311p. These results suggest that an epigenetic gene regulatory mechanism mediated by Ampk and Ezh2 interactions resulted in reduced H3K27me3 and de-repression of key developmental genes, which could have led to cell fate changes observed in the developing embryo brain cortex due to maternal obesity.

AKT-FoxO1-PCK/ChREBP signaling pathway regulates metabolic liver disease induced by high glucose in largemouth bass.

Starch is widely used in aquaculture because of its low price and the advantages for processing expanded feed. Largemouth bass are naturally type 2 diabetic and intolerant to dietary carbohydrates. In this study, we found that the phosphorylation of AKT and FoxO1 were down-regulated in the fish suffering from metabolic liver disease (MLD). High glucose (25mM) stimulation in hepatocytes significantly reduced AKT and FoxO1 phosphorylation level, while enhancing glycolysis and gluconeogenesis enzyme activities, leading to acute glucose metabolism disorder. However, after treatment of insulin or FoxO1 inhibitor, the related parameters returned to control level. The mRNA levels of ChREBP and lipid synthesis genes were increased after high glucose stimulation, and then decreased after adding FoxO1 inhibitor, accompanied by a reduction of TG content. Furtherly, plasmid transfection, dual-luciferase reporter assay experiments and EMSA proved that AKT positively regulated the phosphorylation of FoxO1 and FoxO1 positively regulated the promoter activities of PCK and ChREBP, and the transcription factor binding sites were found. In summary, these results support a critical role of AKT-FoxO1-PCK/ChREBP signaling pathway in regulating the occurrence of MLD in largemouth bass. Moreover, we identified a novel FoxO1-mediated gene regulation mechanism, revealing a previously unrecognized cross-talk between FoxO1 and ChREBP.

Fisetin Alleviates d-Galactose-Induced Senescence in C2C12 Myoblasts: Metabolic and Gene Regulatory Mechanisms.

Skeletal muscle aging poses a major threat to the health and quality of life of elderly individuals. Fisetin, a natural polyphenolic compound, exhibits various biological activities; however, its role in preventing skeletal muscle cell aging is still unclear. This study aimed to elucidate the effects of fisetin on skeletal muscle aging using a d-galactose-induced C2C12 myoblast senescence model. Fisetin treatment effectively ameliorated d-galactose-induced aging damage and restored cellular functionality by improving cell viability, reducing the accumulation of the senescence marker enzyme SA-β-gal, and decreasing the expression of key aging marker proteins, p16 and p53. NMR-based metabolomics and RNA-seq transcriptomics analyses revealed that fisetin regulates several critical metabolic pathways, including glutathione metabolism, glycine, serine and threonine metabolism, as well as taurine and hypotaurine metabolism. This regulation led to the restoration of amino acid metabolism, stabilization of cellular energy homeostasis, and the preservation of membrane integrity. In addition, fisetin inhibited calcium signaling and JAK-STAT pathways, reduced cellular stress responses and reversed senescence-induced cell cycle arrest. Together, these findings highlight the potential of fisetin as a therapeutic agent to combat skeletal muscle aging and restore cellular homeostasis, offering a promising avenue for the development of antiaging treatments for skeletal muscle degeneration.

Learning Enhancer-Gene associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT.

To reveal gene regulation mechanisms, it is essential to understand the role of regulatory elements, which are possibly distant from gene promoters. Integrative analysis of epigenetic and transcriptomic data can be used to gain insights into gene-expression regulation in specific phenotypes. Here, we discuss STITCHIT, an approach to dissect epigenetic variation in a gene-specific manner across many samples for the identification of regulatory elements without relying on peak calling algorithms. The obtained genomic regions are then further refined using a regularized linear model approach, which can also be used to predict gene expression. We illustrate the use of STITCHIT using H3k27ac ChIP-seq and RNA-seq data from the International Human Epigenome Consortium (IHEC).

CELL REJUVENATION AND DISEASE

Abstract Aging is characterized by the functional decline of tissues and organs and the increased risk of aging-associated disorders. Different rejuvenating interventions have been proposed to delay aging and the onset of age-associated decline and disease to extend healthspan and lifespan. These interventions include metabolic manipulation, heterochronic parabiosis, pharmaceutical administration and senescent cell ablation. As disease and aging are associated with altered epigenetic mechanisms of gene regulation, such as DNA methylation, histone modification and chromatin remodelling, and non-coding RNAs, the manipulation of these mechanisms might be central to the effectiveness of treating disease as well as age-delaying interventions. I will discuss some of the epigenetic changes that occur during disease and aging and how partial reprogramming by the Yamanaka factors might be a potential avenue to restore cell health and resilience through cellular rejuvenation programming to reverse disease, injury, and the disabilities that can occur throughout life.

Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding.

The P-glycoprotein efflux pump, encoded by the MDR1 gene, is an ATP-driven transporter capable of expelling a diverse array of compounds from cells. Overexpression of this protein is implicated in the multi-drug resistant phenotype observed in various cancers. Numerous studies have attempted to decipher the impact of genetic variants within MDR1 on P-glycoprotein expression, functional activity, and clinical outcomes in cancer patients. Among these, three specific single nucleotide polymorphisms-T1236C, T2677G, and T3435C - have been the focus of extensive research efforts, primarily through in vitro cell line models and clinical cohort analyses. However, the findings from these studies have been remarkably contradictory. In this study, we employ a computational, data-driven approach to systematically evaluate the effects of these three variants on principal stages of the gene expression process. Leveraging current knowledge of gene regulatory mechanisms, we elucidate potential mechanisms by which these variants could modulate P-glycoprotein levels and function. Our findings suggest that all three variants significantly change the mRNA folding in their vicinity. This change in mRNA structure is predicted to increase local translation elongation rates, but not to change the protein expression. Nonetheless, the increased translation rate near T3435C is predicted to affect the protein's co-translational folding trajectory in the region of the second ATP binding domain. This potentially impacts P-glycoprotein conformation and function. Our study demonstrates the value of computational approaches in elucidating the functional consequences of genetic variants. This framework provides new insights into the molecular mechanisms of MDR1 variants and their potential impact on cancer prognosis and treatment resistance. Furthermore, we introduce an approach which can be systematically applied to identify mutations potentially affecting mRNA folding in pathology. We demonstrate the utility of this approach on both ClinVar and TCGA and identify hundreds of disease related variants that modify mRNA folding at essential positions.

Transcriptional regulation of the piRNA pathway by Ovo in animal ovarian germ cells.

The gene-regulatory mechanisms controlling the expression of the germline PIWI-interacting RNA (piRNA) pathway components within the gonads of metazoan species remain largely unexplored. In contrast to the male germline piRNA pathway, which in mice is known to be activated by the testis-specific transcription factor A-MYB, the nature of the ovary-specific gene-regulatory network driving the female germline piRNA pathway remains a mystery. Here, using Drosophila as a model, we combined multiple genomics approaches to reveal the transcription factor Ovo as regulator of the germline piRNA pathway in ovarian germ cells. Ectopic expression of Ovo in ovarian somatic cells activates germline piRNA pathway components, including the ping-pong factors Aubergine, Argonaute-3, and Vasa, leading to assembly of perinuclear cellular structures resembling nuage bodies of germ cells. We found that in ovarian somatic cells, transcription of ovo is repressed by l(3)mbt, thus preventing expression of germline piRNA pathway genes in the soma. Cross-species ChIP-seq and motif analyses demonstrate that Ovo is binding to genomic CCGTTA motifs within the promoters of germline piRNA pathway genes, suggesting a regulation by Ovo in ovaries analogous to that of A-MYB in testes. Our results also show consistent engagement of the Ovo transcription factor family at ovarian piRNA clusters across metazoan species, reflecting a deep evolutionary conservation of this regulatory paradigm from insects to humans.

Metabolic labeling of RNA using ribonucleoside analogs enables the evaluation of RNA synthesis and degradation rates.

Long noncoding RNAs (lncRNAs) are transcripts exceeding 200 nucleotides that do not encode proteins. Despite lacking protein-coding capabilities, lncRNAs play crucial roles in cellular processes, including gene-expression modulation and structural maintenance. The study of lncRNAs has evolved significantly since 2009, with advancements in analytical methodologies providing new insights into their functions and dynamics. Key developments include BRIC-Seq, SLAM-Seq, TUC-Seq, TimeLapse-seq, and Dyrec-Seq. These methodologies have enabled researchers to investigate lncRNA behavior under various conditions, including cellular stress responses and complex biologic systems. Future challenges include developing comprehensive techniques for identifying lncRNA-interacting proteins and advancing in vivo methodologies using model organisms. As the field progresses, integrating these technologies will enhance our understanding of lncRNA biology, potentially leading to novel therapeutic strategies and deeper insights into gene-regulation mechanisms.

Plant response to intermittent heat stress involves modulation of mRNA translation efficiency.

Acquired thermotolerance (also known as priming) is the ability of cells or organisms to survive acute heat stress if preceded by a milder one. In plants, acquired thermotolerance has been studied mainly at the transcriptional level, including recent descriptions of sophisticated regulatory circuits that are essential for this learning capacity. Here, we tested the involvement of polysome-related processes (translation and cotranslational mRNA decay (CTRD)) in Arabidopsis (Arabidopsis thaliana) thermotolerance using two heat stress regimes with and without a priming event. We found that priming is essential to restore the general translational potential of plants shortly after acute heat stress. We observed that mRNAs not involved in heat stress suffered from reduced translation efficiency at high temperatures, whereas heat stress-related mRNAs were translated more efficiently under the same condition. We also showed that the induction of the unfolded protein response (UPR) pathway in acute heat stress is favored by a previous priming event and that, in the absence of priming, ER-translated mRNAs become preferential targets of CTRD. Finally, we present evidence that CTRD can specifically regulate more than a thousand genes during heat stress and should be considered as an independent gene regulatory mechanism.

InPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data.

Alternative cleavage and polyadenylation (APA) is a crucial post-transcriptional gene regulation mechanism that regulates gene expression in eukaryotes by increasing the diversity and complexity of both the transcriptome and proteome. Despite the development of more than a dozen experimental methods over the last decade to identify and quantify APA events, widespread adoption of these methods has been limited by technical, financial, and time constraints. Consequently, APA remains poorly understood in most eukaryotes. However, RNA sequencing (RNA-seq) technology has revolutionized transcriptome profiling and recent studies have shown that RNA-seq data can be leveraged to identify and quantify APA events. To fully capitalize on the exponentially growing RNA-seq data, we developed InPAS (Identification of Novel alternative PolyAdenylation Sites), an R/Bioconductor package for accurate identification of novel and known cleavage and polyadenylation sites (CPSs), as well as quantification of APA from RNA-seq data of various experimental designs. Compared to other APA analysis tools, InPAS offers several important advantages, including the ability to detect both novel proximal and distal CPSs, to fine tune positions of CPSs using a naïve Bayes classifier based on flanking sequence features, and to identify APA events from RNA-seq data of complex experimental designs using linear models. We benchmarked the performance of InPAS and other leading tools using simulated and experimental RNA-seq data with matched 3'-end RNA-seq data. Our results reveal that InPAS frequently outperforms existing tools in terms of precision, sensitivity, and specificity. Furthermore, we demonstrate its scalability and versatility by applying it to large, diverse RNA-seq datasets. InPAS is an efficient and robust tool for identifying and quantifying APA events using readily accessible conventional RNA-seq data. Its versatility opens doors to explore APA regulation across diverse eukaryotic systems with various experimental designs. We believe that InPAS will drive APA research forward, deepening our understanding of its role in regulating gene expression, and potentially leading to the discovery of biomarkers or therapeutics for diseases.

E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism.

Transcription factors (TFs) may activate or repress gene expression through an interplay of different mechanisms, including RNA polymerase (RNAP) recruitment, exclusion, and initiation. TFs often have drastically different regulatory behaviors depending on promoter context and interacting cofactors. However, the detailed mechanisms by which each TF affects transcription and produce promoter-dependent regulation is unclear. Here, we discover that a simple model explains the regulatory effects of E. coli TFs in a range of contexts. Specifically, we measure the relationship between basal promoter activity and its regulation by diverse TFs and find that the contextual changes in TF function are determined entirely by the basal strength of the regulated promoter: TFs exert lower fold-change on stronger promoters under a precise inverse scaling. Remarkably, this scaling relationship holds for both activators and repressors, indicating a universal mechanism of gene regulation. Our data, which spans between 100-fold activation to 1000-fold repression, is consistent with a model of regulation driven by stabilization of RNAP at the promoter for every TF. Crucially, this indicates that TFs naturally act to maintain homeostatic expression levels across genetic or environmental perturbations, ensuring robust expression of regulated genes .

Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function.

Interactions between distal loci, including those involving enhancers and promoters, are a central mechanism of gene regulation in mammals, yet the protein regulators of these interactions remain largely undetermined. The zinc-finger transcription factor (TF) ZNF143/ZFP143 has been strongly implicated as a regulator of chromatin interactions, functioning either with or without CTCF. However, how ZNF143/ZFP143 functions as a looping factor is not well understood. Here, we tagged both CTCF and ZNF143/ZFP143 with dual-purpose degron/imaging tags to combinatorially assess their looping function and effect on each other. We find that ZNF143/ZFP143, contrary to prior reports, possesses no general looping function in mouse and human cells and that it largely functions independently of CTCF. Instead, ZNF143/ZFP143 is an essential and highly conserved transcription factor that largely binds promoters proximally, exhibits an extremely stable chromatin dwell time (>20min), and regulates an important subset of mitochondrial and ribosomal genes.

Evaluation of ALKBH2 and ALKBH3 gene regulation in patients with adult T-cell leukemia/lymphoma

BackgroundHuman T-cell leukemia virus type 1 (HTLV-1) is an oncogenic virus that causes malignant adult T-cell leukemia/lymphoma (ATL). Patients infected with HTLV-1 are considered HTLV-1 carriers, and a small proportion of patients progress to life-threatening ATL after a long asymptomatic phase. No antiviral agent or preventive vaccine specific for HTLV-1 infection is established in current situation. For development of countermeasures to combat HTLV-1 infection and ATL, it is essential to expand our knowledge about their pathogenesis. Recently, AlkB homolog (ALKBH) family have been shown to participate in the oncogenesis of various cancer types.MethodsTo investigate the potential role of ALKBH family members in the pathogenesis of ATL, we analyzed their gene expression dynamics in HTLV-1-infected T-cell lines and peripheral blood mononuclear cell-derived clinical specimens obtained from asymptomatic HTLV-1 carriers and patients with acute-type ATL. Epigenetic analysis was performed to dissect the mechanisms of ALKBH3 gene regulation using cultivated cells and a public dataset.ResultsThe mRNA expression levels of ALKBH2 and ALKBH3 were significantly or suggestively decreased in asymptomatic HTLV-1 carriers, but reverted in acute-type ATL patients, correlating with HTLV-1 basic leucine zipper factor gene expression. Intriguingly, the pre-mRNA expression of ALKBH2 and ALKBH3 was significantly suppressed in patients infected with HTLV-1, but not in healthy controls. Epigenetic analysis was performed to dissect the mechanisms of ALKBH3 gene regulation. In vitro analysis suggested a possible relationship between DNA methylation and ALKBH3 gene expression. Investigation of a public dataset revealed that specific CpG sites exhibited characteristically regulated methylation states in HTLV-1-infected T-cell subsets.ConclusionWe discovered dynamically regulated patterns of ALKBH2 and ALKBH3 gene expression in patients infected with HTLV-1, and specific CpG sites epigenetically regulated by HTLV-1 infection. This study provides novel insights into HTLV-1 infection and contributes to the elucidation of ATL pathogenesis.

Erythropoietin Production in Embryonic Neural Cells is Controlled by Hypoxia Signaling and Histone Deacetylases with an Undifferentiated Cellular State.

During mammalian development, production sites of the erythroid growth factor erythropoietin (EPO) shift from the neural tissues to the liver in embryos and to the kidneys in adults. Embryonic neural EPO-producing (NEP) cells, a subpopulation of neuroepithelial and neural crest cells, express the Epo gene between embryonic day (E) 8.5 and E11.5 to promote primitive erythropoiesis in mice. While Epo gene expression in the liver and kidneys is induced under hypoxic conditions through hypoxia-inducible transcription factors (HIFs), the Epo gene regulatory mechanisms in NEP cells remain to be elucidated. Here, we confirmed the presence of cells co-expressing EPO and HIFs in mouse neural tubes, where the hypoxic microenvironment activates HIFs. Chemical activation and inhibition of HIFs demonstrated the hypoxic regulation of EPO expression in human fetal neural progenitors and mouse embryonic neural tissues. In addition, we found that histone deacetylase inhibitors can reactivate EPO production in cell lines derived from NEP cells and human neuroblastoma, as well as in mouse primary neural crest cells, while rejuvenating these cells. Furthermore, the ability of the rejuvenated cells to produce EPO was maintained in hypoxia. Thus, EPO production is controlled by epigenetic mechanisms and hypoxia signaling in the immature state of hypoxic NEP cells.

Reading m6A marks in mRNA: A potent mechanism of gene regulation in plants.

Modifications to RNA have recently been recognized as a pivotal regulator of gene expression in living organisms. More than 170 chemical modifications have been identified in RNAs, with N6-methyladenosine (m6A) being the most abundant modification in eukaryotic mRNAs. The addition and removal of m6A marks are catalyzed by methyltransferases (referred to as "writers") and demethylases (referred to as "erasers"), respectively. In addition, the m6A marks in mRNAs are recognized and interpreted by m6A-binding proteins (referred to as "readers"), which regulate the fate of mRNAs, including stability, splicing, transport, and translation. Therefore, exploring the mechanism underlying the m6A reader-mediated modulation of RNA metabolism is essential for a much deeper understanding of the epigenetic role of RNA modification in plants. Recent discoveries have improved our understanding of the functions of m6A readers in plant growth and development, stress response, and disease resistance. This review highlights the latest developments in m6A reader research, emphasizing the diverse RNA-binding domains crucial for m6A reader function and the biological and cellular roles of m6A readers in the plant response to developmental and environmental signals. Moreover, we propose and discuss the potential future research directions and challenges in identifying novel m6A readers and elucidating the cellular and mechanistic role of m6A readers in plants.