Molecular mechanisms of noncoding RNA and epigenetic regulation in obesity with consequent diabetes mellitus development

Diabetes mellitus(DM)and obesity have become two of the most prevalent and challenging diseases worldwide,with increasing incidence and serious complications.Recent studies have shown that noncoding RNA(ncRNA)and epigenetic regulation play crucial roles in the pathogenesis of DM complicated by obesity.Identification of the involvement of ncRNA and epigenetic regulation in the pathogenesis of diabetes with obesity has opened new avenues of investigation.Targeting these mechanisms with small molecules or RNA-based therapies may provide a more precise and effective approach to diabetes treatment than traditional therapies.In this review,we discuss the molecular mechanisms of ncRNA and epigenetic regulation and their potential therapeutic targets,and the research prospects for DM complicated with obesity.

Epigenetic regulation of dental pulp stem cells and its potential in regenerative endodontics

Regenerative endodontics(RE)therapy means physiologically replacing damaged pulp tissue and regaining functional dentin–pulp complex.Current clinical RE procedures recruit endogenous stem cells from the apical papilla,periodontal tissue,bone marrow and peripheral blood,with or without application of scaffolds and growth factors in the root canal space,resulting in cementum-like and bone-like tissue formation.Without the involvement of dental pulp stem cells(DPSCs),it is unlikely that functional pulp regeneration can be achieved,even though acceptable repair can be acquired.DPSCs,due to their specific odontogenic potential,high proliferation,neurovascular property,and easy accessibility,are considered as the most eligible cell source for dentin–pulp regeneration.The regenerative potential of DPSCs has been demonstrated by recent clinical progress.DPSC transplantation following pulpectomy has successfully reconstructed neurovascularized pulp that simulates the physiological structure of natural pulp.The self-renewal,proliferation,and odontogenic differentiation of DPSCs are under the control of a cascade of transcription factors.Over recent decades,epigenetic modulations implicating histone modifications,DNA methylation,and noncoding(nc)RNAs have manifested as a new layer of gene regulation.These modulations exhibit a profound effect on the cellular activities of DPSCs.In this review,we offer an overview about epigenetic regulation of the fate of DPSCs;in particular,on the proliferation,odontogenic differentiation,angiogenesis,and neurogenesis.We emphasize recent discoveries of epigenetic molecules that can alter DPSC status and promote pulp regeneration through manipulation over epigenetic profiles.

The landscape of epigenetic regulation and therapeutic application of N^(6)-methyladenosine modifications in non-coding RNAs

RNA N^(6)-methyladenosine(m^(6)A)methylation is the most abundant and conserved RNA modification in eukaryotes.It participates in the regulation of RNA metabolism and various pathophysiological processes.Non-coding RNAs(ncRNAs)are defined as small or long transcripts which do not encode proteins and display numerous biological regulatory functions.Similar to mRNAs,m^(6)A deposition is observed in ncRNAs.Studying RNA m^(6)A modifications on ncRNAs is of great importance specifically to deepen our understanding of their biological roles and clinical implications.In this review,we summarized the recent research findings regarding the mutual regulation between RNA m^(6)A modification and ncRNAs(with a specific focus on microRNAs,long non-coding RNAs,and circular RNAs)and their functions.We also discussed the challenges of m^(6)A-containing ncRNAs and RNA m^(6)A as therapeutic targets in human diseases and their future perspective in translational roles.

Epigenetic changes in the regulation of carotenoid metabolism during honeysuckle flower development

Flower development is one of the most vital pathways in plant development, during which the epigenetic regulation of gene expression is essential. DNA methylation, the most conserved epigenetic modification, participates in gene expression regulation and transposable element silencing. Honeysuckle(Lonicera japonica) is an important medicinal plant renowned for its colorful and fragrant flowers. Honeysuckle flowers change color from white to gold as a result of carotenoid accumulation during development. However, the role of DNA methylation in flower color changes is not well understood in L. japonica. Here, we performed whole-genome bisulfite sequencing and transcriptome sequencing during flowering development in honeysuckle. The results showed that a decrease in the levels of genome-wide average DNA methylation during flower development and changes in DNA methylation were associated with the expression of demethylase genes. Moreover, many genes involved in carotenoid biosynthesis and degradation, such as Lj PSY1, LjPDS1, LjLCYE, and LjCCD4, have altered expression levels because of hypomethylation, indicating that DNA methylation plays an important role in flower color changes in honeysuckle. Taken together, our data provide epigenetic insights into flower development and color change in honeysuckles.

Recent advances in understanding of the epigenetic regulation of plant regeneration

Ever since the concept of"plant cell totipotency"was first proposed in the early twentieth century,plant regeneration has been a major focus of study.Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture.Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration.The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation.Here,we summarize how various aspects of epigenetic regulation,including histone modifications and variants,chromatin accessibility dynamics,DNA methylation,and microRNAs,modulate plant regeneration.As the mechanisms of epigenetic regulation are conserved in many plants,research in this field has potential applications in boosting crop breeding,especially if coupled with emerging single-cell omics technologies.

Disease resistance conferred by components of essential chrysanthemum oil and the epigenetic regulation of OsTPS1

The sesquiterpene alpha-bisabolol is the predominant active ingredient in essential oils that are highly valued in the cosmetics industry due to its wound healing,anti-inflammatory,and skin-soothing properties.Alpha-bisabolol was thought to be restricted to Compositae plants.Here we reveal that alpha-bisabolol is also synthesized in rice,a non-Compositae plant,where it acts as a novel sesquiterpene phytoalexin.Overexpressing the gene responsible for the biosynthesis of alpha-bisabolol,Os TPS1,conferred bacterial blight resistance in rice.Phylogenomic analyses revealed that alpha-bisabolol-synthesizing enzymes in rice and Compositae evolved independently.Further experiments demonstrated that the natural variation in the disease resistance level was associated with differential transcription of Os TPS1 due to polymorphisms in its promoter.We demonstrated that Os TPS1 was regulated at the epigenetic level by JMJ705 through the methyl jasmonate pathway.These data reveal the cross-family accumulation and regulatory mechanisms of alpha-bisabolol production.

Oxidative stress,epigenetic regulation and pathological processes of lens epithelial cells underlying diabetic cataract

Background:Cataract is a blinding disease worldwide.It is an age-related disease that mainly occurs in people over 65 years old.Cataract is also prevalent in patients with diabetes mellites(DM).The pathological mechanisms underlying diabetic cataract(DC)are more complex than that of age-related cataract.Studies have identified that polyol pathway,advanced glycation end products(AGEs)and oxidative stress are the primary pathogenesis of DC.In recent years,molecular-level regulations and pathological processes of lens epithelial cells(LECs)have been confirmed to play roles in the initiation and progression of DC.A comprehensive understanding and elucidation of how chronic hyperglycemia drives molecular-level regulations and cytopathological processes in the lens will shed lights on the prevention,delay and treatment of DC.Main text:Excessive glucose in the lens enhances polyol pathway and AGEs formation.Polyol pathway causes imbalance in the ratio of NADPH/NADPt and NADH/NADt.Decrease in NADPH/NADPt ratio compromises antioxidant enzymes,while increase in NADH/NADt ratio promotes reactive oxygen species(ROS)overproduction in mitochondria,resulting in oxidative stress.Oxidative stress in the lens causes oxidation of DNA,proteins and lipids,leading to abnormalities in their structure and functions.Glycation of proteins by AGEs decreases solubility of proteins.High glucose triggered epigenetic regulations directly or indirectly affect expressions of genes and proteins in LECs.Changes in autophagic activity,increases in fibrosis and apoptosis of LECs destroy the morphological structure and physiological functions of the lens epithelium,disrupting lens homeostasis.Conclusions:In both diabetic animal models and diabetics,oxidative stress plays crucial roles in the formation of cataract.Epigenetic regulations,include lncRNA,circRNA,microRNA,methylation of RNA and DNA,histone acetylation and pathological processes,include autophagy,fibrosis and apoptosis of LECs also involved in DC.

Epigenetic regulation of N-hydroxypipecolic acid biosynthesis by the AIPP3-PHD2-CPL2 complex

N-Hydroxypipecolic acid(NHP)is a signaling molecule crucial for systemic acquired resistance(SAR),a systemic immune response in plants that provides long-lasting and broad-spectrum protection against secondary pathogen infections.To identify negative regulators of NHP biosynthesis,we performed a forward genetic screen to search for mutants with elevated expression of the NHP biosynthesis gene FLAVIN-DEPENDENT MONOOXYGENASE 1(FMO1).Analysis of two constitutive expression of FMO1(cef)and one induced expression of FMO1(ief)mutants revealed that the AIPP3–PHD2–CPL2 protein complex,which is involved in the recognition of the histone modification H3K27me3 and transcriptional repression,contributes to the negative regulation of FMO1 expression and NHP biosynthesis.Our study suggests that epigenetic regulation plays a crucial role in controlling FMO1 expression and NHP levels in plants.

Rice melatonin deficiency causes premature leaf senescence via DNA methylation regulation

In a study of DNA methylation changes in melatonin-deficient rice mutants,mutant plants showed premature leaf senescence during grain-filling and reduced grain yield.Melatonin deficiency led to transcriptional reprogramming,especially of genes involved in chlorophyll and carbon metabolism,redox regulation,and transcriptional regulation,during dark-induced leaf senescence.Hypomethylation of mCG and mCHG in the melatonin-deficient rice mutants was associated with the expression change of both protein-coding genes and transposable element-related genes.Changes in gene expression and DNA methylation in the melatonin-deficient mutants were compensated by exogenous application of melatonin.A decreased S-adenosyl-L-methionine level may have contributed to the DNA methylation variations in rice mutants of melatonin deficiency under dark conditions.

MicroRNA-206 as a promising epigenetic approach to modulate tumor-associated macrophages in hepatocellular carcinoma

This letter comments on the recently published manuscript by Huang et al in the World Journal of Gastroenterology,which focused on the immunomodulatory effect of Calculus bovis on hepatocellular carcinoma(HCC)tumor microenvironments(TME)by inhibiting M2-tumor-associated macrophage(M2-TAM)polarization via Wnt/β-catenin pathway modulation.Recent research highlights the crucial role of TAMs and their polarization towards the M2 phenotype in promoting HCC progression.Epigenetic regulation,particularly through microRNAs(miR),has emerged as a key factor in modulating immune responses and TAM polarization in the TME,influencing treatment responses and tumor progression.This editorial focuses on miR-206,which has been found to inhibit HCC cell proliferation and migration and promote apoptosis.Moreover,miR-206 enhances anti-tumor immune responses by promoting M1-polarization of Kupffer cells,facilitating CD8+T cell recruitment and suppressing liver cancer stem cell expansion.However,challenges remain in understanding the precise mechanisms regulating miR-206 and its potential as a therapeutic agent.Targeting epigenetic mechanisms and improving strategies,whether through pharmacological or genetic approaches,offer promising avenues to sensitize tumor cells to chemotherapy.Understanding the intricate interactions between cancer and non-coding RNA regulation opens new avenues for developing targeted therapies,potentially improving HCC prognosis.

Navigating the autophagic landscape:Epigenetic modulation in gastrointestinal cancer

This editorial comments on the manuscript by Chang et al,focusing on the still elusive interplay between epigenetic regulation and autophagy in gastrointestinal diseases,particularly cancer.Autophagy,essential for cellular homeostasis,exhibits diverse functions ranging from cell survival to death,and is particularly implicated in physiological gastrointestinal cell functions.However,its role in pathological backgrounds remains intricate and context-dependent.Studies underscore the dual nature of autophagy in cancer,where its early suppressive effects in early stages are juxtaposed with its later promotion,contributing to chemoresistance.This discrepancy is attributed to the dysregulation of autophagy-related genes and their intricate involvement in cellular processes.Epigenetic modifications and regulations of gene expression,including non-coding RNAs(ncRNAs),emerge as critical players in exerting regulatory control over autophagy flux,influencing treatment responses and tumor progression.Targeting epigenetic mechanisms and improving strategies involving the inhibition or induction of autophagy through pharmacological or genetic means present potential avenues to sensitize tumor cells to chemotherapy.Additionally,nanocarrier-based delivery of ncRNAs offers innovative therapeutic approaches.Understanding the intricate interaction between autophagy and ncRNA regula-tion opens avenues for the development of targeted therapies,thereby improving the prognosis of gastrointestinal malignancies with poor outcomes.

Large-scale loss-of-function perturbations reveal a comprehensive epigenetic regulatory network in breast cancer

Objective:Epigenetic abnormalities have a critical role in breast cancer by regulating gene expression;however,the intricate interrelationships and key roles of approximately 400 epigenetic regulators in breast cancer remain elusive.It is important to decipher the comprehensive epigenetic regulatory network in breast cancer cells to identify master epigenetic regulators and potential therapeutic targets.Methods:We employed high-throughput sequencing-based high-throughput screening(HTS^(2))to effectively detect changes in the expression of 2,986 genes following the knockdown of 400 epigenetic regulators.Then,bioinformatics analysis tools were used for the resulting gene expression signatures to investigate the epigenetic regulations in breast cancer.Results:Utilizing these gene expression signatures,we classified the epigenetic regulators into five distinct clusters,each characterized by specific functions.We discovered functional similarities between BAZ2B and SETMAR,as well as CLOCK and CBX3.Moreover,we observed that CLOCK functions in a manner opposite to that of HDAC8 in downstream gene regulation.Notably,we constructed an epigenetic regulatory network based on the gene expression signatures,which revealed 8 distinct modules and identified 10 master epigenetic regulators in breast cancer.Conclusions:Our work deciphered the extensive regulation among hundreds of epigenetic regulators.The identification of 10 master epigenetic regulators offers promising therapeutic targets for breast cancer treatment.

The effects of diabetes on male fertility and epigenetic regulation during spermatogenesis

The effects of diabetes mellitus include long-term damages, dysfunctions, and failures of various organs. An important complication of diabetes is the disturbance in the male reproductive system. Glucose metabolism is an important event in spermatogenesis. Moreover, glucose metabolism is also important for maintaining basic cell activity, as well as specific functions, such as motility and fertilization ability in mature sperm. Diabetic disease and experimentally induced diabetes both demonstrated that either type 1 diabetes or type 2 diabetes could have detrimental effects on male fertility, especially on sperm quality, such as sperm motility, sperm DNA integrity, and ingredients of seminal plasma. Epigenetic modifications are essential during spermatogenesis. The epigenetic regulation represents chromatin modifications including DNA methylation, histone modifications, remodeling of nucleosomes and the higher-order chromatin reorganization and noncoding RNAs. If spermatogenesis is affected during the critical developmental window, embryonic gonadal development, and germline differentiation, environmentally-induced epigenetic modifications may become permanent in the germ line epigenome and have a potential impact on subsequent generations through epigenetic transgenerational inheritance. Diabetes may influence the epigenetic modification during sperm spermatogenesis and that these epigenetic dysregulation may be inherited through the male germ line and passed onto more than one generation, which in turn may increase the risk of diabetes in offspring.

Epigenetic regulation by polycomb group complexes:focus on roles of CBX proteins

Polycomb group （PCG） complexes are epigenetic regulatory complexes that conduct transcriptional repression of target genes via modifying the chromatin. The two best characterized forms of PCG complexes, polycomb repressive complexes 1 and 2 （PRC1 and PRC2）, are required for maintaining the sternness of embryonic stem cells and many types of adult stem cells. The spectra of target genes for PRCs are dynamically changing with cell differentiation, which is essential for proper decisions on cell fate during developmental processes, Chromobox （CBX） family proteins are canonical components in PRC1, responsible for targeting PRC1 to the chromatin. Recent studies highlight the function specifications among CBX family members in undifferentiated and differentiated stem cells, which reveal the interplay between compositional diversity and functional specificity of PRCI. In this review, we summarize the current knowledge about targeting and functional mechanisms of PRCs, emphasizing the recent breakthroughs related to CBX proteins under a number of physiological and pathological conditions.

Epigenetic regulation of adipocyte differentiation and adipogenesis

It is generally agreed that adipocytes originate from mesenchymal stem cells in what can be divided into two processes:determination and differentiation.In the past decade,many factors associated with epigenetic signals have been proved to be pivotal for the appropriate timing of adipogenesis progression.A large number of coregulators at critical gene promoters set up specific patterns of DNA methylation,histone acetylation and methylation,and nucleosome rearrangement,that act as an epigenetic code to modulate the correct progress of adipocyte differentiation and adipogenesis during adipogenesis.In this review,we focus on the functions and roles of epigenetic processes in preadipocyte differentiation and adipogenesis.

Chromatin and epigenetic regulation of the telomerase reverse transcriptase gene

Telomerase expression and telomere maintenance are critical for long-term cell proliferation and survival,and they play important roles in development,aging,and cancer.Cumulating evidence has indicated that regulation of the rate-limiting subunit of human telomerase reverse transcriptase gene(hTERT)is a complex process in normal cells and many cancer cells.In addition to a number of transcriptional activators and repressors,the chromatin environment and epigenetic status of the endogenous hTERT locus are also pivotal for its regulation in normal human somatic cells and in tumorigenesis.

Epigenetic regulation of B cells and its role in autoimmune pathogenesis

B cells play a pivotal role in the pathogenesis of autoimmune diseases.Although previous studies have shown many genetic polymorphisms associated with B-cell activation in patients with various autoimmune disorders,progress in epigenetic research has revealed new mechanisms leading to B-cell hyperactivation.Epigenetic mechanisms,including those involving histone modifications,DNA methylation,and noncoding RNAs,regulate B-cell responses,and their dysregulation can contribute to the pathogenesis of autoimmune diseases.Patients with autoimmune diseases show epigenetic alterations that lead to the initiation and perpetuation of autoimmune inflammation.Moreover,many clinical and animal model studies have shown the promising potential of epigenetic therapies for patients.In this review,we present an up-to-date overview of epigenetic mechanisms with a focus on their roles in regulating functional B-cell subsets.Furthermore,we discuss epigenetic dysregulation in B cells and highlight its contribution to the development of autoimmune diseases.Based on clinical and preclinical evidence,we discuss novel epigenetic biomarkers and therapies for patients with autoimmune disorders.

Metabolic-epigenetic nexus in regulation of stem cell fate

Stem cell fate determination is one of the central questions in stem cell biology,and although its regulation has been studied at genomic and proteomic levels,a variety of biological activities in cells occur at the metabolic level.Metabolomics studies have established the metabolome during stem cell differentiation and have revealed the role of metabolites in stem cell fate determination.While metabolism is considered to play a biological regulatory role as an energy source,recent studies have suggested the nexus between metabolism and epigenetics because several metabolites function as cofactors and substrates in epigenetic mechanisms,including histone modification,DNA methylation,and microRNAs.Additionally,the epigenetic modification is sensitive to the dynamic metabolites and consequently leads to changes in transcription.The nexus between metabolism and epigenetics proposes a novel stem cell-based therapeutic strategy through manipulating metabolites.In the present review,we summarize the possible nexus between metabolic and epigenetic regulation in stem cell fate determination,and discuss the potential preventive and therapeutic strategies via targeting metabolites.

Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis

Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context.Previous studies have shown that a protein complex,the ASI1-AIPP1-EDM2(AAE)complex,participates in polyadenylation regulation of several intronic heterochromatin-containing genes.However,the genome-wide functions of AAE are still unknown.Here,we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome-wide level and preferentially interacts with genetic heterochromatin.Polyadenylation(poly(A)sequencing reveals that AAE complex has a substantial influence on poly(A)site usage of heterochromatin-containing genes,includingnotonlyintronicheterochromatincontaining genes but also the genes showing overlap with heterochromatin.Intriguingly,AAE is also involved in the alternative splicing regulation of a number of heterochromatin-overlapping genes,such as the disease resistance gene RPP4.We provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing regulation.In addition to conferring RNA processing regulation at genic heterochromatin-containing genes,AAE also targets some transposable elements(TEs)outside of genes(including TEs sandwiched by genes and island TEs)for epigenetic silencing.Our results reveal new functions of AAE in RNA processing and epigenetic silencing,and thus representimportantadvancesinepigenetic regulation.

Epigenetic Regulation of Serotonin Transporter in Psychiatric Disorders

SLC6A4 （solute carrier family 6, member 4） gene encodes a serotonin transporter （5-hydroxytryptamine transporter, HTT）, which transports synaptic serotonin into presynaptic terminal. SLC6A4 is known to be the target of antidepressants such as selective serotonin reuptake inhibitors （SSRIs）. Inhibition of HTT increases synaptic serotonin concentration and thereby exerts antidepressant efficacy. A large number of genetic studies suggest the contribution of genetic variations of SLC6A4 to various psychiatric disorders. The most studied genetic variation, HTT-linked polymorphic region （HTTLPR）,