Regulate Target Gene Expression Research Articles

Integration of Alzheimer\u2019s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

Genome-wide association studies (GWAS) have identified more than 40 loci associated with Alzheimer’s disease (AD), but the causal variants, regulatory elements, genes and pathways remain largely unknown, impeding a mechanistic understanding of AD pathogenesis. Previously, we showed that AD risk alleles are enriched in myeloid-specific epigenomic annotations. Here, we show that they are specifically enriched in active enhancers of monocytes, macrophages and microglia. We integrated AD GWAS with myeloid epigenomic and transcriptomic datasets using analytical approaches to link myeloid enhancer activity to target gene expression regulation and AD risk modification. We identify AD risk enhancers and nominate candidate causal genes among their likely targets (including AP4E1, AP4M1, APBB3, BIN1, MS4A4A, MS4A6A, PILRA, RABEP1, SPI1, TP53INP1, and ZYX) in twenty loci. Fine-mapping of these enhancers nominates candidate functional variants that likely modify AD risk by regulating gene expression in myeloid cells. In the MS4A locus we identified a single candidate functional variant and validated it in human induced pluripotent stem cell (hiPSC)-derived microglia and brain. Taken together, this study integrates AD GWAS with multiple myeloid genomic datasets to investigate the mechanisms of AD risk alleles and nominates candidate functional variants, regulatory elements and genes that likely modulate disease susceptibility.

A bioinformatics pipeline for processing CLIP-seq data of RNA-binding proteins and its application

<p indent=0mm>UV cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) has emerged to be a powerful tool in dissecting mechanisms of RNA-binding proteins (RBP). Based on a recently developed eCLIP method by Yeo lab at UCSD, we performed target identifications and motif analyses on several RNA-binding proteins and established a bioinformatic pipeline for CLIP-seq data of RNA-binding proteins. By integrating the analysis software and scripts from different sources and analyzing RNA-binding protein PUMILIO1(PUM1) CLIP-seq data from a human cancer cell line, we identified 1189 RNA targets and found that PUM1 preferentially bound to the 3′ untranslated region (3′ UTR) and transcription termination sites (TTS) of its target mRNAs. The motif UGUAHAUA (H stands for A/U/C) is consistent with the canonical motif sequence of PUM1 for target recognition. Hence PUM1 may be involved in the proliferation and differentiation of cancer cells by regulating target gene expression at the post-transcriptional level via binding to the 3′ UTR.

Therapeutic Targeting of MicroRNAs in the Tumor Microenvironment.

The tumor-microenvironment (TME) is an amalgamation of various factors derived from malignant cells and infiltrating host cells, including cells of the immune system. One of the important factors of the TME is microRNAs (miRs) that regulate target gene expression at a post transcriptional level. MiRs have been found to be dysregulated in tumor as well as in stromal cells and they emerged as important regulators of tumorigenesis. In fact, miRs regulate almost all hallmarks of cancer, thus making them attractive tools and targets for novel anti-tumoral treatment strategies. Tumor to stroma cell cross-propagation of miRs to regulate protumoral functions has been a salient feature of the TME. MiRs can either act as tumor suppressors or oncogenes (oncomiRs) and both miR mimics as well as miR inhibitors (antimiRs) have been used in preclinical trials to alter cancer and stromal cell phenotypes. Owing to their cascading ability to regulate upstream target genes and their chemical nature, which allows specific pharmacological targeting, miRs are attractive targets for anti-tumor therapy. In this review, we cover a recent update on our understanding of dysregulated miRs in the TME and provide an overview of how these miRs are involved in current cancer-therapeutic approaches from bench to bedside.

Prolactin Drives a Dynamic STAT5A/HDAC6/HMGN2 Cis-Regulatory Landscape Exploitable in ER+ Breast Cancer.

The hormone prolactin has been implicated in breast cancer pathogenesis and regulates chromatin engagement by the transcription factor, STAT5A. STAT5A is known to inducibly bind promoters and cis-regulatory elements genome-wide, though the mechanisms by which it exerts specificity and regulation of target gene expression remain enigmatic. We previously identified HDAC6 and HMGN2 as cofactors that facilitate prolactin-induced, STAT5A-mediated gene expression. Here, multicondition STAT5A, HDAC6, and HMGN2 chromatin immunoprecipitation and sequencing with parallel condition RNA-seq are utilized to reveal the cis-regulatory landscape and cofactor dynamics underlying prolactin-stimulated gene expression in breast cancer. We find that prolactin-regulated genes are significantly enriched for cis-regulatory elements bound by HDAC6 and HMGN2, and that inducible STAT5A binding at enhancers, rather than promoters, conveys specificity for prolactin-regulated genes. The selective HDAC6 inhibitor, ACY-241, blocks prolactin-induced STAT5A chromatin engagement at cis-regulatory elements as well as a significant proportion of prolactin-stimulated gene expression. We identify functional pathways known to contribute to the development and/or progression of breast cancer that are activated by prolactin and inhibited by ACY-241. Additionally, we find that the DNA sequences underlying shared STAT5A and HDAC6 binding sites at enhancers are differentially enriched for estrogen response elements (ESR1 and ESR2 motifs) relative to enhancers bound by STAT5A alone. Gene set enrichment analysis identifies significant overlap of ERα-regulated genes with genes regulated by prolactin, particularly prolactin-regulated genes with promoters or enhancers co-occupied by both STAT5A and HDAC6. Lastly, the therapeutic efficacy of ACY-241 is demonstrated in in vitro and in vivo breast cancer models, where we identify synergistic ACY-241 drug combinations and observe differential sensitivity of ER+ models relative to ER- models.

Effect of miR-21 on Renal Fibrosis Induced by Nano-SiO₂ in Diabetic Nephropathy Rats via PTEN/AKT Pathway.

MicroRNAs are a type of non-coding single-stranded RNA that can mediate target mRNA degradation or inhibit target mRNA translation, thereby regulating target gene expression and have an important role in physiological and pathological processes. At present, miRs have been confirmed to be closely related to kidneys and kidney diseases, and have been involved in the occurrence, development and prognosis of renal fibrosis. Now we review the research progress of miRs in renal fibrosis in recent years, and provide references for the future diagnosis and treatment of renal fibrosis. The incidence of diabetic nephropathy (DN) is increasing year by year, the pathogenesis is complicated, and renal fibrosis occurs during the progress of the disease, which is very difficult to treat. The protein encoded by the PTEN gene has lipid phosphatase and protein phosphatase activity and is the PTEN/AKT and FAK pathway important negative regulators. It can play an anti-fibrotic effect by negatively regulating the PTEN/AKT pathway. Studies show that during the pathogenesis of DN, the expression of PTEN protein is reduced, and the PI3K/AKT pathway is activated to exert multiple fibrotic effects, but affect PTEN. The regulatory factors of expression are still not clear; moreover, the specific mechanism of the decrease in PTEN protein expression in DN pathogenesis. Therefore, this study intends to Intervention of the expression level of miRs in renal tissues, to study its regulation of PTEN and its effect on renal fibrosis, and at the same time, observe the effects on renal tubular epithelial cell phenotype and fibrotic lesions under high glucose conditions by up-regulating and down-regulating PTEN expression. Further elucidate the pathogenesis of DN renal fibrosis, and explore new effective targets for the prevention and treatment of DN.

Profiling of MicroRNAs and Their Targets in Roots and Shoots Reveals a Potential MiRNA-Mediated Interaction Network in Response to Phosphate Deficiency in the Forestry Tree Betula luminifera.

Inorganic phosphate (Pi) is often lacking in natural and agro-climatic environments, which impedes the growth of economically important woody species. Plants have developed strategies to cope with low Pi (LP) availability. MicroRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Transcriptomic libraries, small RNA (sRNA) libraries, and a mixed degradome cDNA library of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. Analysis of the transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA–target pairs were further validated in the roots and shoots, respectively, using degradome sequencing. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the “ascorbate and aldarate metabolism” pathway responded to LP, suggesting miRNA-target pairs might participating in the removing of reactive oxidative species under LP stress. Moreover, a putative network of miRNA–target interactions involved in responses to LP stress in B. luminifera is proposed. Taken together, these findings provide useful information to decipher miRNA functions and establish a framework for exploring P signaling networks regulated by miRNAs in B. luminifera and other woody plants. It may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.

Antitumor and Protective Effects of Melatonin: The Potential Roles of MicroRNAs.

MicroRNAs (miRNAs) are endogenous short noncoding RNAs with approximately 22 nucleotides. The primary function of miRNAs is the negative regulation of target gene expression via mRNA degradation or translation inhibition. During recent years, much attention has been made toward miRNAs' role in different disorders; particularly cancer and compounds with modulatory effects on miRNAs are of interest. Melatonin is one of these compounds which is secreted by the pineal gland. Also, melatonin is present in the leaves, fruits, and seeds of plants. Melatonin has several valuable biological activities such as antioxidant, anti-inflammation, antitumor, and antiaging activities. This important agent is extensively used to treat different disorders such as cancer and neurodegenerative and cardiovascular diseases. This review aims to describe the modulatory effect of melatonin on miRNAs as novel targets.

MicroRNA 452 regulates ASB8, NOL8, and CDR2 expression in colorectal cancer cells

MicroRNAs play important roles in the pathogenesis of human diseases by regulating target gene expression in specific cells or tissues. Previously, we identified microRNA 452 (MIR452), which was specifically up-regulated in early stage human colorectal cancer (CRC) tissue. The current study aims to identify and verify the target genes of MIR452 associated with CRC. A luciferase reporter system was used to confirm the effect of MIR452 on ASB8, NOL8, and CDR2 expression. The expression levels of MIR452 and the target genes were evaluated by quantitative RT-PCR (qRT-PCR) and western blotting. We verified the association between MIR452 and three genes, ASB8, NOL8, and CDR2, and showed that their transcripts were down-regulated by MIR452. Up-regulated MIR452 also down-regulated ASB8, NOL8, and CDR2 mRNA and protein levels in CRC cells. CDR2 protein expression was decreased in CRC tissues compared to adjacent non-tumor tissues. These results suggest that ASB8, NOL8, and CDR2 were target genes of MIR452 in CRC cells and that up-regulated MIR452 in CRC tissue regulated ASB8, NOL8, and CDR2 expression during colorectal carcinogenesis.

An integrated epigenomic-transcriptomic landscape of lung cancer reveals novel methylation driver genes of diagnostic and therapeutic relevance.

Background: Aberrant DNA methylation occurs commonly during carcinogenesis and is of clinical value in human cancers. However, knowledge of the impact of DNA methylation changes on lung carcinogenesis and progression remains limited.Methods: Genome-wide DNA methylation profiles were surveyed in 18 pairs of tumors and adjacent normal tissues from non-small cell lung cancer (NSCLC) patients using Reduced Representation Bisulfite Sequencing (RRBS). An integrated epigenomic-transcriptomic landscape of lung cancer was depicted using the multi-omics data integration method.Results: We discovered a large number of hypermethylation events pre-marked by poised promoter in embryonic stem cells, being a hallmark of lung cancer. These hypermethylation events showed a high conservation across cancer types. Eight novel driver genes with aberrant methylation (e.g., PCDH17 and IRX1) were identified by integrated analysis of DNA methylome and transcriptome data. Methylation level of the eight genes measured by pyrosequencing can distinguish NSCLC patients from lung tissues with high sensitivity and specificity in an independent cohort. Their tumor-suppressive roles were further experimentally validated in lung cancer cells, which depend on promoter hypermethylation. Similarly, 13 methylation-driven ncRNAs (including 8 lncRNAs and 5 miRNAs) were identified, some of which were co-regulated with their host genes by the same promoter hypermethylation. Finally, by analyzing the transcription factor (TF) binding motifs, we uncovered sets of TFs driving the expression of epigenetically regulated genes and highlighted the epigenetic regulation of gene expression of TCF21 through DNA methylation of EGR1 binding motifs.Conclusions: We discovered several novel methylation driver genes of diagnostic and therapeutic relevance in lung cancer. Our findings revealed that DNA methylation in TF binding motifs regulates target gene expression by affecting the binding ability of TFs. Our study also provides a valuable epigenetic resource for identifying DNA methylation-based diagnostic biomarkers, developing cancer drugs for epigenetic therapy and studying cancer pathogenesis.

MicroRNA regulation of fruit development, quality formation and stress response

Fruits, as the reproductive organs of many higher plants, are an integral part of a balanced diet, providing rich nutrients and bioactive substances for our health. Over the years, the research on fruit development, quality formation and stress response has deepened, which sheds light on the regulatory mechanism and application of fruit quality improvement. Among the many regulatory factors, microRNAs (miRNAs) are a class of short non-coding RNAs, ranging from 20 to 24-nt, which post-transcriptionally regulate target gene expression. miRNAs and their functions have been extensively examined in plants especially in model species, and they play critical roles in the regulation of diverse biological processes in response to endogenous developmental signals and external environmental cues, respectively. In fruit crops, the function of miRNAs and their regulation have also been under intensive study. In particular, the novel roles of miRNAs that have not been revealed in the model annual species have been unraveling, which reflect the genetic, physiological, and developmental complexity of gene regulation in fruit crops. Here we review the current research progress achieved, specifically in fruit crops, with a focus on the function of miRNAs in the control of fruit development and quality as well as response to various stresses. The future prospects of miRNAs for quality-targeted fruit breeding are also discussed.

Therapeutic perspectives of extracellular vesicles and extracellular microRNAs in atherosclerosis.

Extracellular signaling molecules, such as growth factors, cytokines, and hormones, regulate cell behaviors and fate through endocrine, paracrine, and autocrine actions and play essential roles in maintaining tissue homeostasis. MicroRNAs, an important class of posttranscriptional modulators, could stably present in extracellular space and body fluids and participate in intercellular communication in health and diseases. Indeed, recent studies demonstrated that microRNAs could be secreted through vesicular and non-vesicular routes, transported in body fluids, and then transmitted to recipient cells to regulate target gene expression and signaling events. Over the past decade, a great deal of effort has been made to investigate the functional roles of extracellular vesicles and extracellular microRNAs in pathological conditions. Emerging evidence suggests that altered levels of extracellular vesicles and extracellular microRNAs in body fluids, as part of the cellular responses to atherogenic factors, are associated with the development of atherosclerosis. This review article provides a brief overview of extracellular vesicles and perspectives of their applications as therapeutic tools for cardiovascular pathologies. In addition, we highlight the role of extracellular microRNAs in atherogenesis and offer a summary of circulating microRNAs in liquid biopsies associated with atherosclerosis.

Bazı Psikiyatrik ve Nörodejeneratif Bozuklukların Tanısında Potansiyel Bir Biyobelirteç MikroRNA’ ların İncelenmesi

MicroRNAs (miRNAs) are a large endogenous, non-coding RNA class of 19-25 nucleotides. Mature miRNAs regulate target gene expression at both transcriptional and translational levels. As a current area of interest in molecular diagnostic research, microRNAs (miRNAs) have recently been shown to be effective circulatory biomarkers for many diseases. Major depressive disorder, Bipolar disorder, Schizophrenia, Obsessive compulsive disorder, Alzheimer's disease and Parkinson's disease are among the most common psychiatric and neurodegenerative disorders known to be a serious public health problem in terms of morbidity, mortality and functional handicap. MicroRNAs are aware of the events occurring in the cell as normal mechanical, physical and biochemical functions due to many psychiatric and other medical diseases, and are very promising as a biomarker for emerging disorders and neuropathological changes.

Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications.

Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering.

Regulatory microRNAs and vascular cognitive impairment and dementia.

Vascular cognitive impairment and dementia (VCID) is defined as a progressive dementia disease related to cerebrovascular injury and often occurs in aged populations. Despite decades of research, effective treatment for VCID is still absent. The pathological processes of VCID are mediated by the molecular mechanisms that are partly modulated at the post‐transcriptional level. As small endogenous non‐coding RNAs, microRNAs (miRs) can regulate target gene expression through post‐transcriptional gene silencing. miRs have been reported to play an important role in the pathology of VCID and have recently been suggested as potential novel pharmacological targets for the development of new diagnosis and treatment strategies in VCID. In this review, we summarize the current understanding of VCID, the possible role of miRs in the regulation of VCID and attempt to envision future therapeutic strategies. Since manipulation of miR levels by either pharmacological or genetic approaches has shown therapeutic effects in experimental VCID models, we also emphasize the potential therapeutic value of miRs in clinical settings.

Tiny Regulators of Massive Tissue: MicroRNAs in Skeletal Muscle Development, Myopathies, and Cancer Cachexia.

Skeletal muscles are the largest tissues in our body and the physiological function of muscle is essential to every aspect of life. The regulation of development, homeostasis, and metabolism is critical for the proper functioning of skeletal muscle. Consequently, understanding the processes involved in the regulation of myogenesis is of great interest. Non-coding RNAs especially microRNAs (miRNAs) are important regulators of gene expression and function. MiRNAs are small (~22 nucleotides long) noncoding RNAs known to negatively regulate target gene expression post-transcriptionally and are abundantly expressed in skeletal muscle. Gain- and loss-of function studies have revealed important roles of this class of small molecules in muscle biology and disease. In this review, we summarize the latest research that explores the role of miRNAs in skeletal muscle development, gene expression, and function as well as in muscle disorders like sarcopenia and Duchenne muscular dystrophy (DMD). Continuing with the theme of the current review series, we also briefly discuss the role of miRNAs in cancer cachexia.

MiR-421 Aggravates Neurotoxicity and Promotes Cell Death in Parkinson's Disease Models by Directly Targeting MEF2D.

Parkinson's disease (PD) is a severe neurodegenerative disease characterized by selective loss of dopaminergic neurons, which reduces quality of life of patients and poses a heavy burden to the society. The pathological mechanism of PD remains unclear, and increasing efforts are aimed to solve this problem. MiRNAs are a kind of small noncoding RNA regulating target gene expression. Previous studies have shown that dysregulation of miRNAs is involved in the development of PD. In the present study, we determined that miR-421 and MEF2D are increased and decreased, respectively, in a cellular model of PD. The data on the mechanism of action indicate that miR-421 directly binds to MEF2D mRNA and negatively regulates MEF2D expression. An increase in miR-421 disrupted the Bcl2/Bax system. Functional assays indicated that enhanced miR-421 promotes cell death by negative modulation of MEF2D expression. Inhibition of miR-421 or restoration of MEF2D protected neurons from neurotoxicity in cellular and animal models of PD. Our study is the first to demonstrate that miR-421 is decreased in PD models and to determine a novel putative mechanism of PD pathogenesis.

Advances in the role of miRNAs in the occurrence and development of osteosarcoma.

Osteosarcoma (OS) is the most common primary malignant tumor of the skeletal system in the clinic. It mainly occurs in adolescent patients and the pathogenesis of the disease is very complicated. The distant metastasis may occur in the early stage, and the prognosis is poor. MicroRNAs (miRNAs) are non-coding RNAs of about 18–25 nt in length that are involved in post-transcriptional regulation of genes. miRNAs can regulate target gene expression by promoting the degradation of target mRNAs or inhibiting the translation process, thereby the proliferation of OS cells can be inhibited and the apoptosis can be promoted; in this way, miRNAs can affect the metabolism of OS cells and can also participate in the occurrence, invasion, metastasis, and recurrence of OS. Some miRNAs have already been found to be closely related to the prognosis of patients with OS. Unlike other reviews, this review summarizes the miRNA molecules closely related to the development, diagnosis, prognosis, and treatment of OS in recent years. The expression and influence of miRNA molecule on OS were discussed in detail, and the related research progress was summarized to provide a new research direction for early diagnosis and treatment of OS.

DNMT3A inhibits E2F1-induced arterial marker expression and impairs angiogenesis in human umbilical artery endothelial cells.

Arterial marker genes EphrinB2 and HEY2 are essential for cardiovascular development and postnatal neovascularization. Our previous study confirmed that E2F1 could activate the transcription of EphrinB2 and HEY2 in human mesenchymal stem cells; however, the detailed mechanism has not been resolved yet. In this study, we focused on the interaction between E2F1 and DNMT3A, a de novo DNA methyltransferase, on regulating the expression of EphrinB2 and HEY2, and explored the potential mechanisms. Gain- and loss-of-function experiments implicated the positive effect of E2F1 on the expression of EphrinB2 and HEY2 and tube formation in human umbilical artery endothelial cells. Accumulation of DNMT3A decreased the levels of EphrinB2 and HEY2, and impaired tube formation induced by E2F1, while inhibiting DNMT3A by RNA interference augmented their expression and angiogenesis in E2F1-trasfected cells. We then asked whether the low expressions of EphrinB2 and HEY2 induced by DNMT3A are related to the methylation status of their promoters. Surprisingly, the methylation status of the CpG islands in the promoter region was not significantly affected by overexpression of exogenous DNMT3A. Furthermore, the interaction between E2F1 and DNMT3A was confirmed by co-immunoprecipitation. DNMT3A could inhibit the transcription of EphrinB2 and HEY2 promoters by affecting the binding of E2F1 to its recognition sequences as revealed by luciferase reporter assay and chromatin immunoprecipitation. These results identified a novel mechanism underlying the cooperation of DNMT3A with E2F1 on regulating target gene expression, and revealed their roles in the angiogenic process.

Photoregulation of Gene Expression with Amantadine-Modified Caged siRNAs through Host-Guest Interactions.

RNA interference is an essential and powerful tool for targeting and verifying specific gene functions. Conditional control of small interfering RNA (siRNA) activity, especially using light activation, is a potential method for regulating target gene expression and functions. In this study, a series of photolabile siRNAs with amantadine modification have been rationally designed and developed through host-guest interactions between amantadine and β-cyclodextrin derivatives to enhance the blocking effect of siRNA binding and/or RNA-induced silencing complex processing. These caged siRNAs with amantadine modification at the 5' end of antisense-strand RNA were efficiently inactivated through the host-guest interactions between amantadine and β-cyclodextrin. Photomodulation of the gene silencing activity of these amantadine-modified caged siRNAs targeting both exogenous and endogenous genes was successfully achieved, which indicates that host-guest interactions could be a new strategy for developing new caged siRNAs for gene photoregulation with low leaking activity.

Epigenetic Regulation of Spermatogonial Stem Cell Homeostasis: From DNA Methylation to Histone Modification.

Spermatogonial stem cells(SSCs)are the ultimate germline stem cells with the potential of self-renewal and differentiation, and a dynamic balance of SSCs play an essential role in spermatogenesis. During the gene expression process, genomic DNA and nuclear protein, working together, contribute to SSC homeostasis. Recently, emerging studies have shown that epigenome-related molecules such as chromatin modifiers play an important role in SSC homeostasis through regulating target gene expression. Here, we focus on two types of epigenetic events, including DNA methylation and histone modification, and summarize their function in SSC homeostasis. Understanding the molecular mechanism during SSC homeostasis will promote the recognition of epigenetic biomarkers in male infertility, and bring light into therapies of infertile patients.Graphical Abstract.