Coordinated actions of microRNAs with other epigenetic factors regulate skeletal muscle development and adaptation

Epigenetics plays a pivotal role in regulating gene expression in development, in response to cellular stress or in disease states, in virtually all cell types. MicroRNAs (miRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate gene expression. miRNAs were discovered in 1993 and have been extensively studied ever since. They can be expressed in a tissue-specific manner and play a crucial role in tissue development and many biological processes. miRNAs are responsible for changes in the cell epigenome because of their ability to modulate gene expression post-transcriptionally. Recently, numerous studies have shown that miRNAs and other epigenetic factors can regulate each other or cooperate in regulating several biological processes. On the one hand, the expression of some miRNAs is silenced by DNA methylation, and histone modifications have been demonstrated to modulate miRNA expression in many cell types or disease states. On the other hand, miRNAs can directly target epigenetic factors, such as DNA methyltransferases or histone deacetylases, thus regulating chromatin structure. Moreover, several studies have reported coordinated actions between miRNAs and other epigenetic mechanisms to reinforce the regulation of gene expression. This paper reviews multiple interactions between miRNAs and epigenetic factors in skeletal muscle development and in response to stimuli or disease

Current epigenetic aspects the clinical kidney researcher should embrace

Chronic kidney disease (CKD), affecting 10-12% of the world's adult population, is associated with a considerably elevated risk of serious comorbidities, in particular, premature vascular disease and death. Although a wide spectrum of causative factors has been identified and/or suggested, there is still a large gap of knowledge regarding the underlying mechanisms and the complexity of the CKD phenotype. Epigenetic factors, which calibrate the genetic code, are emerging as important players in the CKD-associated pathophysiology. In this article, we review some of the current knowledge on epigenetic modifications and aspects on their role in the perturbed uraemic milieu, as well as the prospect of applying epigenotype-based diagnostics and preventive and therapeutic tools of clinical relevance to CKD patients. The practical realization of such a paradigm will require that researchers apply a holistic approach, including the full spectrum of the epigenetic landscape as well as the variability between and within tissues in the uraemic milieu

MiR-185 Targets the DNA Methyltransferases 1 and Regulates Global DNA Methylation in human glioma

<p>Abstract</p> <p>Background</p> <p>Perturbation of DNA methylation is frequent in cancers and has emerged as an important mechanism involved in tumorigenesis. To determine how DNA methylation is modified in the genome of primary glioma, we used Methyl-DNA immunoprecipitation (MeDIP) and Nimblegen CpG promoter microarrays to identify differentially DNA methylation sequences between primary glioma and normal brain tissue samples.</p> <p>Methods</p> <p>MeDIP-chip technology was used to investigate the whole-genome differential methylation patterns in glioma and normal brain tissues. Subsequently, the promoter methylation status of eight candidate genes was validated in 40 glioma samples and 4 cell lines by Sequenom's MassARRAY system. Then, the epigenetically regulated expression of these genes and the potential mechanisms were examined by chromatin immunoprecipitation and quantitative real-time PCR.</p> <p>Results</p> <p>A total of 524 hypermethylated and 104 hypomethylated regions were identified in glioma. Among them, 216 hypermethylated and 60 hypomethylated regions were mapped to the promoters of known genes related to a variety of important cellular processes. Eight promoter-hypermethylated genes (ANKDD1A, GAD1, HIST1H3E, PCDHA8, PCDHA13, PHOX2B, SIX3, and SST) were confirmed in primary glioma and cell lines. Aberrant promoter methylation and changed histone modifications were associated with their reduced expression in glioma. In addition, we found loss of heterozygosity (LOH) at the miR-185 locus located in the 22q11.2 in glioma and induction of miR-185 over-expression reduced global DNA methylation and induced the expression of the promoter-hypermethylated genes in glioma cells by directly targeting the DNA methyltransferases 1.</p> <p>Conclusion</p> <p>These comprehensive data may provide new insights into the epigenetic pathogenesis of human gliomas.</p

Epigenetic alteration of microRNAs in DNMT3B-mutated patients of ICF syndrome

Immunodeficiency, Centromeric region instability, Facial anomalies (ICF; OMIM #242860) syndrome, due to mutations in the DNMT3B gene, is characterized by inheritance of aberrant patterns of DNA methylation and heterochromatin defects. Patients show variable agammaglobulinemia and a reduced number of T cells, making them prone to infections and death before adulthood. Other variable symptoms include facial dysmorphism, growth and mental retardation. Despite the recent advances in identifying the dysregulated genes, the molecular mechanisms, which underlie the altered gene expression causing ICF phenotype complexity, are not well understood. Held the recently-shown tight correlation between epigenetics and microRNAs (miRNAs), we searched for miRNAs regulated by DNMT3B activity, comparing cell lines from ICF patients with those from healthy individuals. We observe that eighty-nine miRNAs, some of which involved in immune function, development and neurogenesis, are dysregulated in ICF (LCLs) compared to wild-type cells. Significant DNA hypomethylation of miRNA CpG islands was not observed in cases of miRNA up-regulation in ICF cells, suggesting a more subtle effect of DNMT3B deficiency on their regulation; however, a modification of histone marks, especially H3K27 and H3K4 trimethylation, and H4 acetylation, was observed concomitantly with changes in microRNA expression. Functional correlation between miRNA and mRNA expression of their targets allow us to suppose a regulation either at mRNA level or at protein level. These results provide a better understanding of how DNA methylation and histone code interact to regulate the class of microRNA genes and enable us to predict molecular events possibly contributing to ICF condition

The miR-139-5p regulates proliferation of supratentorial paediatric low-grade gliomas by targeting the PI3K/AKT/mTORC1 signalling

Paediatric low-grade gliomas (pLGGs) are a heterogeneous group of brain tumours associated with a high overall survival: however, they are prone to recur and supratentorial lesions are difficult to resect, being associated with high percentage of disease recurrence. Our aim was to shed light on the biology of pLGGs

Maternal folic acid supplementation and its effects on metabolic and epigenetic regulatory gene networks in offspring

Periconceptional folic acid supplementation is a highly prevalent public health intervention and is known to reduce the incidence of neural tube defects (NTDs) and the risk of small for gestational age (SGA) infants. Increased maternal folate status during mid-gestation is associated with increased adiposity and insulin resistance in children. In rodents, maternal folic acid supplementation (MFAS) reduces plasma triacylglyceride (TAG) and cholesterol in adolescent and adult offspring but increases plasma glucose in adult female offspring. Overall, this suggests that MFAS, while beneficial perinatally, may affect metabolic regulation and susceptibility of offspring to chronic metabolic disease long term; however, the potential mechanisms involved remain incompletely understood. One mechanism by which MFAS may alter long-term metabolic regulation in offspring is perturbed DNA methylation. DNA methylation is a heritable form of epigenetic modification, which establishes a signature of inactive gene expression via the addition of a methyl group to the 5’ position of a cytosine residue; folate, a key methyl group donor, may modulate this epigenetic process and state. Consistently, MFAS, before and during gestation, increases DNA methylation in the regulatory region of IGF2 in blood of the newborn infant. In rodents, MFAS, during pregnancy and lactation, decreases hepatic activity of DNA methyltransferases (DNMTs), which are key enzymes for maintaining and establishing DNA methylation, in adult offspring. Maternal folic acid supplementation may act through such pathways to affect epigenetic state and phenotype of offspring long term. Besides affecting protein-coding genes, DNA methylation also regulates the expression of small non-coding microRNAs (miRs). These short single-stranded RNA molecules can repress post-transcriptional expression of their mRNA targets through 3’UTR base-pairing interactions. Many miRs target genes are involved in glucose, lipid and cholesterol metabolism; miRs can act in concert to orchestrate co-ordinated post-transcriptional changes by targeting multiple sites and, in turn, forming regulatory networks. In addition, miRs can target repressors in DNA methylation, enabling for dynamic regulation between these two distinct epigenetic processes. This may be a third pathway whereby MFAS influences phenotype of offspring. The present thesis describes studies, in the rodent, of the effects of MFAS, from preconception to term, on the expression of key metabolic regulatory genes, DNMTs and non-coding miRs in the major glucoregulatory tissues, liver and skeletal muscle, of offspring during prenatal and postnatal stages of development. Maternal folic acid supplementation altered hepatic expression of 13 genes (P < 0.05) in all adult offspring as well as in a sexually dimorphic manner, as shown by microarray analysis. Maternal folic acid supplementation altered the hepatic mRNA transcriptome of adult offspring, with 22 genes in males and 36 genes in females being differentially expressed (P < 0.05). Gene ontology analysis revealed that the differentially expressed genes in liver of offspring following MFAS were closely associated with lipid and cholesterol metabolism. Maternal folic acid supplementation increased hepatic expression of Ppara, an upstream regulator of genes closely related to lipid metabolism, in all offspring in late gestation (1.22 fold, P = 0.024) but reduced it in adulthood (-0.41 fold, P = 0.002). Maternal folic acid supplementation also altered hepatic expression of lipogenic genes in offspring in a sexually dimorphic and age-dependent manner. In male offspring, MFAS decreased hepatic expression of Acaca in late gestation (-0.32 fold, P = 0.018) but increased it in adulthood (1.56 fold, P = 0.011); in female offspring, it was not affected by MFAS in late gestation nor in adulthood. Maternal folic acid supplementation decreased hepatic expression of Scd1 in the female offspring in late gestation (-0.37 fold, P = 0.017) but increased it in adulthood (1.38 fold, P = 0.035); in male offspring, it was not affected by MFAS in late gestation nor in adulthood. Maternal folic acid supplementation altered expression of genes involved in cholesterogenesis in female offspring in an age-dependent manner, with hepatic expression of Sc4mol being increased in late gestation (1.92 fold, P = 0.003), but it was unchanged in adulthood. Maternal folic acid supplementation also decreased hepatic expression of a cholesterogenic gene, Idi1 (-0.64 fold, P < 0.0001), in adult female offspring. In terms of associations, hepatic expression of Ppara was positively correlated with that of Idi1 (r = 0.434, P = 0.036) and Sqle (r = 0.528, P = 0.012) in the adult female offspring. Hepatic expression of Akr1b10 and Acaca (r = 0.846, P < 0.0001) were also positively correlated in the adult female offspring. Collectively, MFAS induces distinct changes in hepatic expression of genes related to lipid and cholesterol metabolism and their regulatory networks in offspring during prenatal and postnatal stages of development, particularly, in a manner that appears to augment the capacity for hepatic lipid and cholesterol homeostasis in later life. Maternal folic acid supplementation reduced hepatic expression of Dnmt1 (-0.36 fold, P = 0.039) and Dnmt3b (-0.21 fold, P < 0.0001) in the female foetus in late gestation. In addition, MFAS altered hepatic miR expression of 36 miRs (P < 0.05) in the female foetus in late gestation, with four miRs being up-regulated (1.18 to 1.22 fold) and 32 miRs being down-regulated (-0.21 to -1.18 fold). Maternal folic acid supplementation did not alter hepatic expression of DNMTs nor that of miRs in the male foetus. This suggests that MFAS could partly mediate its effects on hepatic gene expression in a sexually dimorphic manner through altering the capacity to regulate DNA methylation and miR expression in female foetuses but not in males. Effects of MFAS on hepatic expression of miRs and DNMTs in the adult offspring remain to be further determined. Maternal folic acid supplementation also altered skeletal muscle expression of six genes (P < 0.05) in adult offspring, as shown by microarray analysis. Gene ontology analysis further revealed these differentially expressed genes in offspring following MFAS were closely associated with lipid metabolism, cytoskeletal remodelling and potassium ion homeostasis. Overall, these observations show that MFAS alters hepatic and skeletal muscle expression of genes related to lipid and cholesterol metabolism in the offspring during prenatal and postnatal development. Maternal folic acid supplementation induces sex-specific differences in hepatic expression of DNMTs and non-coding miRs in foetal life, with these changes suggested to contribute towards altered expression of metabolic regulatory genes and, in effect, an altered capacity for lipid and cholesterol homeostasis after birth.Thesis (Ph.D.) -- University of Adelaide, Adelaide Medical School, 201