Promoter Regions Of Candidate Genes Research Articles

Association Between Promoter Methylation of Vitamin D Metabolic Pathway Genes and Tuberculosis and Diabetes Comorbidity in a Chinese Han Population: A Case-Control Study.

Deficiency vitamin D and hyperglycemia could be related to weakened innate immune response and aggravate the progression of tuberculosis (TB). This study hypothesized that DNA promoter methylation of the pivotal genes in the vitamin D metabolic pathway might be related to diabetes and tuberculosis co-morbidity (TB-DM) susceptibility. A total of 50 TB-DM and 50 healthy subjects (HS) were included in the present study. Targeted bisulfite sequencing was applied to detect the methylation of the promoter regions of candidate genes in the vitamin D metabolic pathway (CYP24A1, CYP27B1, CYP2R1, DHCR7, and VDR) in whole blood. The overall methylation level of candidate genes in this study was lower in patients with TB-DM than HS, except for CYP2R1. The results of the ROC demonstrated the potential of CYP24A1, CYP27B1, DHCR7, and VDR promoter methylation as a biomarker for diagnosing TB-DM, with all the AUC above 0.7. In subgroup analysis, we found that lower circulating vitamin D is related to a low level of CYP24A1, CYP27B1, and DHCR7 promoter methylation in patients with TB-DM. With decreasing methylation level, risk of TB-DM was significantly increased (odds ratio, 95% CI 0.343, 0.144-0.821 for CYP24A1; 0.461, 0.275-0.773 for CYP27B1; 0.09, 0.015-0.530 for DHCR7; 0.006, 0.0003-0.115 for VDR). Besides, our results revealed that there was a significant correlation between DNA promoter methylation of selected genes in the vitamin D metabolic pathway and platelet indices in TB-DM. However, there was no correlation between DNA methylation of the four genes and fasting glucose and HbA1c. Our results could suggest that the selected genes in the vitamin D metabolic pathway may be involved in the pathological process of TB-DM, but independent of the process of hyperglycemia to impaired immune responses to Mtb.

The Class II KNOX family members KNAT3 and KNAT7 redundantly participate in Arabidopsis seed coat mucilage biosynthesis.

The production of Arabidopsis seed mucilage involves complex polysaccharide biosynthetic pathways and developmental processes in seed epidermal cells. Although the polysaccharide components of Arabidopsis seed mucilage have been identified, their regulatory mechanism requires further investigation. Here, we show that Class II KNOX gene family members KNAT3 and KNAT7 play an essential role in regulating mucilage production in the early developmental stages of Arabidopsis seeds. Double mutant knat3knat7 resulted in defective seed mucilage production and columellae formation, whereas knat3 showed a normal phenotype compared with wild type, and the mucilage thickness in knat7 was slightly disturbed. Rhamnogalacturonan I (RG-I) and its biosynthetic substrates galacturonic acid and rhamnose were reduced in both the adherent and soluble mucilage of knat3knat7. Comparative transcriptome analysis on whole seeds suggested that polysaccharide, glucosinolate and anthocyanin biosynthetic pathways were specifically repressed in knat3knat7. Transient co-expression of KNAT3 and KNAT7 with promoter regions of candidate genes in Arabidopsis protoplasts revealed that both KNAT3 and KNAT7 act as positive regulators of the RG-I biosynthetic gene MUCILAGE-MODIFIED 4 (MUM4, AT1G53500). Collectively, our results demonstrate that KNAT3 and KNAT7 are multifunctional transcription factors in secondary cell wall development and redundantly modulate mucilage biosynthesis in Arabidopsis seeds.

Hypermethylated promoters of genes UNC5D and KCNA1 as potential novel diagnostic biomarkers in colorectal cancer.

Aim: Identification of aberrant hypermethylation in promoter regions of candidate genes to discover potential biomarkers for colorectal cancer. Materials & Methods: Genes BMP2, IRF4, KCNA1, LRRC7, NRG3, SLC27A6 and UNC5D were pre-selected in a bioinformatics study for their hypermethylation status in colorectal cancer. Methylation analysis was performed on 202 cancer tissue specimens to validate candidate genes. Results: Genes KCNA1 and UNC5D displayed methylation in 95.3and 99.7% of TheCancer Genome Atlas dataset samplesand in 96 and 98% of our experimentally tested samples, respectively. Conclusion:KCNA1 and UNC5D promoter hypermethylation holds diagnostic biomarker potential in patients with early colorectal cancer.

Effects of histone methyltransferase inhibition in endometriosis.

Although the histone methyltransferase EZH2 and its product H3K27me3 are well studied in cancer, little is known about their role and potential as therapeutic targets in endometriosis. We have previously reported that endometriotic lesions are characterized by global enrichment of H3K27me3. Therefore, we aimed to (1) characterize the expression levels of EZH2 in endometriotic tissues; (2) assess H3K27me3 enrichment in candidate genes promoter regions; and (3) determine if pharmacological inhibition of EZH2 impacts migration, proliferation, and invasion of endometriotic cells. Immunohistochemistry of an endometriosis-focused tissue microarray was used to assess the EZH2 protein levels in tissues. Chromatin immunoprecipitation-qPCR was conducted to assess enrichment of H3K27me3 in candidate gene promoter regions in tissues. Immunofluorescence was performed to assess the effect of an EZH2-specific pharmacological inhibitor on H3K27me3 global enrichment in cell lines. To measure effects of the inhibitor in migration, proliferation, and invasion in vitro we used Scratch, BrdU, and Matrigel assays, respectively. Endometriotic lesions had significantly higher EZH2α nuclear immunostaining levels compared to eutopic endometrium from patients (glands, stroma) and controls (glands). H3K27me3 was enriched within promoter regions of candidate genes in some but not all of the endometriotic lesions. Inhibition of EZH2 reduced H3K27me3 levels in the endometriotic cells specifically, and also reduced migration, proliferation but not invasion of endometriotic epithelial cells (12Z). These findings support future preclinical studies to determine in vivo efficacy of EZH2 inhibitors as promising nonhormonal treatments for endometriosis, still an incurable gynecological disease.

DNA methylation in candidate genes for handedness predicts handedness direction

ABSTRACTHandedness is a complex trait influenced by both genetic and non-genetic factors. Asymmetries of DNA methylation and gene expression in the developing foetus are thought to underlie its development. However, its molecular epigenetics are not well understood. We collected buccal cells from adult left- and right-handers (n = 60) to investigate whether epigenetic biomarkers of handedness can be identified in non-neuronal tissue. We associated DNA methylation in promoter regions of candidate genes with handedness direction. Results indicate that DNA methylation of genes asymmetrically expressed in the foetal brain or spinal cord might play a role within such a multifactorial model. Moreover, we provide tentative evidence that birth stress might be a factor that affects DNA methylation in NEUROD6, a gene that is asymmetrically expressed in foetal brains.

Promoter polymorphisms in genes involved in porcine myogenesis influence their transcriptional activity.

BackgroundSuccess of meat production and selection for improvement of meat quality is among the primary aims in animal production. Meat quality traits are economically important in swine; however, the underlying genetic nature is very complex. Therefore, an improved pork production strongly depends on identifying and studying how genetic variations contribute to modulate gene expression. Promoters are key regions in gene modulation as they harbour several binding motifs to transcription regulatory factors. Therefore, polymorphisms in these regions are likely to deeply affect RNA levels and consequently protein synthesis. In this study, we report the identification of single nucleotide polymorphisms (SNPs) in promoter regions of candidate genes involved in development, cellular differentiation and muscle growth in Sus scrofa. We identified SNPs in the promoter regions of genes belonging to the Myogenic Regulatory Factors (MRF) gene family (the Myogenic Differentiation gene, MYOD1) and to Growth and Differentiation Factors (GDF) gene family (Myostatin gene, MSTN, GDF8), in Casertana and Large White breeds. The purpose of this study was to investigate if polymorphisms in the promoters could affect the transcriptional activity of these genes. With this aim, we evaluated in vitro the functional activity of the luciferase reporter gene luc2 activity, driven by two constructs carrying different promoter haplotypes.ResultsWe tested the effects of the G302A (U12574) transition on the promoter efficiency in MYOD1 gene. We ascertained a difference in transcription efficiency for the two variants. A stronger activity of the A-carrying construct is more evident in C2C12. The luciferase expression driven by the MYOD1-A allelic variant displayed a 3.8-fold increased transcriptional activity. We investigated the activity of two haplotype variants (AY527152) in the promoter of GDF8 gene. The haploptype-1 (A435-A447-A879) up-regulated the expression of the reporter gene by a two-fold increase, and hence presumably of the GDF8 gene, in both CHO and C2C12 cultured cells.ConclusionsIn vitro the MYOD1-A allelic variant could up-regulate the expression of MYOD1 gene. Additionally, we could assess a different response of in vitro gene expression according to cell type used to transfect constructs, suggesting that MyoD activation is regulated by mechanisms that are specific of myoblasts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0119-2) contains supplementary material, which is available to authorized users.

Variation of DNA methylation in candidate age-related targets on the mitochondrial-telomere axis in cord blood and placenta

BackgroundEpigenetics is tissue-specific and potentially even cell-specific, but little information is available from human reproductive studies about the concordance of DNA methylation patterns in cord blood and placenta, as well as within-placenta variations. We evaluated methylation levels at promoter regions of candidate genes in biological ageing pathways (SIRT1, TP53, PPARG, PPARGC1A, and TFAM), a subtelomeric region (D4Z4) and the mitochondrial genome (MT-RNR1, D-loop). MethodsNinety individuals were randomly chosen from the ENVIRONAGE birth cohort to evaluate methylation concordance between cord blood and placenta using highly quantitative bisulfite-PCR pyrosequencing. In a subset of nineteen individuals, a more extensive sampling scheme was performed to examine within-placenta variation. ResultsThe DNA methylation levels of the subtelomeric region and mitochondrial genome showed concordance between cord blood and placenta with correlation coefficients ranging from r = 0.31 to 0.43, p ≤ 0.005, and also between the maternal and foetal sides of placental tissue (r = 0.53 to 0.72, p ≤ 0.05). For the majority of targets, an agreement in methylation levels between four foetal biopsies was found (with intra-class correlation coefficients ranging from 0.16 to 0.72), indicating small within-placenta variation. ConclusionsThe methylation levels of the subtelomeric region (D4Z4) and mitochondrial genome (MT-RNR1, D-loop) showed concordance between cord blood and placenta, suggesting a common epigenetic signature of these targets between tissues. Concordance was lacking between the other genes that were studied. In placental tissue, methylation patterns of most targets on the mitochondrial-telomere axis were not strongly influenced by sample location.

Endometriosis Is Characterized by a Distinct Pattern of Histone 3 and Histone 4 Lysine Modifications

The histone modification patterns in endometriosis have not been fully characterized. This gap in knowledge results in a poor understanding of the epigenetic mechanisms (and potential therapeutic targets) at play. We aimed to (1) assess global acetylation status of histone 3 (H3) and histone 4 (H4), (2) measure levels of H3 and H4 lysine (K) acetylation and methylation, and (3) to identify histone acetylation patterns in promoter regions of candidate genes in tissues from patients and controls. Global and K-specific acetylation/methylation levels of histones were measured in 24 lesions, 15 endometrium from patients, and 26 endometrium from controls. Chromatin immunoprecipitation (ChIP)-polymerase chain reaction was used to determine the histone acetylation status of the promoter regions of candidate genes in tissues. The lesions were globally hypoacetylated at H3 (but not H4) compared to eutopic endometrium from controls. Lesions had significantly lower levels of H3K9ac and H4K16ac compared to eutopic endometrium from patients and controls. Tissues from patients were hypermethylated at H3K4, H3K9, and H3K27 compared to endometrium from controls. The ChIP analysis showed hypoacetylation of H3/H4 within promoter regions of candidate genes known to be downregulated in endometriosis (e.g., HOXA10, ESR1, CDH1, and p21 (WAF1/Cip1) ) in lesions versus control endometrium. The stereoidogenic factor 1 (SF1) promoter region was enriched for acetylated H3 and H4 in lesions versus control tissues, correlating with its reported high expression in lesions. This study describes the histone code of lesions and endometrium from patients with endometriosis and provides support for a possible role of histone modification in modulation of gene expression in endometriosis.

Epigenetics and eating disorders

Eating disorders are complex psychiatric disorders in which genes, environment, and gene-environment interactions (G×E) have a role. Such G×E may occur in adulthood or during development. They may also be modified by factors such as (mal)nutrition or stress and this may result in acute or long-term epigenetic modifications. This review discusses the potential for recent developments in epigenetics to address ongoing aetiological issues in eating disorders. Epigenetic studies in eating disorders have focussed on the DNA methylation status of promoter regions of candidate genes: differences have been reported between people with eating disorders and healthy controls, and between subtypes of eating disorders. Animal studies related to eating disorders have focussed on understanding the acute and long-term effects of environmental manipulation on epigenetic changes and on the resultant phenotypes: these studies are promising, but they have also identified some of the complexity of epigenetic processing. Because of the difficulties in obtaining brain samples, epigenetic studies in eating disorders (like in other psychiatric illnesses) have used peripheral tissues, usually blood: this raises various problems. It is likely, therefore, that in the immediate future, animal, rather than human studies will guide the progress in epigenetics studies of eating disorders and other psychiatric disorders.

Pro-/anti-inflammatory cytokine gene polymorphisms and chronic kidney disease: a cross-sectional study

BackgroundThe aim of this study was to explore the associations between common potential functional promoter polymorphisms in pro-/anti-inflammatory cytokine genes and kidney function/chronic kidney disease (CKD) prevalence in a large Japanese population.MethodsA total of 3,323 subjects aged 35-69 were genotyped for all 10 single nucleotide polymorphisms (SNPs) in the promoter regions of candidate genes with minor allele frequencies of > 0.100 in Japanese populations. The estimated glomerular filtration rate (eGFR) and CKD prevalence (eGFR < 60 ml/min/1.73 m2) of the subjects were compared among the genotypes.ResultsA higher eGFR and lower prevalence of CKD were observed for the homozygous variants of IL4 -33CC (high IL-4 [anti-inflammatory cytokine]-producing genotype) and IL6 -572GG (low IL-6 [pro-inflammatory cytokine]-producing genotype). Subjects with IL4 CC + IL6 GG showed the highest mean eGFR (79.1 ml/min/1.73 m2) and lowest CKD prevalence (0.0%), while subjects carrying IL4 TT + IL6 CC showed the lowest mean eGFR (73.4 ml/min/1.73 m2) and highest CKD prevalence (17.9%).ConclusionsThe functional promoter polymorphisms IL4 T-33C (rs2070874) and IL6 C-572G (rs1800796), which are the only SNPs that affect the IL-4 and IL-6 levels in Japanese subjects, were associated with kidney function and CKD prevalence in a large Japanese population.

Tissue-specific gene expression analysis of silkworm (Bombyx mori) by quantitative real-time RT-PCR

The Bombyx mori Microarray Database (BmMDB; http://silkworm.swu.edu.cn/microarray) provides information for tissue-specific gene expression by using the whole-genome oligonucleotide microarray in the silkworm. We analyzed the tissue-specific expression patterns in the silk gland, fat body, and midgut five days of fifth instar larvae during the development of B. mori. To verify the tissue-specific expression, analysis was conducted using quantitative Real-time RT-PCR and the highly expressed endogenous Actin RNA as an intrinsic reference. Finally, we confirmed five genes, (sw15872, sw00692, sw20990, sw05300,and sw2250), out of 18 candidates expressed in two different tissues, which was consistent with the data published by Dr. Xiang's group, thereby supporting the BmMDB. Further studies for promoter regions of candidate genes can be applied in creating transgenic silkworms as biomedical insects for use in producing biomaterials, and to serve as well-characterized models for understanding the mechanism for the genetic regulation of tissue-specific development.

Tissue-specific gene expression analysis of silkworm (Bombyx mori) by quantitative real-time RT-PCR

The Bombyx mori Microarray Database (BmMDB; http://silkworm.swu.edu.cn/microarray) provides information for tissue-specific gene expression by using the whole-genome oligonucleotide microarray in the silkworm. We analyzed the tissue-specific expression patterns in the silk gland, fat body, and midgut five days of fifth instar larvae during the development of B. mori. To verify the tissue-specific expression, analysis was conducted using quantitative Real-time RT-PCR and the highly expressed endogenous Actin RNA as an intrinsic reference. Finally, we confirmed five genes, (sw15872, sw00692, sw20990, sw05300,and sw2250), out of 18 candidates expressed in two different tissues, which was consistent with the data published by Dr. Xiang's group, thereby supporting the BmMDB. Further studies for promoter regions of candidate genes can be applied in creating transgenic silkworms as biomedical insects for use in producing biomaterials, and to serve as well-characterized models for understanding the mechanism for the genetic regulation of tissue-specific development.

Cell cultures harbouring constructs of different pig promoter polymorphisms show different transcriptional efficiency in gene reporter systems

Production traits variability among and within breeds, differences among developmental stages or the response to different environments are in part due to genetic factors that affect gene expression. Within the context of an Italian FIRB project, whose objective is to identify genes and molecular mechanisms affecting meat quality and production traits in pig, we studied the promoter regions of candidate genes selected on the basis of their physiological role in animal tissue development or composition. Genomic DNA was isolated from liver or muscle tissue of individuals belonging to Large White and Casertana breed. PCR primers were designed to amplify 5’ upstream region of SCD (Stearoyl-CoA Desaturase), LDLR (Low Density Lipoprotein Receptor), LEP (Leptin), MSTN (Myostatin), ACTA1 (Alpha-actin) and HFABP (Heart Fatty Acid Binding Protein) genes using sequences available at NCBI. A total of 19 single nucleotide polymorphisms (SNPs) not previously described were characterised. Some haplotypes, harbouring SNPs located within, or closely flanking potential cis-acting elements, were used to carry out an in vitro analysis of the efficiency of promoter natural variants. Up to 1200 bases upstream the translation start codon were cloned in pGL3 basic vector in phase with the downstream luciferase reporter gene. The different luminescence intensities showed by constructs harbouring allelic variants suggest transcriptional efficiency influenced by polymorphism. The knowledge of a correlation between a different transcriptional activity and a particular haplotype could be a useful tool to identify variation at genes controlling important traits in pig.