161 Epigenetic Changes in Poultry Due to Reprogramming of the Gut Microbiota at an Early Stage of Embryonic Development

Abstract Epigenetic regulation of the gene expression is an interaction of the external environment with the genetic information. They are potentially heritable changes in the gene expression which does not involve alteration in DNA sequence and can be triggered by microRNA activity and DNA methylation. MicroRNA is fraction of small RNA molecules that have a fundamental impact on gene expression. DNA methylation inhibits DNA transcription by addition of the methyl residues to the cysteine within the CpG islands of the gene promoters. These processes can be modulated by environmental factors, such as intestinal microbiota modification. In poultry, the microbiota can be reprogrammed using in ovo technology at an early stage of embryo development. The intestinal microbiota is therefore stimulated and rearranged by injecting bioactive substances into air chamber of eggs on the day 12 of incubation. We have proved that the administration of lactic acid bacteria strains and galactooligosaccharide in ovo is effective in modulating of the intestinal microbiota. The administration of bioactive compounds has been demonstrated to influence gene expression in immune, intestinal and metabolic tissues. However, it has been noticed that a significant part of genes is silenced. In our experiment after in ovo administration of the substances in different genotypes (chicken broiler and native Polish breed) the range of tissues was collected: liver, caecal tonsils, spleen. By performing the bioinformatic analysis of the expression microarray, silenced genes and active miRNAs were selected. Methylation was analysed using the global and MSP-qPCR method, and analysis of miRNA activity using miRCURY LNA PCR Systems. We confirmed that negative regulation of the gene expression have epigenetic character and its mechanism depends on the genotype and the substance administered in ovo. Epigenetic nature of research is new direction of host-microbiome interaction. Research was financed by grant UMO-2017/25/N/NZ9/01822 funded by National Science Centre (Poland).

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Hepatic DNA Methylation in Response to Early Stimulation of Microbiota with Lactobacillus Synbiotics in Broiler Chickens

Genes ◽

10.3390/genes11050579 ◽

2020 ◽

Vol 11 (5) ◽

pp. 579 ◽

Cited By ~ 1

Author(s):

Aleksandra Dunislawska ◽

Anna Slawinska ◽

Maria Siwek

Keyword(s):

Dna Methylation ◽

Intestinal Microbiota ◽

Broiler Chickens ◽

Cpg Islands ◽

Gene Promoters ◽

In Ovo ◽

Lactobacillus Salivarius ◽

Egg Incubation ◽

Metabolic Gene Expression ◽

Stimulation Of

DNA methylation inhibits DNA transcription by the addition of methyl residues to cysteine within the CpG islands of gene promoters. The process of DNA methylation can be modulated by environmental factors such as intestinal microbiota. In poultry, the composition of the intestinal microbiota can be stimulated by in ovo delivery of synbiotics. The present study aims to determine the effect of Lactobacillus synbiotics delivered in ovo on the level of hepatic DNA methylation in broiler chickens. In ovo stimulation was performed on day 12 of egg incubation. Bioactive compounds delivered in ovo included (S1)—Lactobacillus salivarius with GOS and (S2)—Lactobacillus plantarum with RFO. Samples were collected from six individuals from each group on day 42 post-hatching. DNA methylation of five genes selected on the basis of the transcriptome data were analyzed using the qMSP method. Significant changes were observed in DNA methylation of genes in liver including ANGPTL4 and NR4A3, after S2 delivery. The obtained results confirm that the downregulation of metabolic gene expression in the liver mediated by in ovo stimulation had epigenetic characteristics.

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Interaction between early in ovo stimulation of the gut microbiota and chicken host – splenic changes in gene expression and methylation

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-021-00602-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

A. Dunislawska ◽

A. Slawinska ◽

M. Gryzinska ◽

M. Siwek

Keyword(s):

Gene Expression ◽

Epigenetic Regulation ◽

Regulation Of Gene Expression ◽

Gene Promoters ◽

Gene Methylation ◽

In Ovo ◽

Bioactive Substances ◽

Global Methylation ◽

D 12 ◽

Methylation Patterns

Abstract Background Epigenetic regulation of the gene expression results from interaction between the external environment and transcription of the genetic information encoded in DNA. Methylated CpG regions within the gene promoters lead to silencing of the gene expression in most cases. Factors contributing to epigenetic regulation include intestinal microbiota, which in chicken can be potently modified by in ovo stimulation. The main aim of this study was to determine global and specific methylation patterns of the spleen under the influence of host-microbiome interaction. Results Fertilized eggs of two genotypes: Ross 308 and Green-legged Partridgelike were in ovo stimulated on d 12 of incubation. The injected compounds were as follows: probiotic – Lactococcus lactis subsp. cremoris IBB477, prebiotic – galactooligosaccharides, and synbiotic – combination of both. Chickens were sacrificed on d 42 post-hatching. Spleen was collected, RNA and DNA were isolated and intended to gene expression, gene methylation and global methylation analysis. We have proved that negative regulation of gene expression after administration of bioactive substances in ovo might have epigenetic character. Epigenetic changes depend on the genotype and the substance administered in ovo. Conclusion Epigenetic nature of microbial reprogramming in poultry and extension of issues related to host-microbiome interaction is a new direction of this research.

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Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte

10.1101/2021.03.11.434836 ◽

2021 ◽

Author(s):

Courtney W. Hanna ◽

Jiahao Huang ◽

Christian Belton ◽

Susanne Reinhardt ◽

Andreas Dahl ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Gene Expression Analysis ◽

Cpg Islands ◽

Conditional Knockout ◽

Epigenetic Mark ◽

Gene Promoters ◽

Downregulated Gene ◽

Mammalian Development ◽

Histone 3

SummaryHistone 3 lysine 4 trimethylation (H3K4me3) is an epigenetic mark found at gene promoters and CpG islands. H3K4me3 is essential for mammalian development, yet mechanisms underlying its genomic targeting are poorly understood. H3K4me3 methyltransferases SETD1B and MLL2 are essential for oogenesis. We investigated changes in H3K4me3 in Setd1b conditional knockout (cKO) GV oocytes using ultra-low input ChIP-seq, in conjunction with DNA methylation and gene expression analysis. Setd1b cKO oocytes showed a redistribution of H3K4me3, with a marked loss at active gene promoters associated with downregulated gene expression. Remarkably, many regions gained H3K4me3 in Setd1b cKOs, in particular those that were DNA hypomethylated, transcriptionally inactive and CpG-rich - hallmarks of MLL2 targets. Thus, loss of SETD1B appears to enable enhanced MLL2 activity. Our work reveals two distinct, complementary mechanisms of genomic targeting of H3K4me3 in oogenesis, with SETD1B linked to gene expression in the oogenic program and MLL2 to CpG content.

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Do age-related changes in DNA methylation play a role in the development of age-related diseases?

Biochemical Society Transactions ◽

10.1042/bst20120358 ◽

2013 ◽

Vol 41 (3) ◽

pp. 803-807 ◽

Cited By ~ 26

Author(s):

Sanne D. van Otterdijk ◽

John C. Mathers ◽

Gordon Strathdee

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Cpg Islands ◽

Large Body ◽

Epigenetic Mechanism ◽

Aberrant Methylation ◽

Gene Promoters ◽

Cpg Sites ◽

Pathological Conditions ◽

Age Related

DNA methylation is an important epigenetic mechanism in mammalian cells. It occurs almost exclusively at CpG sites and has a key role in a number of biological processes. It plays an important part in regulating chromatin structure and has been best studied for its role in controlling gene expression. In particular, hypermethylation of gene promoters which have high levels of CpG sites, known as CpG islands, leads to gene inactivation. In healthy cells, however, it appears that only a small number of genes are controlled through promoter hypermethylation, such as genes on the inactivated X-chromosome or at imprinted loci, and most promoter-associated CpG islands remain methylation-free regardless of gene expression status. However, a large body of evidence has now shown that this protection from methylation not only breaks down in a number of pathological conditions (e.g. cancer), but also already occurs during the normal process of aging. The present review focuses on the methylation changes that occur during healthy aging and during disease development, and the potential links between them. We focus especially on the extent to which the acquisition of aberrant methylation changes during aging could underlie the development of a number of important age-related pathological conditions.

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Interaction Between Early in Ovo Stimulation of the Gut Microbiota and Chicken Host – Splenic Changes in Gene Expression and Methylation

10.21203/rs.3.rs-114215/v1 ◽

2020 ◽

Author(s):

Aleksandra Dunislawska ◽

Anna Slawinska ◽

Magdalena Gryzinska ◽

Maria Siwek

Keyword(s):

Gene Expression ◽

Epigenetic Regulation ◽

Regulation Of Gene Expression ◽

Gene Promoters ◽

Gene Methylation ◽

In Ovo ◽

Bioactive Substances ◽

Global Methylation ◽

Methylation Patterns ◽

Rna And Dna

Abstract Epigenetic regulation of the gene expression results from interaction between the external environment and transcription of the genetic information encoded in DNA. Methylated CpG regions within the gene promoters lead to silencing of the gene expression. Factors contributing to epigenetic regulation include intestinal microbiota, which in chicken can be potently modified by in ovo stimulation. The main aim of this study was to determine global and specific methylation patterns for the spleen under the influence of host-microbiome interaction. Incubating eggs were in ovo stimulated on day 12 of incubation in two chicken genotypes: Ross broilers and Green-legged Partridgelike. The injected compounds included: probiotic – Lactococcus lactis subsp. cremoris, prebiotic – galactooligosaccharides, and synbiotic – combination of both. Chickens were sacrificed on day 42 post-hatching. Spleen was collected, RNA and DNA were isolated and intended to gene expression, gene methylation and global methylation analysis. We have proved that negative regulation of gene expression after administration of bioactive substances in ovo might have epigenetic character. Epigenetic changes depend on the genotype and the substance administered in ovo. Epigenetic nature of microbial reprogramming in poultry and extension of issues related to host-microbiome interaction is a new direction of this research.

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Interaction between Early in Ovo Stimulation of the Gut Microbiota and Chicken Host – Splenic Changes in Gene Expression and Methylation

10.21203/rs.3.rs-142257/v1 ◽

2021 ◽

Author(s):

Aleksandra Dunislawska ◽

Anna Slawinska ◽

Magdalena Gryzinska ◽

Maria Siwek

Keyword(s):

Gene Expression ◽

Epigenetic Regulation ◽

Regulation Of Gene Expression ◽

Gene Promoters ◽

Gene Methylation ◽

In Ovo ◽

Bioactive Substances ◽

Global Methylation ◽

Methylation Patterns ◽

Rna And Dna

Abstract Background: Epigenetic regulation of the gene expression results from interaction between the external environment and transcription of the genetic information encoded in DNA. Methylated CpG regions within the gene promoters lead to silencing of the gene expression. Factors contributing to epigenetic regulation include intestinal microbiota, which in chicken can be potently modified by in ovo stimulation. The main aim of this study was to determine global and specific methylation patterns for the spleen under the influence of host-microbiome interaction. Results: Incubating eggs were in ovo stimulated on day 12 of incubation in two chicken genotypes: Ross broilers and Green-legged Partridgelike. The injected compounds included: probiotic – Lactococcus lactis subsp. cremoris, prebiotic – galactooligosaccharides, and synbiotic – combination of both. Chickens were sacrificed on day 42 post-hatching. Spleen was collected, RNA and DNA were isolated and intended to gene expression, gene methylation and global methylation analysis. We have proved that negative regulation of gene expression after administration of bioactive substances in ovo might have epigenetic character. Epigenetic changes depend on the genotype and the substance administered in ovo. Conclusion: Epigenetic nature of microbial reprogramming in poultry and extension of issues related to host-microbiome interaction is a new direction of this research.

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Abstract 40: Disturbed Flow Alters Genomewide DNA Methylation Patterns, Regulating Endothelial Gene Expression and Atherosclerosis

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.34.suppl_1.40 ◽

2014 ◽

Vol 34 (suppl_1) ◽

Author(s):

Jessilyn Dunn ◽

Haiwei Qiu ◽

Soyeon Kim ◽

Daudi Jjingo ◽

Ryan Hoffman ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Dna Methyltransferase ◽

Methylation Status ◽

Western Diet ◽

Dependent Manner ◽

Gene Promoters ◽

Genome Wide ◽

Methylation Patterns ◽

Endothelial Gene Expression

Atherosclerosis preferentially occurs in arterial regions of disturbed blood flow (d-flow), which alters gene expression, endothelial function, and atherosclerosis. Here, we show that d-flow regulates genome-wide DNA methylation patterns in a DNA methyltransferase (DNMT)-dependent manner. We found that d-flow induced expression of DNMT1, but not DNMT3a or DNMT3b, in mouse arterial endothelium in vivo and in cultured endothelial cells by oscillatory shear (OS) compared to unidirectional laminar shear in vitro. The DNMT inhibitor 5-Aza-2’deoxycytidine (5Aza) or DNMT1 siRNA significantly reduced OS-induced endothelial inflammation. Moreover, 5Aza reduced lesion formation in two atherosclerosis models using ApoE-/- mice (western diet for 3 months and the partial carotid ligation model with western diet for 3 weeks). To identify the 5Aza mechanisms, we conducted two genome-wide studies: reduced representation bisulfite sequencing (RRBS) and transcript microarray using endothelial-enriched gDNA and RNA, respectively, obtained from the partially-ligated left common carotid artery (LCA exposed to d-flow) and the right contralateral control (RCA exposed to s-flow) of mice treated with 5Aza or vehicle. D-flow induced DNA hypermethylation in 421 gene promoters, which was significantly prevented by 5Aza in 335 genes. Systems biological analyses using the RRBS and the transcriptome data revealed 11 mechanosensitive genes whose promoters were hypermethylated by d-flow but rescued by 5Aza treatment. Of those, five genes contain hypermethylated cAMP-response-elements in their promoters, including the transcription factors HoxA5 and Klf3. Their methylation status could serve as a mechanosensitive master switch in endothelial gene expression. Our results demonstrate that d-flow controls epigenomic DNA methylation patterns in a DNMT-dependent manner, which in turn alters endothelial gene expression and induces atherosclerosis.

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Micro-biopsy for detection of gene expression changes in ischemic swine myocardium: A pilot study

PLoS ONE ◽

10.1371/journal.pone.0250582 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0250582

Author(s):

Arvin Chireh ◽

Rikard Grankvist ◽

Mikael Sandell ◽

Abdul Kadir Mukarram ◽

Fabian Arnberg ◽

...

Keyword(s):

Gene Expression ◽

Pilot Study ◽

Early Stage ◽

Cell Types ◽

Bioinformatic Analysis ◽

Balloon Occlusion ◽

Deconvolution Analysis ◽

Infarcted Area ◽

Tissue Changes ◽

Apoptosis And Inflammation

Micro-endomyocardial biopsy (micro-EMB) is a novel catheter-based biopsy technique, aiming to increase flexibility and safety compared to conventional EMB. The technique was developed and evaluated in healthy swine. Therefore, the ability to detect disease related tissue changes could not be evaluated. The aim of the present pilot study was to investigate the ability to detect disease related gene expression changes using micro-EMB. Myocardial infarction was induced in three swine by coronary artery balloon occlusion. Micro-EMB samples (n = 164) were collected before, during, and after occlusion. RNA-sequencing was performed on 85 samples, and 53 of these were selected for bioinformatic analysis. A large number of responding genes was detected from the infarcted area (n = 1911). The early responding genes (n = 1268) were mostly related to apoptosis and inflammation. There were fewer responding genes two days after infarction (n = 6), which were related to extra-cellular matrix changes, and none after 14 days. In contrast to the infarcted area, samples harvested from a non-infarcted myocardial region showed considerably fewer regulated genes (n = 33). Deconvolution analysis, to estimate the proportion of different cell types, revealed a higher proportion of fibroblasts and a reduced proportion of cardiomyocytes two days after occlusion compared to baseline (p < 0.02 and p < 0.01, respectively. S5 File). In conclusion, this pilot study demonstrates the capabilities of micro-EMB to detect local gene expression responses at an early stage after ischemia, but not at later timepoints.

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Effects of in ovo feeding of vitamin C on post-hatch performance, immune status and DNA methylation-related gene expression in broiler chickens

British Journal Of Nutrition ◽

10.1017/s000711452000210x ◽

2020 ◽

Vol 124 (9) ◽

pp. 903-911 ◽

Cited By ~ 1

Author(s):

Yufei Zhu ◽

Shizhao Li ◽

Yulan Duan ◽

Zhouzheng Ren ◽

Xin Yang ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Vitamin C ◽

Antioxidant Capacity ◽

Broiler Chickens ◽

Immune Status ◽

Stimulation Index ◽

Average Daily Gain ◽

Related Gene ◽

In Ovo

AbstractThis study aimed to evaluate the effect of in ovo feeding (IOF) of vitamin C at embryonic age 11 (E11) on post-hatch performance, immune status and DNA methylation-related gene expression in broiler chickens. A total of 240 Arbor Acres breeder eggs (63 (sem 0·5) g) were randomly divided into two groups: normal saline and vitamin C (VC) groups. After incubation, newly hatched chicks from each group were randomly divided into six replicates with ten chicks per replicate. Hatchability, average daily feed intake (D21–42 and D1–42), and average daily gain and feed conversion ratio (D1–21) were improved by vitamin C treatment (P < 0·05). IOF of vitamin C increased vitamin C content (D1), total antioxidant capacity (D42), IgA (D1), IgM (D1 and D21), stimulation index for T lymphocyte (D35) and lysozyme activity (D21) in plasma (P < 0·05). On D21, vitamin C increased the splenic expression of IL-4 and DNMT1 and decreased IL-1β, Tet2, Tet3 and Gadd45β expression (P < 0·05). On D42, vitamin C increased the splenic expression of IL-4 and DNMT3A and decreased IFN-γ, Tet3, MBD4 and TDG expression (P < 0·05). In conclusion, the vitamin C via in ovo injection can be absorbed by broiler’s embryo and IOF of vitamin C at E11 improves the post-hatch performance and immune status and, to some extent, the antioxidant capacity of broiler chickens. The expression of enzyme-related DNA methylation and demethylation indicates that the level of DNA methylation may increase in spleen in the VC group and whether the fluctuating expression of pro- and anti-inflammatory cytokines is related to DNA methylation change remained to be further investigated.

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