Integrative analysis of genome‐wide DNA methylation and gene expression profiles reveals important epigenetic genes related to milk production traits in dairy cattle

2021 ◽  
Author(s):  
Wanting Dong ◽  
Jie Yang ◽  
Yu Zhang ◽  
Shuli Liu ◽  
Chao Ning ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dairy Cattle ◽  
Milk Production ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Integrative Analysis ◽  
Production Traits ◽  
Milk Production Traits ◽  
Genome Wide

scholarly journals Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 850
Author(s):  
Marcello Del Corvo ◽  
Silvia Bongiorni ◽  
Bruno Stefanon ◽  
Sandy Sgorlon ◽  
Alessio Valentini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Nervous System ◽  
Dairy Cattle ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing ◽  
Regulatory Functions ◽  
Cattle Health

Dairy cattle health, wellbeing and productivity are deeply affected by stress. Its influence on metabolism and immune response is well known, but the underlying epigenetic mechanisms require further investigation. In this study, we compared DNA methylation and gene expression signatures between two dairy cattle populations falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine marker of stress in dairy cows. Reduced Representation Bisulfite Sequencing was used to obtain a methylation map from blood samples of these animals. The high and low groups exhibited similar amounts of methylated CpGs, while we found differences among non-CpG sites. Significant methylation changes were detected in 248 genes. We also identified significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) analysis showed that genes of both groups act together in several pathways, such as nervous system activity, immune regulatory functions and glucocorticoid metabolism. These preliminary results suggest that, in livestock, cortisol secretion could act as a trigger for epigenetic regulation and that peripheral changes in methylation can provide an insight into central nervous system functions.

scholarly journals Integrated analysis of genome-wide DNA methylation and gene expression profiles identifies potential novel biomarkers of rectal cancer

Oncotarget ◽  
2016 ◽  
Vol 7 (38) ◽  
pp. 62547-62558 ◽  
Author(s):  
Jiufeng Wei ◽  
Guodong Li ◽  
Jinning Zhang ◽  
Yuhui Zhou ◽  
Shuwei Dang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Rectal Cancer ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Integrated Analysis ◽  
Genome Wide ◽  
Novel Biomarkers

scholarly journals Monozygotic Twins Discordant for Immunoglobulin A Nephropathy Display Differences in DNA Methylation and Gene Expression

2020 ◽  
pp. 1-10
Author(s):  
Min Wei ◽  
Sijun Meng ◽  
Sufang Shi ◽  
Lijun Liu ◽  
Xujie Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Profiles ◽  
Immunoglobulin A ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Genome Wide ◽  
Mz Twins

<b><i>Introduction:</i></b> Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis. It involves both genetic and environmental factors, among which DNA methylation, the most studied epigenetic modification, was shown to play a role. Here, we assessed genome-wide DNA methylation and gene expression profiles in 2 pairs of IgAN-discordant monozygotic (MZ) twins, in order to characterize methylation changes and their potential influences on gene expression in IgAN. <b><i>Methods:</i></b> Genome-wide DNA methylation and gene expression profiles were evaluated in peripheral blood mononuclear cells obtained from 2 IgAN-discordant MZ twins. Differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were detected, and an integrated analysis was performed. Finally, functional enrichment analysis was done for DMR-associated genes and DEGs. <b><i>Results:</i></b> Totally 521 DMRs were detected for 2 IgAN-discordant MZ twins. Among them, 9 DMRs were found to be mapped to genes that differentially expressed in 2 MZ twins, indicating the potential regulatory mechanisms of expression for these 9 genes (<i>MNDA</i>, <i>DYSF</i>, <i>IL1R2</i>, <i>TLR6</i>, <i>TREML2</i>, <i>TREM1</i>, <i>IL32</i>, <i>S1PR5</i>, and <i>ADGRE3</i>) in IgAN. Biological process analysis of them showed that they were mostly involved in the immune system process. Functional enrichment analysis of DEGs and DMR-associated genes both identified multiple pathways relevant to inflammatory and immune responses. And DMR-associated genes were significantly enriched in terms related to T-cell function. <b><i>Conclusions:</i></b> Our findings indicate that changes in DNA methylation patterns were involved in the pathogenesis of IgAN. Nine target genes detected in our study may provide new ideas for the exploration of molecular mechanisms of IgAN.

Abstract 40: Transcriptome and DNA Methylation Changes in Patients with Subarachnoid Hemorrhage Undergoing Remote Ischemic Preconditioning

Stroke ◽  
2015 ◽  
Vol 46 (suppl_1) ◽  
Author(s):  
Elina Nikkola ◽  
Arthur Ko ◽  
Mark J Connolly ◽  
Yinn Cher Ooi ◽  
Päivi Pajukanta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Profiles ◽  
Methylation Status ◽  
Gene Expression Profiles ◽  
Reduced Representation ◽  
Ischemic Conditioning ◽  
Genome Wide ◽  
Reduced Representation Bisulfite Sequencing ◽  
Before And After

Background: Remote ischemic conditioning (RIC) is a phenomenon by which brief periods of sublethal ischemia in one tissue confers protection from ischemia to distant tissues. We hypothesize that RIC triggers a cascade of integrated gene expression and methylation changes, leading to neuroprotection in subarachnoidal hemorrhage (SAH) patients. Our goal was to identify and compare changes in DNA methylation and gene expression profiles before and after RIC. Methods: Patients enrolled in a clinical trial of RIC after SAH, receiving RIC by limb cuff transient ischemia sessions. Fourteen SAH patients (64% female, mean age 51) underwent 3-4 RIC sessions and gave a blood sample before and after RIC, seven days apart. The transcriptome analysis of whole blood was performed using paired-end, 100-bp RNA-sequencing. We employed STAR and HTSeq to align and count reads; EdgeR to normalize the counts and detect differential expression (DE); and David to search for functional categories of the DE genes. Genome-wide DNA methylation profiles were assessed using reduced representation bisulfite sequencing (RRBS); Bismark with Bowtie to align the RRBS data, and the differential methylation analysis package (DMAP) to call the methylation status of CpG sites. Bedtools was used to overlap the DE genes with differentially methylated regions. Results: Of the 12,411 genes passing QC, 168 genes were differentially expressed after RIC (FDR<0.05). These genes were enriched for pathways involving mitosis and nuclear division (P50% after RIC in at least one individual. Of the 8,069 sites, 723 were differentially methylated (Bonferroni P<0.05). Our overlap analysis showed that 88 of the significantly altered methylation sites resided in 39 DE genes, including CEACAM8 and CRISP3, both implicated previously for stroke. Conclusions: Our data suggest that RIC alters expression of a specific set of genes involved in stroke via changes in regional DNA methylation. Further studies are warranted to replicate these pilot results.

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