scholarly journals Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and transcription factor ZGPAT co-regulate milk production

2020 ◽  
Author(s):  
Jinwei Xin ◽  
Zhixin Chai ◽  
Chengfu Zhang ◽  
Qiang Zhang ◽  
Yong Zhu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Network Analysis ◽  
Milk Production ◽  
Breast Tissue ◽  
Biceps Brachii ◽  
Age Groups ◽  
High Expression ◽  
Differentially Methylated Regions ◽  
Genome Wide ◽  
Gene Correlation

Abstract Background Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiological adaptabilities to high-altitude environment, such as the strong capacity of blood oxygen transportation and high metabolism. The role of DNA methylation and network of gene expression underlying milk production and adaptation to high altitudes of yak need further exploration. Results We performed genome-wide DNA methylome and transcriptome analyses of breast, lung, and biceps brachii muscle from yaks of different ages. We identified differentially methylated regions (DMRs) across age groups within the each tissue. The breast tissue had considerably more differentially methylated regions than that from the three younger age groups. Hypomethylated genes with high expression level might regulate milk production by influencing protein processing in the endoplasmic reticulum. Weighted gene correlation network analysis revealed that the “hub” gene ZGPAT was highly expressed in the post-mature breast tissue. It potentially regulated the transcription of 280 genes, which play roles in regulating protein synthesis, processing, and secretion. Besides, Tissue network analysis indicates that high expression of HIF1A regulates energy metabolism in the lung. Conclusions The results of this comprehensive study provide a solid basis for understanding the epigenetic mechanisms underlying milk production in yaks, which could be helpful to breeding programs aimed at improving milk production.

scholarly journals Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jinwei Xin ◽  
Zhixin Chai ◽  
Chengfu Zhang ◽  
Qiang Zhang ◽  
Yong Zhu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Network Analysis ◽  
Milk Production ◽  
Breast Tissue ◽  
Biceps Brachii ◽  
Age Groups ◽  
High Expression ◽  
Differentially Methylated Regions ◽  
Muscle Tissues ◽  
Gene Correlation

Abstract Background Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiological adaptations to high-altitude environment, including strong blood oxygen transportation capabilities and high metabolism. The roles of DNA methylation and gene expression in milk production and high-altitudes adaptation need further exploration. Results We performed genome-wide DNA methylome and transcriptome analyses of breast, lung, and biceps brachii muscle tissues from yaks of different ages. We identified 432,350 differentially methylated regions (DMRs) across the age groups within each tissue. The post-mature breast tissue had considerably more differentially methylated regions (155,957) than that from the three younger age groups. Hypomethylated genes with high expression levels might regulate milk production by influencing protein processing in the endoplasmic reticulum. According to weighted gene correlation network analysis, the “hub” gene ZGPAT was highly expressed in the post-mature breast tissue, indicating that it potentially regulates the transcription of 280 genes that influence protein synthesis, processing, and secretion. The tissue network analysis indicated that high expression of HIF1A regulates energy metabolism in the lung. Conclusions This study provides a basis for understanding the epigenetic mechanisms underlying milk production in yaks, and the results offer insight to breeding programs aimed at improving milk production.

scholarly journals Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and transcription factor ZGPAT co-regulate milk production

2020 ◽  
Author(s):  
Jinwei Xin ◽  
Zhixin Chai ◽  
Chengfu Zhang ◽  
Qiang Zhang ◽  
Yong Zhu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Network Analysis ◽  
Milk Production ◽  
Breast Tissue ◽  
Age Groups ◽  
High Expression ◽  
Differentially Methylated Regions ◽  
Genome Wide ◽  
Younger Age ◽  
Gene Correlation

Abstract Background Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat, and have evolved numerous physiological adaptabilities to high-altitude landscape, such as strong capacity of blood oxygen transportation and high metabolism. The role of DNA methylation and network of gene expression underlying milk production and adaptation to high altitudes of yak need further exploration. Results We performed genome-wide DNA methylome and transcriptome analyses of breast, lungs, and gluteal muscle from yaks of different ages. We identified differentially methylated regions (DMRs) across age groups within the each tissue, and breast tissue had considerably more differentially methylated regions than that from the three younger age groups. Hypomethylated genes with high expression level might regulate milk production by influencing protein processing in the endoplasmic reticulum. Weighted gene correlation network analysis revealed that the “hub” gene ZGPAT was highly expressed in post-mature breast tissue and that it potentially regulated the transcription of 280 genes, which play roles in regulating protein synthesis, processing, and secretion. Besides, Tissue network analysis indicates that high expression of HIF1A regulates energy metabolism in the lung. Conclusions The results of this comprehensive study provide a solid basis for understanding the epigenetic mechanisms underlying milk production in yaks, which could be helpful to breeding programs aimed at improving milk production.

scholarly journals Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production

2020 ◽  
Author(s):  
Jinwei Xin ◽  
Zhixin Chai ◽  
Chengfu Zhang ◽  
Qiang Zhang ◽  
Yong Zhu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Network Analysis ◽  
Milk Production ◽  
Breast Tissue ◽  
Biceps Brachii ◽  
Age Groups ◽  
High Expression ◽  
Differentially Methylated Regions ◽  
Muscle Tissues ◽  
Gene Correlation

Abstract BackgroundDomestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiological adaptations to high-altitude environment, including strong blood oxygen transportation capabilities and high metabolism. The roles of DNA methylation and gene expression in milk production and high-altitudes adaptation need further exploration. Results We performed genome-wide DNA methylome and transcriptome analyses of breast, lung, and biceps brachii muscle tissues from yaks of different ages. We identified 432,350 differentially methylated regions (DMRs) across the age groups within each tissue. The post-mature breast tissue had considerably more differentially methylated regions (155,957) than that from the three younger age groups. Hypomethylated genes with high expression levels might regulate milk production by influencing protein processing in the endoplasmic reticulum. According to weighted gene correlation network analysis, the “hub” gene ZGPAT was highly expressed in the post-mature breast tissue, indicating that it potentially regulates the transcription of 280 genes that influence protein synthesis, processing, and secretion. The tissue network analysis indicated that high expression of HIF1A regulates energy metabolism in the lung. ConclusionsThis study provides a basis for understanding the epigenetic mechanisms underlying milk production in yaks, and the results offer insight to breeding programs aimed at improving milk production.

scholarly journals Methylome and transcriptome analyses of yaks of different ages revealed that DNA methylation and transcription factor ZGPAT co-regulate milk production

2020 ◽  
Author(s):  
Jinwei Xin ◽  
Zhixin Chai ◽  
Chengfu Zhang ◽  
Qiang Zhang ◽  
Yong Zhu ◽  
...  
Keyword(s):  
Network Analysis ◽  
Milk Production ◽  
Breast Tissue ◽  
Molecular Mechanisms ◽  
Age Groups ◽  
High Expression ◽  
Genome Wide ◽  
Different Ages ◽  
Gene Correlation ◽  
Transcriptome Analyses

Abstract Background Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat, and have evolved numerous physiological adaptabilities to high-altitude landscape, such as strong capacity of blood oxygen transportation and high metabolism. The molecular mechanisms underlying milk production and adaptation to high altitudes of yak need further exploration. Results We performed genome-wide DNA methylome and transcriptome analyses of breast, lungs, and gluteal muscle from yaks of different ages. We identified differentially methylated regions (DMRs) across age groups within the each tissue, and breast tissue had considerably more differential methylation than that from the three younger age groups. Hypomethylated genes with high expression level might regulate milk production by influencing protein processing in the endoplasmic reticulum. Weighted gene correlation network analysis revealed that the “hub” gene ZGPAT was highly expressed in adult breast tissue and that it potentially regulated the transcription of 280 genes, which play roles in regulating protein synthesis, processing, and secretion. Besides, Tissue network analysis indicates that high expression of HIF1A regulates energy metabolism in the lung. Conclusions The results of this comprehensive study provide a solid basis for understanding the epigenetic mechanisms underlying milk production in yaks, which could be helpful to breeding programs aimed at improving milk production.

scholarly journals Landscape of genome-wide age-related DNA methylation in breast tissue

Oncotarget ◽  
2017 ◽  
Vol 8 (70) ◽  
pp. 114648-114662 ◽  
Author(s):  
Min-Ae Song ◽  
Theodore M. Brasky ◽  
Daniel Y. Weng ◽  
Joseph P. McElroy ◽  
Catalin Marian ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Breast Tissue ◽  
Age Related ◽  
Genome Wide

1 Whole-genome bisulfite sequencing of bovine gametes and invivo-produced pre-implantation embryos

2019 ◽  
Vol 31 (1) ◽  
pp. 126
Author(s):  
J. E. Duan ◽  
Z. Jiang ◽  
F. Alqahtani ◽  
I. Mandoiu ◽  
H. Dong ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Cell ◽  
Epigenetic Regulation ◽  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Differentially Methylated Regions ◽  
Whole Genome Bisulfite Sequencing ◽  
Cpg Sites ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing

Dynamic changes in DNA methylation are crucial in the epigenetic regulation of mammalian embryogenesis. Global DNA methylation studies in the bovine, however, remain mostly at the immunostaining level. We adopted the single-cell whole-genome bisulfite sequencing method to characterise stage-specific genome-wide DNA methylation in bovine sperm, individual oocytes derived invivo and invitro, and invivo-developed embryos at the 2-, 4-, 8-, and 16-cell stages. This method allowed us to theoretically cover all CpG sites in the genome using a limited number of cells from single embryos. Pools of 20 sperm were selected from a bull with proven fertility. Single oocytes (n=6) and embryos (n=4 per stage) were collected from Holstein cows (n=10). Single-cell whole-genome bisulfite sequencing libraries were prepared and sequenced using the Illumina HiSEqn 4000 platform (Illumina, San Diego, CA, USA). Sequencing reads were filtered and aligned to the bovine reference genome (UMD 3.1.1) using Bismark (Krueger and Andrews 2011Bioinformatics27, 1571-1572, DOI: 10.1093/bioinformatics/btr167).A 300-bp tile-based method was applied to bin the genome into consecutive windows to facilitate comparison across samples. The DNA methylation level was calculated as the fraction of read counts of the total number of cytosines (methylated) in the total read counts of reported cytosines and thymines (methylated and unmethylated), only if more than 3 CpG sites were covered in this tile. Gamete-specific differentially methylated regions were identified when DNA methylation levels were greater than 75% in one type of gamete and less than 25% in the other with false discovery rate-corrected Fisher’s exact test P-values of less than 0.05. The major wave of genome-wide DNA demethylation was complete at the 8-cell stage when de novo methylation became prominent. Sperm and oocytes had numerous differentially methylated regions that were enriched in intergenic regions. Differentially methylated regions were also identified between invivo- and invitro-matured oocytes. Moreover, X chromosome methylation followed the global dynamic patterns. Virtually no (less than 1.5%) DNA methylation was found in mitochondrial DNA. Finally, using our RNA sequencing data generated from the same developmental stages (Jiang et al. 2014 BMC Genomics 15, 756; DOI: 10.1186/1471-2164-15-756), we revealed an inverse correlation between gene expression and promoter methylation. Our study provides the first fully comprehensive analysis of the global dynamics of DNA methylation in bovine gametes and single early embryos using single-cell whole-genome bisulfite sequencing. These data provide insights into the critical features of the methylome of bovine embryos and serve as an important reference for embryos produced by assisted reproduction, such as IVF and cloning, and a model for human early embryo epigenetic regulation.

scholarly journals Use of Two Complementary Bioinformatic Approaches to Identify Differentially Methylated Regions in Neonatal Sepsis

2021 ◽  
Vol 14 (1) ◽  
pp. 144-152
Author(s):  
Paula Navarrete ◽  
María José Garzón ◽  
Sheila Lorente-Pozo ◽  
Salvador Mena-Mollá ◽  
Máximo Vento ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Neonatal Sepsis ◽  
Late Onset ◽  
Underlying Disease ◽  
Methylation Pattern ◽  
Differentially Methylated Regions ◽  
Genome Wide ◽  
Bioinformatic Approaches ◽  
Using Data ◽  
Underlying Mechanisms

Background: Neonatal sepsis is a heterogeneous condition affecting preterm infants whose underlying mechanisms remain unknown. The analysis of changes in the DNA methylation pattern can contribute to improving the understanding of molecular pathways underlying disease pathophysiology. Methylation EPIC 850K BeadChip technology is an excellent tool for genome-wide methylation analyses and the detection of differentially methylated regions (DMRs). Objective: The aim is to identify DNA methylation traits in complex diseases, such as neonatal sepsis, using data from Methylation EPIC 850K BeadChip arrays. Methods: Two different bioinformatic methods, DMRcate (a supervised approach) and mCSEA (an unsupervised approach), were used to identify DMRs using EPIC data from leukocytes of neonatal septic patients. Here, we describe with detail the implementation of both methods as well as their applicability, briefly discussing the results obtained for neonatal sepsis. Results: Differences in methylation levels were observed in neonatal sepsis patients. Moreover, differences were identified between the two subsets of the disease: Early-Onset neonatal Sepsis (EOS) and Late-Onset Neonatal Sepsis (LOS). Conclusion: This approach by using DMRcate and mCSA helped us to gain insight into the intricate mechanisms that may drive EOS and LOS development and progression in newborns.

scholarly journals Epigenetics biomarkers of delirium: immune response, inflammatory response and cholinergic synaptic involvement evidenced by genome-wide DNA methylation analysis of delirious inpatients

2019 ◽  
Author(s):  
Taku Saito ◽  
Hiroyuki Toda ◽  
Gabrielle N. Duncan ◽  
Sydney S. Jellison ◽  
Tong Yu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Immune Response ◽  
Network Analysis ◽  
Tnf Alpha ◽  
Epigenetic Biomarkers ◽  
Genome Wide ◽  
A Genome ◽  
Significant Difference ◽  
Dnam Level

ABSTRACTBackgroundThe authors previously hypothesized the role of epigenetics in pathophysiology of delirium, and tested DNA methylation (DNAm) change among pro-inflammatory cytokines along with aging in blood, glia and neuron. The authors reported that DNAm level of the TNF-alpha decreases along with aging in blood and glia, but not in neuron; however, DNAm differences between delirium cases and non-delirium controls have not been investigated directly. Therefore, in the present study, DNAm differences in blood between delirium patients and controls without delirium were examined.MethodsA case-control study with 92 subjects was conducted. Whole blood samples were collected and genome-wide DNAm was measured by the Infinium HumanMethylationEPIC BeadChip arrays. The correlation between DNAm levels in the TNF-alpha and age, network analysis, and the correlation between age and DNAm age were tested.ResultsOnly delirium cases showed 3 CpGs sites in the TNF-alpha significantly correlated to age after multiple corrections. A genome-wide significant CpG site near the gene of LDLRAD4 was identified. In addition, network analysis showed several significant pathways with false discovery rate adjusted p-value < 0.05. The top pathway with GO was immune response, and the second top pathway with KEGG was cholinergic synapse. Although there was no statistically significant difference, DNAm age among non-delirium controls showed “slower aging” compared to delirium cases.ConclusionsDNAm differences were shown both at gene and network levels between delirium cases and non-delirium controls. This finding indicates that DNAm status in blood has a potential to be used as epigenetic biomarkers for delirium.

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