Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates

Abstract Background Use of cannabidiol (CBD), the primary non-psychoactive compound found in cannabis, has recently risen dramatically, while relatively little is known about the underlying molecular mechanisms of its effects. Previous work indicates that direct CBD exposure strongly impacts the brain, with anxiolytic, antidepressant, antipsychotic, and other effects being observed in animal and human studies. The epigenome, particularly DNA methylation, is responsive to environmental input and can direct persistent patterns of gene regulation impacting phenotype. Epigenetic perturbation is particularly impactful during embryogenesis, when exogenous exposures can disrupt critical resetting of epigenetic marks and impart phenotypic effects lasting into adulthood. The impact of prenatal CBD exposure has not been evaluated; however, studies using the psychomimetic cannabinoid Δ9-tetrahydrocannabinol (THC) have identified detrimental effects on psychological outcomes in developmentally exposed adult offspring. We hypothesized that developmental CBD exposure would have similar negative effects on behavior mediated in part by the epigenome. Nulliparous female wild-type Agouti viable yellow (Avy) mice were exposed to 20 mg/kg CBD or vehicle daily from two weeks prior to mating through gestation and lactation. Coat color shifts, a readout of DNA methylation at the Agouti locus in this strain, were measured in F1 Avy/a offspring. Young adult F1 a/a offspring were then subjected to tests of working spatial memory and anxiety/compulsive behavior. Reduced-representation bisulfite sequencing was performed on both F0 and F1 cerebral cortex and F1 hippocampus to identify genome-wide changes in DNA methylation for direct and developmental exposure, respectively. Results F1 offspring exposed to CBD during development exhibited increased anxiety and improved memory behavior in a sex-specific manner. Further, while no significant coat color shift was observed in Avy/a offspring, thousands of differentially methylated loci (DMLs) were identified in both brain regions with functional enrichment for neurogenesis, substance use phenotypes, and other psychologically relevant terms. Conclusions These findings demonstrate for the first time that despite positive effects of direct exposure, developmental CBD is associated with mixed behavioral outcomes and perturbation of the brain epigenome.

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Epigenome-wide association study of seizures in childhood and adolescence

Clinical Epigenetics ◽

10.1186/s13148-019-0793-z ◽

2020 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Doretta Caramaschi ◽

Charlie Hatcher ◽

Rosa H. Mulder ◽

Janine F. Felix ◽

Charlotte A. M. Cecil ◽

...

Keyword(s):

Dna Methylation ◽

Genetic Variants ◽

Mendelian Randomization ◽

Independent Study ◽

Childhood And Adolescence ◽

Parents And Children ◽

Genome Wide ◽

Common Genetic Variants ◽

The Brain ◽

Avon Longitudinal Study

AbstractThe occurrence of seizures in childhood is often associated with neurodevelopmental impairments and school underachievement. Common genetic variants associated with epilepsy have been identified and epigenetic mechanisms have also been suggested to play a role. In this study, we analyzed the association of genome-wide blood DNA methylation with the occurrence of seizures in ~ 800 children from the Avon Longitudinal Study of Parents and Children, UK, at birth (cord blood), during childhood, and adolescence (peripheral blood). We also analyzed the association between the lifetime occurrence of any seizures before age 13 with blood DNA methylation levels. We sought replication of the findings in the Generation R Study and explored causality using Mendelian randomization, i.e., using genetic variants as proxies. The results showed five CpG sites which were associated cross-sectionally with seizures either in childhood or adolescence (1–5% absolute methylation difference at pFDR < 0.05), although the evidence of replication in an independent study was weak. One of these sites was located in the BDNF gene, which is highly expressed in the brain, and showed high correspondence with brain methylation levels. The Mendelian randomization analyses suggested that seizures might be causal for changes in methylation rather than vice-versa. In conclusion, we show a suggestive link between seizures and blood DNA methylation while at the same time exploring the limitations of conducting such study.

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Epigenome-wide association study of seizures in childhood and adolescence

10.1101/19005116 ◽

2019 ◽

Author(s):

Doretta Caramaschi ◽

Charlie Hatcher ◽

Rosa H. Mulder ◽

Janine F. Felix ◽

Charlotte A. M. Cecil ◽

...

Keyword(s):

Dna Methylation ◽

Genetic Variants ◽

Cognitive Skills ◽

Mendelian Randomization ◽

Independent Study ◽

Childhood And Adolescence ◽

Parents And Children ◽

Genome Wide ◽

Common Genetic Variants ◽

The Brain

ABSTRACTThe occurrence of seizures in childhood is often associated with neurodevelopmental impairments and school underachievement. Common genetic variants associated with epilepsy have been identified and epigenetic mechanisms have also been suggested to play a role. In this study we analysed the association of genome-wide blood DNA methylation with the occurrence of seizures in ∼800 children from the Avon Longitudinal Study of Parents and Children, UK, at birth (cord blood), during childhood and adolescence (peripheral blood). We also analysed the association between the lifetime occurrence of any seizures before age 13 with blood DNA methylation levels. We sought replication of the findings in the Generation R Study and explored causality using Mendelian randomization, i.e. using genetic variants as proxies. The results showed five CpG sites which were associated cross-sectionally with seizures either in childhood or adolescence (1-5% absolute methylation difference at pFDR<0.05), although the evidence of replication in an independent study was weak. One of these sites was located in the BDNF gene, which is highly expressed in the brain, and showed high correspondence with brain methylation levels. The Mendelian randomization analyses suggested that seizures might be causal for changes in methylation rather than vice-versa. In addition, seizure-associated methylation changes could affect other outcomes such as growth, cognitive skills and educational attainment. In conclusion, we present a link between seizures and DNA methylation which suggests that DNA methylation changes might mediate some of the effects of seizures on growth and neurodevelopment.

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

Reproduction Fertility and Development ◽

10.1071/rdv31n1ab1 ◽

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.

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Leukocyte methylomic imprints of exposure to the genocide against the Tutsi in Rwanda: a pilot epigenome-wide analysis

Epigenomics ◽

10.2217/epi-2021-0310 ◽

2021 ◽

Author(s):

Clarisse Musanabaganwa ◽

Agaz H Wani ◽

Janelle Donglasan ◽

Segun Fatumo ◽

Stefan Jansen ◽

...

Keyword(s):

Dna Methylation ◽

Quality Control ◽

Association Study ◽

Comparison Group ◽

In Utero ◽

Differentially Methylated Regions ◽

The Brain

We conducted a pilot epigenome-wide association study of women from Tutsi ethnicity exposed to the genocide while pregnant and their resulting offspring, and a comparison group of women who were pregnant at the time of the genocide but living outside of Rwanda. Fifty-nine leukocyte-derived DNA samples survived quality control: 33 mothers (20 exposed, 13 unexposed) and 26 offspring (16 exposed, 10 unexposed). Twenty-four significant differentially methylated regions (DMRs) were identified in mothers and 16 in children. In utero genocide exposure was associated with CpGs in three of the 24 DMRs: BCOR, PRDM8 and VWDE, with higher DNA methylation in exposed versus unexposed offspring. Of note, BCOR and VWDE show significant correlation between brain and blood DNA methylation within individuals, suggesting these peripherally derived signals of genocide exposure may have relevance to the brain.

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Genome-wide DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) residing in mouse pluripotent stem cells

Genes to Cells ◽

10.1111/j.1365-2443.2010.01404.x ◽

2010 ◽

Vol 15 (6) ◽

pp. 607-618 ◽

Cited By ~ 22

Author(s):

Shinya Sato ◽

Shintaro Yagi ◽

Yoshikazu Arai ◽

Keiji Hirabayashi ◽

Naoko Hattori ◽

...

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Pluripotent Stem Cells ◽

Methylation Profile ◽

Differentially Methylated Regions ◽

Genome Wide ◽

Dna Methylation Profile

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

10.21203/rs.3.rs-20775/v2 ◽

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.

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

The Open Bioinformatics Journal ◽

10.2174/1875036202114010144 ◽

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.

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

10.21203/rs.3.rs-20775/v3 ◽

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.

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Pre-Implantation Alcohol Exposure Induces Lasting Sex-Specific DNA Methylation Programming Errors in the Developing Forebrain

10.1101/2020.12.07.415208 ◽

2020 ◽

Author(s):

LM Legault ◽

K Doiron ◽

M Breton-Larrivée ◽

A Langford-Avelar ◽

A Lemieux ◽

...

Keyword(s):

Dna Methylation ◽

De Novo ◽

Prenatal Alcohol Exposure ◽

Alcohol Exposure ◽

Fetal Alcohol ◽

Developmental Program ◽

Genome Wide ◽

Fetal Alcohol Spectrum ◽

The Brain

ABSTRACTPrenatal alcohol exposure is recognized for altering DNA methylation profiles of brain cells during development, and to be part of the molecular basis underpinning Fetal Alcohol Spectrum Disorder (FASD) etiology. However, we have negligible information on the effects of alcohol exposure during pre-implantation, the early embryonic window marked with dynamic DNA methylation reprogramming, and on how this may rewire the brain developmental program. Using a pre-clinical in vivo mouse model, we show that pre-implantation alcohol exposure leads to adverse developmental outcomes that replicate clinical characteristics observed in children with FASD. Genome-wide DNA methylation analyses of fetal forebrains uncovered sex-specific alterations, including partial loss of DNA methylation maintenance at imprinting control regions, and abnormal de novo DNA methylation profiles in various biological pathways (e.g., neural/brain development). These findings support the contribution of alcohol-induced DNA methylation programming deviations during pre-implantation to the manifestation of neurodevelopmental phenotypes associated with FASD.

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