Whole genome DNA methylation sequencing of the chicken retina, cornea and brain

Epigenetic regulation is a key component of stress responses, acclimatization and adaptation processes in plants. DNA methylation is a stable mark plausible for the inheritance of epigenetic traits, such that it is a potential scheme for plant breeding. However, the effect of modulators of stress responses, as hydrogen peroxide (H2O2), in the methylome status has not been elucidated. A transgenic tobacco model to the CchGLP gene displayed high H2O2 endogen levels correlated with biotic and abiotic stresses resistance. The present study aimed to determine the DNA methylation status changes in the transgenic model to obtain more information about the molecular mechanism involved in resistance phenotypes. The Whole-genome bisulfite sequencing analysis revealed a minimal impact of overall levels and distribution of methylation. A total of 9432 differential methylated sites were identified in distinct genome regions, most of them in CHG context, with a trend to hypomethylation. Of these, 1117 sites corresponded to genes, from which 83 were also differentially expressed in the plants. Several genes were associated with respiration, energy, and calcium signaling. The data obtained highlighted the relevance of the H2O2 in the homeostasis of the system in stress conditions, affecting at methylation level and suggesting an association of the H2O2 in the physiological adaptation to stress functional linkages may be regulated in part by DNA methylation.

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A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation

Genetics ◽

10.1534/genetics.116.195008 ◽

2017 ◽

Vol 205 (4) ◽

pp. 1443-1458 ◽

Cited By ~ 10

Author(s):

Owen J. L. Rackham ◽

Sarah R. Langley ◽

Thomas Oates ◽

Eleni Vradi ◽

Nathan Harmston ◽

...

Keyword(s):

Dna Methylation ◽

Bayesian Approach ◽

Bisulfite Sequencing ◽

Whole Genome ◽

Sequencing Data ◽

Whole Genome Bisulfite Sequencing ◽

Genome Bisulfite Sequencing ◽

Bisulfite Sequencing Data

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Whole genome DNA methylation: beyond genes silencing

Oncotarget ◽

10.18632/oncotarget.13562 ◽

2016 ◽

Vol 8 (3) ◽

pp. 5629-5637 ◽

Cited By ~ 52

Author(s):

Roberto Tirado-Magallanes ◽

Khadija Rebbani ◽

Ricky Lim ◽

Sriharsa Pradhan ◽

Touati Benoukraf

Keyword(s):

Dna Methylation ◽

Whole Genome

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Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles

Human Molecular Genetics ◽

10.1093/hmg/ddaa218 ◽

2020 ◽

Author(s):

Benjamin I Laufer ◽

Hyeyeon Hwang ◽

Julia M Jianu ◽

Charles E Mordaunt ◽

Ian F Korf ◽

...

Keyword(s):

Dna Methylation ◽

Down Syndrome ◽

Early Life ◽

Trisomy 21 ◽

Bisulfite Sequencing ◽

Dried Blood Spots ◽

Whole Genome ◽

Genome Wide ◽

Low Pass ◽

Genome Bisulfite Sequencing

Abstract Neonatal dried blood spots (NDBS) are a widely banked sample source that enables retrospective investigation into early life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early life Down syndrome (DS) DNA methylation profiles. DS represents an example of genetics shaping epigenetics, as multiple array-based studies have demonstrated that trisomy 21 is characterized by genome-wide alterations to DNA methylation. By assaying over 24 million CpG sites, thousands of genome-wide significant (q < 0.05) differentially methylated regions (DMRs) that distinguished DS from typical development and idiopathic developmental delay were identified. Machine learning feature selection refined these DMRs to 22 loci. The DS DMRs mapped to genes involved in neurodevelopment, metabolism, and transcriptional regulation. Based on comparisons with previous DS methylation studies and reference epigenomes, the hypermethylated DS DMRs were significantly (q < 0.05) enriched across tissues while the hypomethylated DS DMRs were significantly (q < 0.05) enriched for blood-specific chromatin states. A ~28 kb block of hypermethylation was observed on chromosome 21 in the RUNX1 locus, which encodes a hematopoietic transcription factor whose binding motif was the most significantly enriched (q < 0.05) overall and specifically within the hypomethylated DMRs. Finally, we also identified DMRs that distinguished DS NDBS based on the presence or absence of congenital heart disease (CHD). Together, these results not only demonstrate the utility of low-pass WGBS on NDBS samples for epigenome-wide association studies, but also provide new insights into the early life mechanisms of epigenomic dysregulation resulting from trisomy 21.

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Erratum to: Whole Genome DNA Methylation Analysis of Brachypodium distachyon Using Next-Generation Sequencing (BS-seq)

Brachypodium Genomics - Methods in Molecular Biology ◽

10.1007/978-1-4939-7278-4_19 ◽

2018 ◽

pp. E1-E1

Author(s):

I-Hsuan Lin

Keyword(s):

Dna Methylation ◽

Next Generation Sequencing ◽

Brachypodium Distachyon ◽

Whole Genome ◽

Next Generation ◽

Methylation Analysis ◽

Dna Methylation Analysis ◽

Generation Sequencing

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A Bayesian approach for analysis of whole-genome bisulphite sequencing data identifies disease-associated changes in DNA methylation

10.1101/041715 ◽

2016 ◽

Author(s):

Owen J.L. Rackham ◽

Sarah R. Langley ◽

Thomas Oates ◽

Eleni Vradi ◽

Nathan Harmston ◽

...

Keyword(s):

Dna Methylation ◽

Epigenetic Modification ◽

Promoter Hypermethylation ◽

Whole Genome ◽

Sequencing Data ◽

Accurate Identification ◽

Bisulphite Sequencing ◽

Consistent Change ◽

Rat Strain ◽

Differential Transcription

ABSTRACTDNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulphite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome whilst taking into account the distance between CpG sites as a covariate. Our simulation study shows that ABBA has greater power to detect DMRs than existing methods, providing an accurate identification of DMRs in the large majority of simulated cases. To empirically demonstrate the method’s efficacy in generating biological hypotheses, we performed WGBS of primary macrophages derived from an experimental rat system of glomerulonephritis and used ABBA to identify >1,000 disease-associated DMRs. Investigation of these DMRs revealed differential DNA methylation localized to a 600bp region in the promoter of the Ifitm3 gene. This was confirmed by ChIP-seq and RNA-seq analyses, showing differential transcription factor binding at the Ifitm3 promoter by JunD (an established determinant of glomerulonephritis) and a consistent change in Ifitm3 expression. Our ABBA analysis allowed us to propose a new role for Ifitm3 in the pathogenesis of glomerulonephritis via a mechanism involving promoter hypermethylation that is associated with Ifitm3 repression in the rat strain susceptible to glomerulonephritis.

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Whole-Genome Methylation Analysis Revealed ART-Specific DNA Methylation Pattern of Neuro- and Immune-System Pathways in Chinese Human Neonates

Frontiers in Genetics ◽

10.3389/fgene.2021.696840 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zongzhi Liu ◽

Wei Chen ◽

Zilong Zhang ◽

Junyun Wang ◽

Yi-Kun Yang ◽

...

Keyword(s):

Dna Methylation ◽

Immune System ◽

Cord Blood ◽

Genetic Model ◽

Housekeeping Genes ◽

Normal Pregnancy ◽

Methylation Pattern ◽

Whole Genome ◽

Maternal Cell ◽

Dna Methylation Pattern

The DNA methylation of human offspring can change due to the use of assisted reproductive technology (ART). In order to find the differentially methylated regions (DMRs) in ART newborns, cord blood maternal cell contamination and parent DNA methylation background, which will add noise to the real difference, must be removed. We analyzed newborns’ heel blood from six families to identify the DMRs between ART and natural pregnancy newborns, and the genetic model of methylation was explored, meanwhile we analyzed 32 samples of umbilical cord blood of infants born with ART and those of normal pregnancy to confirm which differences are consistent with cord blood data. The DNA methylation level was lower in ART-assisted offspring at the whole genome-wide level. Differentially methylated sites, DMRs, and cord blood differentially expressed genes were enriched in the important pathways of the immune system and nervous system, the genetic patterns of DNA methylation could be changed in the ART group. A total of three imprinted genes and 28 housekeeping genes which were involved in the nervous and immune systems were significant different between the two groups, six of them were detected both in heel blood and cord blood. We concluded that there is an ART-specific DNA methylation pattern involved in neuro- and immune-system pathways of human ART neonates, providing an epigenetic basis for the potential long-term health risks in ART-conceived neonates.

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Genetic and Epigenetic Changes Are Rapid Responses of the Genome to the Newly Synthesized Autotetraploid Carassius auratus

Frontiers in Genetics ◽

10.3389/fgene.2020.576260 ◽

2021 ◽

Vol 11 ◽

Author(s):

Chongqing Wang ◽

Yuwei Zhou ◽

Huan Qin ◽

Chun Zhao ◽

Li Yang ◽

...

Keyword(s):

Dna Methylation ◽

Carassius Auratus ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Enrichment Analysis ◽

Full Length ◽

Aflp Analysis ◽

Whole Genome ◽

Epigenetic Alterations ◽

Fish Genome

Whole genome duplication events have occurred frequently during the course of vertebrate evolution. To better understand the influence of polyploidization on the fish genome, we herein used the autotetraploid Carassius auratus (4n = 200, RRRR) (4nRR) resulting from the whole genome duplication of Carassius auratus (2n = 100, RR) (RCC) to explore the genomic and epigenetic alterations after polyploidization. We subsequently performed analyses of full-length transcriptome dataset, amplified fragment length polymorphism (AFLP) and methylation sensitive amplification polymorphism (MSAP) on 4nRR and RCC. By matching the results of 4nRR and RCC isoforms with reference genome in full-length transcriptome dataset, 649 and 1,971 novel genes were found in the RCC and 4nRR full-length geneset, respectively. Compared to Carassius auratus and Megalobrama amblycephala, 4nRR presented 3,661 unexpressed genes and 2,743 expressed genes. Furthermore, GO enrichment analysis of expressed genes in 4nRR revealed that they were enriched in meiosis I, whereas KEGG enrichment analysis displayed that they were mainly enriched in proteasome. Using AFLP analysis, we noted that 32.61% of RCC fragments had disappeared, while 32.79% of new bands were uncovered in 4nRR. Concerning DNA methylation, 4nRR exhibited a lower level of global DNA methylation than RCC. Additionally, 60.31% of methylation patterns in 4nRR were altered compared to RCC. These observations indicated that transcriptome alterations, genomic changes and regulation of DNA methylation levels and patterns had occurred in the newly established autotetraploid genomes, suggesting that genetic and epigenetic alterations were influenced by autotetraploidization. In summary, this study provides valuable novel insights into vertebrate genome evolution and generates relevant information for fish breeding.

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Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling

PLoS ONE ◽

10.1371/journal.pone.0254971 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0254971

Author(s):

Federico Rossi ◽

Alessandro Crnjar ◽

Federico Comitani ◽

Rodrigo Feliciano ◽

Leonie Jahn ◽

...

Keyword(s):

Dna Methylation ◽

Tree Ring ◽

High Throughput ◽

Environmental Conditions ◽

High Throughput Sequencing ◽

Wood Formation ◽

Whole Genome ◽

Library Preparation ◽

Bisulfite Treatment ◽

Standing Trees

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.

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164 Genome-wide DNA Methylation Profiling in in Utero Heat-stressed Pigs as Measured by Whole-genome Bisulfite Sequencing

Journal of Animal Science ◽

10.1093/jas/skab235.157 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 87-88

Author(s):

Luiz F Brito ◽

Jacob M Maskal ◽

Shi-Yi Chen ◽

Hinayah R Oliveira ◽

Jason R Graham ◽

...

Keyword(s):

Dna Methylation ◽

Heat Stress ◽

Cellular Response ◽

Bisulfite Sequencing ◽

Cholesterol Biosynthesis ◽

In Utero ◽

Whole Genome ◽

Whole Genome Bisulfite Sequencing ◽

Differentially Methylated Genes ◽

Genome Bisulfite Sequencing

Abstract In utero heat stress (IUHS) has several postnatal consequences in pigs that compromise health, increase stress response, and reduce performance. These phenotypes may be caused by epigenetic modifications such as DNA methylation, which are heritable molecular modifications that impact gene expression and phenotypic outcomes without changing the DNA sequence. Therefore, we aimed to compare the DNA methylation profiles between in-utero thermoneutral (IUTN) and IUHS pigs to identify differentially methylated regions. Twenty-four pregnant gilts were evenly assigned to either a thermoneutral (17.5 ± 2.1°C) or heat stress (cycling 26 to 36°C) chamber from d 0 to 59 of gestation, followed by thermoneutral conditions (20.9 ± 2.3°C) for the rest of gestation and until the piglets were weaned. At 105 d of age, 10 IUTN and 10 IUHS piglets were euthanized and Longissimus dorsi muscle samples were collected and used to perform whole-genome bisulfite sequencing (WGBS). Purified genomic DNA was fragmented and bisulfite conversion was performed. Illumina platforms were used to sequence WGBS libraries. All pigs had similar proportions of methylation at CpG sites. Two-hundred-sixty-eight genomic regions were differentially methylated between IUTN and IUHS pigs. These identified regions are located across all pig chromosomes and ranged from 2 (SSC18) to 40 (SSC10). Eighty-five unique differentially-methylated genes were identified. These genes have been reported to be involved in key biological processes such as transcriptional repressor activity and tRNA processing (e.g., SKOR2,TRMT6, TSEN2), cellular response to heat stress (e.g.,CCAR2), placental vascularization (e.g.,FZD5), central nervous system (e.g.,VEPH1), cholesterol biosynthesis (e.g., CYB5R1), insulin receptor substrate (e.g.,IRS2), synaptic transmission (e.g.,RIMBP2), neurotrophic factor receptor activity (e.g.,LIFR), immune response (e.g., CD84), DNA repair (e.g., CHD1L), and cell proliferation and endocrine signaling (e.g., SSTR1, CYB5R1). These findings contribute to a better understanding of the epigenomic mechanisms underlying postnatal consequences of IUHS in pigs.

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