Dynamic changes of genomic methylation profiles at different growth stages in Chinese Tan sheep

Background Tan sheep, an important local sheep breed in China, is famous for their fur quality. One-month-old Tan sheep have white, curly hair with beautiful flower spikes, commonly known as “nine bends”, which has high economic value. However, the “nine bends” characteristic gradually disappears with age; consequently, the economic value of the Tan sheep decreases. Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression. Until now, no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages. In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing, and compared the DNA methylation levels at three different growth stages: 1, 24, and 48 months old (mon1, mon24, and mon48, respectively). Results In this study, 11 skin samples from three growth stages (four for mon1, four for mon24, and three for mon48) were used for DNA methylation analysis and gene expression profiling. There were 52, 288 and 236 differentially methylated genes (DMGs) identified between mon1 and mon24, mon1 and mon48, and mon24 and mon48, respectively. Of the differentially methylated regions, 1.11%, 7.61%, and 7.65% were in the promoter in mon1 vs. mon24, mon24 vs. mon48, and mon1 vs. mon48, respectively. DMGs were enriched in the MAPK and WNT signaling pathways, which are related to age growth and hair follicle morphogenesis processes. There were 51 DMGs associated with age growth and curly fleece formation. Four DMGs between mon1 and mon48 (KRT71, CD44, ROR2 and ZDHHC13) were further validated by bisulfite sequencing. Conclusions This study revealed dynamic changes in the genomic methylation profiles of mon1, mon24, and mon48 sheep, and the percentages of methylated cytosines were 3.38%, 2.85% and 4.17%, respectively. Of the DMGs, KRT71 and CD44 were highly methylated in mon1, and ROR2 and ZDHHC13 were highly methylated in mon48. These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep.

Advances in the DNA methylation hydroxylase TET1

Background The ten-eleven translocation 1 (TET1) protein is a 5-methylcytosine hydroxylase that belongs to the TET protein family of human α-ketoglutarate oxygenases. TET1 recognizes and binds to regions of high genomic 5′-CpG-3′ dinucleotide density, such as CpG islands, initiates the DNA demethylation program, and maintains DNA methylation and demethylation balance to maintain genomic methylation homeostasis and achieve epigenetic regulation. This article reviews the recent research progress of TET1 in the mechanism of demethylation, stem cells and immunity, various malignant tumours and other clinical diseases. Conclusion TET1 acts as a key factor mediating demethylation, the mechanism of which still remains to be investigated in detail. TET1 is also critical in maintaining the differentiation pluripotency of embryonic stem cells and plays anti- or oncogenic roles in combination with different signalling pathways in different tumours. In certain tumours, its role is still controversial. In addition, the noncatalytic activity of TET1 has gradually attracted attention and has become a new direction of research in recent years.

Correcting Methylation Calls in Clinically Relevant Low-Mappability Regions

DNA methylation is an important component in vital biological functions such as embryonic development, carcinogenesis, and heritable regulation. Accurate methods to assess genomic methylation status are crucial to its effective use in many scenarios, especially in the detection and diagnosis of disease. Methylation aligners, such as Bismark and bwa-meth, frequently assign significantly higher MapQ values than can be supported by the uniqueness of the region reads are mapped to. These incorrectly high MapQs result in inappropriate methylation calling in repetitive regions. We observe reads that should map to separate locations (possibly having different methylation states) actually end up mapping to the same locus, causing apparent mixed methylation at such loci. Methylation calling can be improved by using Bismap mappability data to filter out insufficiently unique reads. However, simply filtering out Cs in insufficiently unique regions is not adequate as it is prone to over-filtering Cs in small mappability dips. These Cs can in fact often be called using reads anchored in a nearby mappable region. We have created a new feature for the MethylDackel methylation caller to perform read-based filtering. This new methylation calling method resolves some of the apparent mixed methylation to either 0% or 100% methylation and removes many unsupportable methylation calls. We examined methylation calls with and without read-based filtering in or near the 7830 genes containing ClinVar variants in a methylation sequencing data set from the NA12878 cell line. Use of this improved method corrected 41,143 mixed methylation Cs to 0% methylation, and 22,345 to 100% methylation throughout the genome.

TANC1 methylation as a novel biomarker for the diagnosis of patients with anti-tuberculosis drug-induced liver injury

We aimed to elucidate the differences in genomic methylation patterns between ADLI and non-ADLI patients to identify DNA methylation-based biomarkers. Genome-wide DNA methylation patterns were obtained using Infinium MethylationEPIC (EPIC) BeadChip array to analyze 14 peripheral blood samples (7 ADLI cases, 7 non-ADLI controls). Changes in the mRNA and DNA methylation in the target genes of another 120 peripheral blood samples (60 ADLI cases, 60 non-ADLI controls) were analyzed by real-time polymerase chain reaction and pyrosequencing, respectively. A total of 308 hypermethylated CpG sites and 498 hypomethylated CpG sites were identified. Significantly, hypermethylated CpG sites cg06961147 and cg24666046 in TANC1 associated with ADLI was identified by genome-wide DNA methylation profiling. The mRNA expression of TANC1 was lower in the cases compared to the controls. Pyrosequencing validated these two differentially methylated loci, which was consistent with the results from the EPIC BeadChip array. Receiver operating characteristic analysis indicated that the area under the curve of TANC1 (cg06961147, cg24666046, and their combinations) was 0.812, 0.842, and 0.857, respectively. These results indicate that patients with ADLI have different genomic methylation patterns than patients without ADLI. The hypermethylated differentially methylated site cg06961147 combined with cg24666046 in TANC1 provides evidence for the diagnosis of ADLI.

Epigenetic models predict age and aging in plains zebras and other equids

ABSTRACTFive of the seven extant wild species of the genus Equus are species of significant conservation concern. Effective conservation and management of such threatened wildlife populations depends on the ability to estimate demographic trends and population viability and therefore requires accurate assessment of age structure. However, reliably aging wildlife is challenging as many methods are highly invasive, inaccurate, or both. Epigenetic aging models, which estimate individual age with high accuracy based on genomic methylation patterns, are promising developments in this regard. Importantly, epigenetic aging models developed for one species can potentially predict age with high accuracy in sister taxa. Using blood and biopsy samples from known age plains zebras (Equus quagga), we developed epigenetic clocks (ECs) to predict chronological age, and epigenetic pacemaker (EPM) models to predict biological age. We tested the ability of our blood-based EC to predict ages of Grevy’s zebras, Somali asses and domestic horses, from blood samples. Because our samples came from a population with a complex pedigree, we also leveraged information from a previous sequencing effort to measure the association between levels of inbreeding (F and ROH) and the age acceleration as measured by DNA methylation. The resulting models describe the trajectory of epigenetic aging in plains zebras and accurately predict the ages of plains zebras and other equids. We found moderate support for a slight acceleration of aging with increased inbreeding.

Clopidogrel Resistance Is Associated With DNA Methylation of Genes From Whole Blood of Humans

Antiplatelet therapy has become a cornerstone in the treatment of coronary heart disease (CHD). However, due to high-residual-platelet-reactivity, clopidogrel resistance (CR) is a common phenomenon, and it is rarely known about the relationship between CR and epigenetic changes. This study compared the whole genomic methylation patterns of blood samples from patients with CR (n = 6) and non-CR (n = 6) with the Human Methylation 850K BeadChip assay. We explored differentially methylated CpG sites, genes, and pathways using bioinformatics profiling. The CR and control groups showed significantly different DNA methylation at 7,098 sites, with 979 sites showing hypermethylation and 6,119 sites showing hypomethylation. The pyrosequencing method was used to validate four differentially methylated CpG loci (cg23371584, cg15971518, cg04481923, cg22507406), confirming that DNA methylation was associated with the risk of CR (30 CR vs. 30 non-CR). The relative mRNA expression of the four genes (BTG2, PRG2, VTRNA2-1, PER3) corresponding to the loci above was also associated with CR, suggesting that alterations in DNA methylation may affect the expression of these four genes, eventually resulting in CR. Additionally, differentially methylated sites are partially related to genes and pathways that play key roles in process of circadian entrainment, insulin secretion, and so on. Hence, the mechanism and biological regulation of CR might be reflected through these epigenetic alterations, but future research will need to address the causal relationships.

Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in osteosarcoma

ABSTRACTBackgroundOsteosarcoma (OSA) is an aggressive malignancy predominantly affecting children and young-adults. Genetic analysis has characterized very few recurrent mutations in OSA, and an improved understanding of interpatient tumor heterogeneity is needed for clinical management.MethodsWe analyzed genome-wide DNA methylation in primary OSA tumors from the NCI Therapeutically Applicable Research to Generate Effective Treatments (TARGET) program (n = 83) profiled using the Illumina 450K methylation array. We tested if broad genomic methylation predicted outcomes and defined supervised methylomic signatures predictive of Recurrence Free Survival (RFS), Chemotherapy Response (CR), and Metastatic disease at Diagnosis (MetDx). We assessed methylation pattern reproducibility in two independent clinical datasets (n = 28 and 34) and in an in vitro dataset (n = 11). Correlations between genomic methylation and transcription were tested using TARGET RNA-seq data. An in silico pharmacogenomic screen was performed to identify agents for future stratified application.ResultsGenome-wide methylation defined two subgroups. Relatively hypomethylated tumors experienced better chemotherapy response (Odds Ratio = 6.429, Fisher’s p = 0.007), longer RFS (metastatic, median 2.3 vs 26.7 months, localized, median 63.5 vs 104.7 months, stratified log-rank p = 0.006), and Overall Survival (p = 5×10-4) than hypermethylated tumors. Robust genomic methylation signatures predictive of RFS and CR were defined, and the signatures’ methylation patterns were reproducible in the independent clinical and in vitro datasets. The RFS signature was enriched for intragenic sites, whereas the CR signature and clinically relevant genome-wide methylation patterns were enriched for intergenic sites. Normal-tissue-like methylation patterns were associated with poor prognosis and in vitro analysis suggested that the methylation signatures are associated with tumor aggressiveness. Downstream transcriptional analysis revealed that genes annotated to the RFS methylation signature were also predictive survival. The transcriptional program represented in the RFS signature included several critical cellular pathways, whereas the CR signature was associated with much fewer known pathways, possibly reflecting a much broader cellular “methylation state” related to chemoresponse. A pharmacogenomic screen identified potential therapies, including epigenomic modifiers, for future stratified clinical application.ConclusionGenomic methylation offers insight into patient prognosis and could be a useful tool for developing alternate adjuvant therapeutic strategies.