swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing

Wang, Zhen; Li, Xianfeng; Jiang, Yi; Shao, Qianzhi; Liu, Qi; Chen, Bingyu; Huang, Dongsheng

doi:10.1371/journal.pone.0132866

Cited by 53 publications

(40 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is consistent with a large body of research that documents spatial clustering among functionally associated CpGs 39 , and with the generally accepted acknowledgement that some of the primary functions of DNA methylation, such as blocking access to the transcription machinery, depend on the accumulation of multiple methyl groups over a stretch of DNA 40,41 , thus contributing to the clustered patterns of methylation that are observed over the genome. As others have proposed 42 , we suggest that this spatial clustering can be used as an additional indicator of biological significance beyond the traditional statistical reliance on the observed strength of the association.…”

Section: Technical Advancesmentioning

confidence: 79%

“…We developed a sliding-window based statistical analysis approach similar to the swDMR method previously described 42 , with the key difference that instead of identifying differentially methylated regions (DMRs) that differ significantly between two groups of subjects as swDMR1 does, we identified methylation regions that are significantly associated with a continuous or quantitative clinical variable, for the analysis of depressive symptoms, attachment style, and history of trauma. The method we developed is as follows: starting from every single CpG locus, a window is defined if more than 5 CpGs are identified within a 1000 bp span.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Epigenetic signatures of attachment insecurity and childhood adversity provide evidence for role transition in the pathogenesis of perinatal depression

et al. 2020

View full text Add to dashboard Cite

Early life adversity and insecure attachment style are known risk factors for perinatal depression. The biological pathways linking these experiences, however, have not yet been elucidated. We hypothesized that overlap in patterns of DNA methylation in association with each of these phenomena could identify genes and pathways of importance. Specifically, we wished to distinguish between allostatic-load and role-transition hypotheses of perinatal depression. We conducted a large-scale analysis of methylation patterns across 5 × 10 6 individual CG dinucleotides in 54 women participating in a longitudinal prospective study of perinatal depression, using clustering-based criteria for significance to control for multiple comparisons. We identified 1580 regions in which methylation density was associated with childhood adversity, 3 in which methylation density was associated with insecure attachment style, and 6 in which methylation density was associated with perinatal depression. Shorter telomeres were observed in association with childhood trauma but not with perinatal depression or attachment insecurity. A detailed analysis of methylation density in the oxytocin receptor gene revealed similar patterns of DNA methylation in association with perinatal depression and with insecure attachment style, while childhood trauma was associated with a distinct methylation pattern in this gene. Clinically, attachment style was strongly associated with depression only in pregnancy and the early postpartum, whereas the association of childhood adversity with depression was time-invariant. We concluded that the broad DNA methylation signature and reduced telomere length associated with childhood adversity could indicate increased allostatic load across multiple body systems, whereas perinatal depression and attachment insecurity may be narrower phenotypes with more limited DNA methylation signatures outside the CNS, and no apparent association with telomere length or, by extension, allostatic load. In contrast, the finding of matching DNA methylation patterns within the oxytocin receptor gene for perinatal depression and attachment insecurity is consistent with the theory that the perinatal period is a time of activation of existing attachment schemas for the purpose of structuring the mother-child relationship, and that such activation may occur in part through specific patterns of methylation of the oxytocin receptor gene.

show abstract

Section: Technical Advancesmentioning

confidence: 79%

Section: Discussionmentioning

confidence: 99%

Epigenetic signatures of attachment insecurity and childhood adversity provide evidence for role transition in the pathogenesis of perinatal depression

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Fisher’s test was implemented to detect DMRs 64 . The distribution of DMRs among genomic features was generated using the ChIPseeker package in R 65 .…”

Section: Methodsmentioning

confidence: 99%

Lineage-specific functions of TET1 in the postimplantation mouse embryo

et al. 2017

View full text Add to dashboard Cite

The mammalian TET enzymes catalyze DNA demethylation. While they have been intensely studied as major epigenetic regulators, little is known about their physiological roles and the extent of functional redundancy following embryo implantation. Here we define non-redundant roles for TET1 at an early postimplantation stage of the mouse embryo, when its paralogs Tet2 and Tet3 are not detectably expressed. TET1 regulates numerous genes defining differentiation programs in the epiblast and extraembryonic ectoderm. In epiblast cells, TET1 demethylates gene promoters via hydroxymethylation and maintains telomere stability. Surprisingly, TET1 represses a majority of epiblast target genes independently of methylation changes, in part through regulation of the gene encoding the transcriptional repressor JMJD8. Dysregulated gene expression in the absence of TET1 causes embryonic defects, which are partially penetrant in an inbred strain but fully lethal in non-inbred mice. Collectively, our study highlights an interplay between the catalytic and non-catalytic activities of TET1 that is essential for normal development.

show abstract

“…First, sequencing adaptors were removed from sequencing reads using Cutadapt (Grassmann, 2019). Second, low‐quality reads were trimmed by using a sliding‐window algorithm (Wang et al , 2015). Third, reads were aligned to the host genome using BWA (http://bio-bwa.sourceforge.net/) to remove host contamination (Li and Durbin, 2009).…”

Section: Methodsmentioning

confidence: 99%

Shifts in microbial community, pathogenicity‐related genes and antibiotic resistance genes during dairy manure piled up

Zhang

Chenjie

Zhang

et al. 2020

Microbial Biotechnology

View full text Add to dashboard Cite

Summary The uncomposted faeces of dairy cow are usually stacked on cow breeding farms, dried under natural conditions and then used as cow bedding material or they may be continuously piled up. However, no information is available to evaluate variations in the human and animal pathogen genes and antibiotic resistance during the accumulation of fresh faeces of dairy cow to manure. Here, we present the metagenomic analysis of fresh faeces and manure from a dairy farm in Ning Xia, showing a unique enrichment of human and animal pathogen genes and antibiotic resistance genes (ARGs) in manure. We found that manure accumulation could significantly increase the diversity and abundance of the pathogenic constituents. Furthermore, pathogens from manure could spread to the plant environment and enphytotic pathogens could affect the yield and quality of crops during the use of manure as a fertilizer. Levels of virulence genes and ARGs increased with the enrichment of microbes and pathogens when faeces accumulated to manure. Accumulated manure was also the transfer station of ARGs to enrich the ARGs in the environment, indicating the ubiquitous presence of environmental antibiotic resistance genes. Our results demonstrate that manure accumulation and usage without effective manure management is an unreasonable approach that could enrich pathogenic microorganisms and ARGs in the environment. The manure metagenome structure allows us to appreciate the overall influence and interaction of animal waste on water, soil and other areas impacted by faecal accumulation and the factors that influence pathogen occurrence in products from dairy cows.

show abstract

swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing

Cited by 53 publications

References 34 publications

Epigenetic signatures of attachment insecurity and childhood adversity provide evidence for role transition in the pathogenesis of perinatal depression

Epigenetic signatures of attachment insecurity and childhood adversity provide evidence for role transition in the pathogenesis of perinatal depression

Lineage-specific functions of TET1 in the postimplantation mouse embryo

Shifts in microbial community, pathogenicity‐related genes and antibiotic resistance genes during dairy manure piled up

Contact Info

Product

Resources

About