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Reduced Representation Bisulfite Sequencing (RRBS)
Reduced representation bisulfite sequencing (RRBS) enriches CpG-rich genomic regions using the MspI restriction enzyme—which cuts DNA at all CCGG...
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Strengths and limitations of reduced representation bisulfite sequencing (RRBS) in the perspective of DNA methylation analysis in fish: a case-study on rainbow trout spermatozoa
DNA methylation in CpG dinucleotides is an important epigenetic mark in fish spermatozoa since it has been shown that some sperm methylome features...
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Smart-RRBS for single-cell methylome and transcriptome analysis
The integration of DNA methylation and transcriptional state within single cells is of broad interest. Several single-cell dual- and multi-omics...
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Generating Sequencing-Based DNA Methylation Maps from Low DNA Input Samples
Reduced representation bisulfite sequencing (RRBS)Reduced representation bisulfite sequencing (RRBS) is a technique used for assessing genome-wide...
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Identification and validation of a DNA methylation-driven gene-based prognostic model for clear cell renal cell carcinoma
BackgroundClear cell renal cell carcinoma (ccRCC) is a malignant tumor with heterogeneous morphology and poor prognosis. This study aimed to...
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Plant-RRBS: DNA Methylome Profiling Adjusted to Plant Genomes, Utilizing Efficient Endonuclease Combinations, for Multi-Sample Studies
In plants, methylation at cytosines often leads to changes in gene expression and inactivation of transposable elements. Changes in cytosine...
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MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation
DNA methylation is a crucial epigenetic modification involved in multiple biological processes and diseases. Current approaches for measuring...
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Swine global genomic resources: insights into wild and domesticated populations
Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to...
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Genome-wide analysis of hepatic DNA methylation reveals impact of epigenetic aging on xenobiotic metabolism and transport genes in an aged mouse model
Hepatic xenobiotic metabolism and transport decline with age, while intact xenobiotic metabolism is associated with longevity. However, few studies...
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SETDB1 deletion causes DNA demethylation and upregulation of multiple zinc-finger genes
BackgroundSETDB1 (SET domain bifurcated-1) is a histone H3-lysine 9 (H3K9)-specific methyltransferase that mediates heterochromatin formation and...
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Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress
BackgroundRegulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for...
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Anchor-based bisulfite sequencing determines genome-wide DNA methylation
Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling. However, this approach is costly as it requires...
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Developmental reprogramming of myometrial stem cells by endocrine disruptor linking to risk of uterine fibroids
BackgroundThe stage, when tissues and organs are growing, is very vulnerable to environmental influences, but it’s not clear how exposure during this...
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CpG DNA methylation changes during epididymal sperm maturation in bulls
BackgroundDuring epididymal transit spermatozoa acquire specific morphological features which enhance their ability to swim in a progressive manner...
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DNA methylation patterns in patients with asthenospermia and oligoasthenospermia
BackgroundSpermatogenesis is a highly regulated and complex process in which DNA methylation plays a crucial role. This study aimed to explore the...
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DNA Methylation Profiling in Aneurysm and Comorbid Atherosclerosis of the Ascending Aorta
AbstractAtherosclerosis and aneurysm of the aorta are relatively common pathological conditions that remain asymptomatic for a long period of time...
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Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity
BackgroundA common issue in CRISPR-Cas9 genome editing is off-target activity, which prevents the widespread use of CRISPR-Cas9 in medical...
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DNMT1 driven by mouse amniotic fluid mesenchymal stem cell exosomes improved corneal cryoinjury via inducing microRNA-33 promoter DNA hypermethylation modification in corneal epithelium cells
Severe corneal cryoinjury can cause permanent corneal swelling and bullous keratopathy, one of the main reason for loss of sight. Mouse amniotic...
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Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify between-group differences in DNA methylation
BackgroundThe combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the...
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Unveiling E2F4, TEAD1 and AP-1 as regulatory transcription factors of the replicative senescence program by multi-omics analysis
Senescence, a stable state of growth arrest, affects many physiological and pathophysiological processes, especially aging. Previous work has...
