Generating Sequencing-Based DNA Methylation Maps from Low DNA Input Samples

Momani, Suzan Al; Rodger, Euan J.; Stockwell, Peter A.; Eccles, Michael R.; Chatterjee, Aniruddha

doi:10.1007/978-1-0716-2140-0_1

Cited by 3 publications

(3 citation statements)

References 44 publications

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“…We used reduced representation bisulfite sequencing (RRBS) to map genome-scale DNA methylation at single nucleotide resolution as we have described previously. 67 , 68 Briefly, genomic DNA was extracted from <20 mg of tissue using the Qiagen QIAamp DNA Mini Kit. The DNA was digested with NEB MspI enzyme followed by end-repair and ligation of Illumina TruSeq sequencing adaptors.…”

Section: Methodsmentioning

confidence: 99%

An epigenetic signature of advanced colorectal cancer metastasis

et al. 2023

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Section: Methodsmentioning

confidence: 99%

An epigenetic signature of advanced colorectal cancer metastasis

et al. 2023

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“…Here we present a detailed protocol for the generation of libraries for reduced representation bisulfite sequencing (RRBS), a technique for comprehensive profiling of genome-scale DNA methylation patterns. 23 , 24 , 25 RRBS library preparation involves digesting genomic DNA with MspI restriction enzyme, which cuts at 5′-C↓CGG-3′ irrespective of the methylation status, to enrich for CpG-dense regions of the genome. Adapter-ligated fragments are bisulfite-converted and amplified by PCR, which allows for sequence-based distinction between methylated and unmethylated CpGs, and then 40–220 bp fragments are size-selected.…”

Section: Step-by-step Methods Detailsmentioning

confidence: 99%

Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens

Rodger,

Stockwell,

Almomani

et al. 2023

STAR Protocols

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“…RRBS libraries were prepared as previously described [ 16 , 37 , 38 ]. Briefly, genomic DNA (500 ng) was digested with 160 U of MSP1 restriction enzyme (NEB, USA).…”

Section: Methodsmentioning

confidence: 99%

Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

Helliwell

Stockwell

Edgar

et al. 2022

IJMS

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Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex disease with variable severity. Patients experience frequent relapses where symptoms increase in severity, leaving them with a marked reduction in quality of life. Previous work has investigated molecular differences between ME/CFS patients and healthy controls, but not the dynamic changes specific to each individual patient. We applied precision medicine here to map genomic changes in two selected ME/CFS patients through a period that contained a relapse recovery cycle. DNA was isolated from two patients and a healthy age/gender matched control at regular intervals and captured the patient relapse in each case. Reduced representation DNA methylation sequencing profiles were obtained spanning the relapse recovery cycle. Both patients showed a significantly larger methylome variability (10–20-fold) through the period of sampling compared with the control. During the relapse, changes in the methylome profiles of the two patients were detected in regulatory-active regions of the genome that were associated, respectively, with 157 and 127 downstream genes, indicating disturbed metabolic, immune and inflammatory functions. Severe health relapses in the ME/CFS patients resulted in functionally important changes in their DNA methylomes that, while differing between the two patients, led to very similar compromised physiology. DNA methylation as a signature of disease variability in ongoing ME/CFS may have practical applications for strategies to decrease relapse frequency.

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Generating Sequencing-Based DNA Methylation Maps from Low DNA Input Samples

Cited by 3 publications

References 44 publications

An epigenetic signature of advanced colorectal cancer metastasis

An epigenetic signature of advanced colorectal cancer metastasis

Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens

Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

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