scholarly journals Systematic benchmarking of tools for CpG methylation detection from Nanopore sequencing

2020 ◽  
Author(s):  
Zaka Wing-Sze Yuen ◽  
Akanksha Srivastava ◽  
Runa Daniel ◽  
Dennis McNevin ◽  
Cameron Jack ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bisulfite Sequencing ◽  
Cpg Methylation ◽  
Genome Integrity ◽  
High Dispersion ◽  
Nanopore Sequencing ◽  
Consensus Approach ◽  
False Negatives ◽  
Control Of Gene Expression ◽  
Improved Accuracy

AbstractDNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives, and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a new consensus approach, METEORE (https://github.com/comprna/METEORE), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are provided for reproducibility and to enable the systematic application of our analyses to other datasets.

scholarly journals Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zaka Wing-Sze Yuen ◽  
Akanksha Srivastava ◽  
Runa Daniel ◽  
Dennis McNevin ◽  
Cameron Jack ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bisulfite Sequencing ◽  
Cpg Methylation ◽  
Genome Integrity ◽  
High Dispersion ◽  
Nanopore Sequencing ◽  
Consensus Approach ◽  
False Negatives ◽  
Control Of Gene Expression ◽  
Improved Accuracy

AbstractDNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a consensus approach, METEORE (https://github.com/comprna/METEORE), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are also provided for reproducibility and to enable the systematic application of our analyses to other datasets.

scholarly journals Oxford Nanopore sequencing-based protocol to detect CpG methylation in human mitochondrial DNA

2021 ◽  
Author(s):  
Iacopo Bicci ◽  
Claudia Calabrese ◽  
Zoe J. Golder ◽  
Aurora Gomez-Duran ◽  
Patrick F Chinnery
Keyword(s):  
Mitochondrial Dna ◽  
Single Molecule ◽  
Bisulfite Sequencing ◽  
Nuclear Dna ◽  
Cpg Methylation ◽  
Nanopore Sequencing ◽  
Single Molecule Level ◽  
Oxford Nanopore ◽  
Genome Bisulfite Sequencing ◽  
Technical Issues

SummaryMethylation on CpG residues is one of the most important epigenetic modifications of nuclear DNA, regulating gene expression. Methylation of mitochondrial DNA (mtDNA) has been studied using whole genome bisulfite sequencing (WGBS), but recent evidence has uncovered major technical issues which introduce a potential bias during methylation quantification. Here, we validate the technical concerns with WGBS, and then develop and assess the accuracy of a protocol for variant-specific methylation identification using long-read Oxford Nanopore Sequencing. Our approach circumvents mtDNA-specific confounders, while enriching for native full-length molecules over nuclear DNA. Variant calling analysis against Illumina deep re-sequencing showed that all expected mtDNA variants can be reliably identified. Methylation calling revealed negligible mtDNA methylation levels in multiple human primary and cancer cell lines. In conclusion, our protocol enables the reliable analysis of epigenetic modifications of mtDNA at single-molecule level at single base resolution, with potential applications beyond methylation.MotivationAlthough whole genome bisulfite sequencing (WGBS) is the gold-standard approach to determine base-level CpG methylation in the nuclear genome, emerging technical issues raise questions about its reliability for evaluating mitochondrial DNA (mtDNA) methylation. Concerns include mtDNA strand asymmetry rendering the C-rich light strand disproportionately vulnerable the chemical modifications introduced with WGBS. Also, short-read sequencing can result in a co-amplification of nuclear sequences originating from ancestral mtDNA with a high nucleotide similarity. Lastly, calling mtDNA alleles with varying proportions (heteroplasmy) is complicated by the C-to-T conversion introduced by WGBS on unmethylated CpGs. Here, we propose an alternative protocol to quantify methyl-CpGs in mtDNA, at single-molecule level, using Oxford Nanopore Sequencing (ONS). By optimizing the standard ONS library preparation, we achieved selective enrichment of native mtDNA and accurate single nucleotide variant and CpG methylation calling, thus overcoming previous limitations.

Cohesin: a regulator of genome integrity and gene expression

2010 ◽  
Vol 428 (2) ◽  
pp. 147-161 ◽  
Author(s):  
Katherine M. Feeney ◽  
Christopher W. Wasson ◽  
Joanna L. Parish
Keyword(s):  
Gene Expression ◽  
Chromosome Segregation ◽  
Sister Chromatid ◽  
Dna Lesions ◽  
Genome Integrity ◽  
Accessory Proteins ◽  
Post Translational Modification ◽  
Control Of Gene Expression ◽  
Chromatid Cohesion ◽  
And Control

Following DNA replication, chromatid pairs are held together by a proteinacious complex called cohesin until separation during the metaphase-to-anaphase transition. Accurate segregation is achieved by regulation of both sister chromatid cohesion establishment and removal, mediated by post-translational modification of cohesin and interaction with numerous accessory proteins. Recent evidence has led to the conclusion that cohesin is also vitally important in the repair of DNA lesions and control of gene expression. It is now clear that chromosome segregation is not the only important function of cohesin in the maintenance of genome integrity.

402: CPG Methylation at Promoter Site -140 Inactivates TGF- β Receptor Type II Gene Expression in Prostate Cancer

2005 ◽  
Vol 173 (4S) ◽  
pp. 110-110
Author(s):  
Kirsten L. Greene ◽  
Hong Zhao ◽  
Hiroaki Shiina ◽  
Long-Cheng Li ◽  
Yuichiro Tanaka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cpg Methylation ◽  
Receptor Type ◽  
Type Ii ◽  
Β Receptor

A Review on Important Histone Acetyltransferase (HAT) Enzymes as Targets for Cancer Therapy

2019 ◽  
Vol 15 (2) ◽  
pp. 120-130
Author(s):  
Mohammad Ghanbari ◽  
Reza Safaralizadeh ◽  
Kiyanoush Mohammadi
Keyword(s):  
Gene Expression ◽  
Histone Acetyltransferase ◽  
Critical Role ◽  
Cancer Treatments ◽  
Control Of Gene Expression ◽  
Post Translational Modifications ◽  
Therapeutic Drugs ◽  
The Status ◽  
Acetyl Group ◽  
Increase Gene Expression

At the present time, cancer is one of the most lethal diseases worldwide. There are various factors involved in the development of cancer, including genetic factors, lifestyle, nutrition, and so on. Recent studies have shown that epigenetic factors have a critical role in the initiation and development of tumors. The histone post-translational modifications (PTMs) such as acetylation, methylation, phosphorylation, and other PTMs are important mechanisms that regulate the status of chromatin structure and this regulation leads to the control of gene expression. The histone acetylation is conducted by histone acetyltransferase enzymes (HATs), which are involved in transferring an acetyl group to conserved lysine amino acids of histones and consequently increase gene expression. On the basis of similarity in catalytic domains of HATs, these enzymes are divided into different groups such as families of GNAT, MYST, P300/CBP, SRC/P160, and so on. These enzymes have effective roles in apoptosis, signaling pathways, metastasis, cell cycle, DNA repair and other related mechanisms deregulated in cancer. Abnormal activation of HATs leads to uncontrolled amplification of cells and incidence of malignancy signs. This indicates that HAT might be an important target for effective cancer treatments, and hence there would be a need for further studies and designing of therapeutic drugs on this basis. In this study, we have reviewed the important roles of HATs in different human malignancies.

Sign in / Sign up

Export Citation Format

Share Document