Anchor-based bisulfite sequencing determines genome-wide DNA methylation

Chapin, Nate; Fernandez, Joseph; Poole, Jason; Delatte, Benjamin

doi:10.1038/s42003-022-03543-1

Cited by 9 publications

(5 citation statements)

References 24 publications

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“…WGBS is the current ideal for DNA methylation analysis, as it provides high-resolution, single-based methylation maps [ 20 ], which enable non-CpG methylation in mammals to be fully understood. Previous studies have suggested that non-CpG methylation is more abundant in stem cells than in differentiated cell types.…”

Section: Discussionmentioning

confidence: 99%

FZD7, Regulated by Non-CpG Methylation, Plays an Important Role in Immature Porcine Sertoli Cell Proliferation

Yang

Yan

Yin

et al. 2023

IJMS

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The regulatory role of non-CpG methylation in mammals has been important in whole-genome bisulfite sequencing. It has also been suggested that non-CpG methylation regulates gene expression to affect the development and health of mammals. However, the dynamic regulatory mechanisms of genome-wide, non-CpG methylation during testicular development still require intensive study. In this study, we analyzed the dataset from the whole-genome bisulfite sequencing (WGBS) and the RNA-seq of precocious porcine testicular tissues across two developmental stages (1 and 75 days old) in order to explore the regulatory roles of non-CpG methylation. Our results showed that genes regulated by non-CpG methylation affect the development of testes in multiple pathways. Furthermore, several hub genes that are regulated by non-CpG methylation during testicular development—such as VEGFA, PECAM1, and FZD7—were also identified. We also found that the relative expression of FZD7 was downregulated by the zebularine-induced demethylation of the first exon of FZD7. This regulatory relationship was consistent with the results of the WGBS and RNA-seq analysis. The immature porcine Sertoli cells were transfected with RNAi to mimic the expression patterns of FZD7 during testicular development. The results of the simulation test showed that cell proliferation was significantly impeded and that cell cycle arrest at the G2 phase was caused by the siRNA-induced FZD7 inhibition. We also found that the percentage of early apoptotic Sertoli cells was decreased by transfecting them with the RNAi for FZD7. This indicates that FZD7 is an important factor in linking the proliferation and apoptosis of Sertoli cells. We further demonstrated that Sertoli cells that were treated with the medium collected from apoptotic cells could stimulate proliferation. These findings will contribute to the exploration of the regulatory mechanisms of non-CpG methylation in testicular development and of the relationship between the proliferation and apoptosis of normal somatic cells.

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Section: Discussionmentioning

confidence: 99%

FZD7, Regulated by Non-CpG Methylation, Plays an Important Role in Immature Porcine Sertoli Cell Proliferation

Yang

Yan

Yin

et al. 2023

IJMS

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“…It is possible that the technical and economic requirements for RRBS or WGBS will soon become lower and more affordable in routine clinical practice. Other approaches could be used, such as anchor-based bisulfite sequencing (ABBS) [ 45 ] and nanopore sequencing [ 46 ].…”

Section: Discussionmentioning

confidence: 99%

Diagnostic Algorithm to Subclassify Atypical Spitzoid Tumors in Low and High Risk According to Their Methylation Status

González-Muñoz,

Sánchez-Sendra,

Monteagudo

2023

IJMS

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Current diagnostic algorithms are insufficient for the optimal clinical and therapeutic management of cutaneous spitzoid tumors, particularly atypical spitzoid tumors (AST). Therefore, it is crucial to identify new markers that allow for reliable and reproducible diagnostic assessment and can also be used as a predictive tool to anticipate the individual malignant potential of each patient, leading to tailored individual therapy. Using Reduced Representation Bisulfite Sequencing (RRBS), we studied genome–wide methylation profiles of a series of Spitz nevi (SN), spitzoid melanoma (SM), and AST. We established a diagnostic algorithm based on the methylation status of seven cg sites located in TETK4P2 (Tektin 4 Pseudogene 2), MYO1D (Myosin ID), and PMF1-BGLAP (PMF1-BGLAP Readthrough), which allows the distinction between SN and SM but is also capable of subclassifying AST according to their similarity to the methylation levels of Spitz nevi or spitzoid melanoma. Thus, our epigenetic algorithm can predict the risk level of AST and predict its potential clinical outcomes.

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“…Notably, the application of GLORI is limited by its relatively high cost as a higher sequencing depth is required compared to enrichment‐based methods. This disadvantage could potentially be mitigated in future improvements by learning from the bisulfite sequencing field, where the development of reduced representation bisulfite sequencing [124] and anchor‐based bisulfite sequencing [125] significantly reduced sequencing cost while preserving a reasonable coverage of the DNA methylome.…”

Section: Special Applications Of M6a‐sequencing Methodsmentioning

confidence: 99%

Unraveling the RNA Tapestry: A Symphony of Innovations in m⁶A Research Technology

Fei,

Fang,

Zhao

2024

Israel Journal of Chemistry

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This review navigates the evolving landscape of N6‐methyladenosine (m6A) research approaches, emphasizing the importance of advanced technology in understanding RNA epigenetics. Beginning with the fundamentals of m6A and the need for high‐ throughput methods, the investigation progresses from low‐throughput approaches to high‐throughput technologies, encompassing antibody‐dependent and antibody‐free sequencing methods, as well as nanopore‐based direct mRNA sequencing and computation methods for m6A detection. Spatial techniques and imaging tools for m6A are also introduced in addition. The discussion of their special applications emphasizes the biological significance of absolute quantification, single‐nucleotide resolution, single‐molecule detection, and single‐cell profiling. The review concludes with a vision of ideal approaches that combine current technologies for comprehensive m6A sequencing, with the potential to further our understanding of gene regulation, cellular diversity, and their roles in health and disease.

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Anchor-based bisulfite sequencing determines genome-wide DNA methylation

Cited by 9 publications

References 24 publications

FZD7, Regulated by Non-CpG Methylation, Plays an Important Role in Immature Porcine Sertoli Cell Proliferation

FZD7, Regulated by Non-CpG Methylation, Plays an Important Role in Immature Porcine Sertoli Cell Proliferation

Diagnostic Algorithm to Subclassify Atypical Spitzoid Tumors in Low and High Risk According to Their Methylation Status

Unraveling the RNA Tapestry: A Symphony of Innovations in m⁶A Research Technology

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Anchor-based bisulfite sequencing determines genome-wide DNA methylation

Cited by 9 publications

References 24 publications

FZD7, Regulated by Non-CpG Methylation, Plays an Important Role in Immature Porcine Sertoli Cell Proliferation

FZD7, Regulated by Non-CpG Methylation, Plays an Important Role in Immature Porcine Sertoli Cell Proliferation

Diagnostic Algorithm to Subclassify Atypical Spitzoid Tumors in Low and High Risk According to Their Methylation Status

Unraveling the RNA Tapestry: A Symphony of Innovations in m6A Research Technology

Contact Info

Product

Resources

About

Unraveling the RNA Tapestry: A Symphony of Innovations in m⁶A Research Technology