Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era

Xie, Shuang; Leung, Amy Wing-Sze; Zheng, Zhenxian; Zhang, Dake; Xiao, Chuan-Le; Luo, Ruibang; Luo, Ming; Zhang, Shoudong

doi:10.1016/j.xinn.2021.100153

Cited by 22 publications

(27 citation statements)

References 191 publications

(329 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nevertheless, the detection sensitivity of this technique may be lower than the PCR-based or sequencing solutions. Recently, nanopore sequencing has been used to directly detect the 5mC in the naïve DNA/RNA sequence without bisulfite treatment, avoiding sample loss and introduced biases during bisulfite conversion [98].…”

Section: Technical Challenges In Future Researchmentioning

confidence: 99%

Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties

Zhang

Guo

Schrodi

2021

IJMS

Self Cite

View full text Add to dashboard Cite

Hepatitis B virus (HBV), the well-studied oncovirus that contributes to the majority of hepatocellular carcinomas (HCC) worldwide, can cause a severe inflammatory microenvironment leading to genetic and epigenetic changes in hepatocyte clones. HBV replication contributes to the regulation of DNA methyltransferase gene expression, particularly by X protein (HBx), and subsequent methylation changes may lead to abnormal transcription activation of adjacent genes and genomic instability. Undoubtedly, the altered expression of these genes has been known to cause diverse aspects of infected hepatocytes, including apoptosis, proliferation, reactive oxygen species (ROS) accumulation, and immune responses. Additionally, pollutant-induced DNA methylation changes and aberrant methylation of imprinted genes in hepatocytes also complicate the process of tumorigenesis. Meanwhile, hepatocytes also contribute to epigenetic modification of the viral genome to affect HBV replication or viral protein production. Meanwhile, methylation levels of HBV integrants and surrounding host regions also play crucial roles in their ability to produce viral proteins in affected hepatocytes. Both host and viral changes can provide novel insights into tumorigenesis, individualized responses to therapeutic intervention, disease progress, and early diagnosis. As such, DNA methylation-mediated epigenetic silencing of cancer-related genes and viral replication is a compelling therapeutic goal to reduce morbidity and mortality from liver cancer caused by chronic HBV infection. In this review, we summarize the most recent research on aberrant DNA methylation associated with HBV infection, which is involved in HCC development, and provide an outlook on the future direction of the research.

show abstract

Section: Technical Challenges In Future Researchmentioning

confidence: 99%

Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties

Zhang

Guo

Schrodi

2021

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…Additionally, the same ONT sequencing datasets can be reprocessed to obtain measurements of modification states of sequenced bases [10]. This allowed for a host of applications for profiling the epigenome in a haplotype resolved whole-genome single-molecule setting [11], which requires software tools for the inference of methylation state as well as interpretation of methylation rates. A number of methylation callers have already been published, including Nanopolish [11], DeepSignal [12] and ONT’s own Megalodon [13].…”

Section: Introductionmentioning

confidence: 99%

“…This allowed for a host of applications for profiling the epigenome in a haplotype resolved whole-genome single-molecule setting [11], which requires software tools for the inference of methylation state as well as interpretation of methylation rates. A number of methylation callers have already been published, including Nanopolish [11], DeepSignal [12] and ONT’s own Megalodon [13]. These methods have been compared and benchmarked elsewhere [14].…”

Section: Introductionmentioning

confidence: 99%

pycoMeth: A toolbox for differential methylation testing from Nanopore methylation calls

Snajder

Stegle

Bonder

2022

Preprint

View full text Add to dashboard Cite

Advances in Nanopore sequencing have opened up the possibility for the simultaneous analysis of genomic and epigenetic variation by way of base-calling and methylation-calling of the same long reads. Methylation analysis based on long read technologies requires a re-evaluation of data storage and analysis approaches previously developed for either CpG-methylation arrays or short-read bisulfite sequencing data. To address this, we here present a toolbox for the segmentation and differential methylation analysis of (haplotyped) methylation calls from Nanopore data. Additionally, we describe a storage format for read-level and reference-anchored methylation call data, which simultaneously allows for efficient storage and rapid data access.

show abstract

“…Currently, PacBio and Oxford Nanopore (ONT) are the most popular 3rd-generation full-length sequencing technologies that can provide more complex transcription and reveal the real structure of sequences during transcription, such as alternative splicing (AS), alternative polyadenylation (APA), and long non-coding RNA (lncRNA) and gene fusion, which can increase the complexity of the transcriptome and proteome. Compared with PacBio sequencing, ONT uses ion current blockades to directly sequence more long-native DNA or full-length RNA molecules ( Cui et al, 2020 ; Xie et al, 2021 ). AS, one of the important steps in post-transcriptional modification, can recognize and eliminate intronic regions of a precursor messenger RNA (pre-mRNA) to generate multiple mRNAs to regulate gene expression that consequently promotes proteome diversity.…”

Section: Introductionmentioning

confidence: 99%

Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response

et al. 2022

View full text Add to dashboard Cite

Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (Glycine max). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, Heterodera glycines) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6.1 GB of clean data and a total of 65,038 transcript sequences. After redundant transcripts were removed, 1,117 novel genes and 41,096 novel transcripts were identified. By analyzing the sequence structure of the novel transcripts, a total of 28,759 complete open reading frame (ORF) sequences, 5,337 transcription factors, 288 long non-coding RNAs, and 40,090 novel transcripts with function annotation were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) revealed that growth hormone, auxin-activated signaling pathway and multidimensional cell growth, and phenylpropanoid biosynthesis pathway were enriched by infection with both nematode races. More DEGs associated with stress response elements, plant-hormone signaling transduction pathway, and plant–pathogen interaction pathway with more upregulation were found in the incompatible reaction with SCN4 infection, and more DEGs with more upregulation involved in cell wall modification and carbohydrate bioprocess were detected in the compatible reaction with SCN5 infection when compared with each other. Among them, overlapping DEGs with a quantitative difference was triggered. The combination of protein–protein interaction with DEGs for the first time indicated that nematode infection activated the interactions between transcription factor WRKY and VQ (valine-glutamine motif) to contribute to soybean defense. The knowledge of the SCN–soybean interaction mechanism as a model will present more understanding of other plant–nematode interactions.

show abstract

Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era

Cited by 22 publications

References 191 publications

Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties

Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties

pycoMeth: A toolbox for differential methylation testing from Nanopore methylation calls

Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response

Contact Info

Product

Resources

About