Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing

Xue, Yue; Xie, Zhiyuan; Li, Yaqian; Wang, Kai; Li, Xiaojing; Zhang, Xiaoqing; Yan, Jian; Yin, Yimeng

doi:10.1038/s41467-022-35650-2

Cited by 15 publications

(9 citation statements)

References 36 publications

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“…We need to delve deeply into the details and deconvolute the complex networks to find faithful disease-driver methylation targets, 280 which is a formidable task. Advances in the technologies, including CRISPR-assisted library screening, 777 , 789 spatial transcriptomics, 790 , 791 and DNA/RNA/protein methylation assays, 792 – 794 will undoubtedly help, however, the field has its intractable problems. The function of methylation pathways is highly context-dependent, making annotation of their role in diseases complex and difficult.…”

Section: Discussionmentioning

confidence: 99%

Methylation across the central dogma in health and diseases: new therapeutic strategies

Liu,

Zhao,

et al. 2023

Sig Transduct Target Ther

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The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control, development, and health. Methylation of DNA, RNAs, histones, and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological processes. Aberrant methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging, necessitating the development of therapies to correct the disease-driver methylation imbalance. In this Review, we summarize the operating system of methylation across the central dogma, which includes writers, erasers, readers, and reader-independent outputs. We then discuss how dysregulation of the system contributes to neurological disorders, cancer, and aging. Current small-molecule compounds that target the modifiers show modest success in certain cancers. The methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity, limiting their therapeutic application, especially for diseases with a monogenic cause or different directions of methylation changes. Emerging tools capable of site-specific methylation manipulation hold great promise to solve this dilemma. With the refinement of delivery vehicles, these new tools are well positioned to advance the basic research and clinical translation of the methylation field.

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Section: Discussionmentioning

confidence: 99%

Methylation across the central dogma in health and diseases: new therapeutic strategies

Liu,

Zhao,

et al. 2023

Sig Transduct Target Ther

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“…For example, Fiber-seq 11 , SMAC-seq 12 , SAMOSA 13 , NanoNOMe 14 , and MeSMLR-seq 15 are all methods that profile chromatin accessibility on long molecules of DNA and can infer protein-DNA binding footprints, although they do not directly measure specific target proteins. Furthermore, recent studies described BIND&MODIFY 16 and nanoHiMe-seq 17 , methods which use similar strategies as DiMeLo-seq to profile protein-DNA interactions, albeit with lower reported sensitivity.…”

Section: Comparison With Other Methodsmentioning

confidence: 99%

Mapping protein-DNA interactions with DiMeLo-seq

Maslan

Altemose

Mishra

et al. 2022

Preprint

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We recently developed Directed Methylation with Long-read sequencing (DiMeLo-seq) to map protein-DNA interactions genome wide. DiMeLo-seq maps multiple interaction sites on single DNA molecules, profiles protein binding in the context of endogenous DNA methylation, and maps protein-DNA interactions in repetitive regions of the genome that are difficult to study with short-read methods. Adenines in the vicinity of a protein of interest are methylated in situ by tethering the Hia5 methyltransferase to an antibody using protein A. Protein-DNA interactions are then detected by direct readout of adenine methylation with long-read, single-molecule, DNA sequencing platforms such as Nanopore sequencing. Here, we present a detailed protocol and guidance for performing DiMeLo-seq. This protocol can be run on nuclei from fresh, lightly fixed, or frozen cells. The protocol requires 1 day for performing in situ targeted methylation, 1-5 days for library preparation depending on desired fragment length, and 1-3 days for Nanopore sequencing depending on desired sequencing depth. The protocol requires basic molecular biology skills and equipment, as well as access to a Nanopore sequencer. We also provide a Python package, dimelo, for analysis of DiMeLo-seq data.

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“…The model‐free nature of nanopore sequencing means that any modification of the genomic or transcriptomic material can be detected – as long as a basecalling algorithm can be trained to detect such a modification beyond the variation in the sequence composition (preprint: Stoiber et al , 2017 ; Wan et al , 2022 ). This has been leveraged to call epigenetic modifications such as DNA methylation and histone modifications (Simpson et al , 2017 ; preprint: Stoiber et al , 2017 ; Yue et al , 2022 ), which provide another rich level of information for assessing biodiversity and its function. Epigenetic variation represents an important part of biodiversity and can provide information about the ecological or environmental components of species and populations (Moore et al , 2013 ; Lacal & Ventura, 2018 ).…”

Section: Monitoring Environmental Healthmentioning

confidence: 99%

Real‐time genomics for One Health

Urban,

Perlas,

Francino

et al. 2023

Molecular Systems Biology

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The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well‐understood. Here, we describe how the advent of real‐time genomic analyses can benefit One Health and how it can enable timely, in‐depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real‐time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real‐time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself – from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real‐time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.

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Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing

Cited by 15 publications

References 36 publications

Methylation across the central dogma in health and diseases: new therapeutic strategies

Methylation across the central dogma in health and diseases: new therapeutic strategies

Mapping protein-DNA interactions with DiMeLo-seq

Real‐time genomics for One Health

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