Mapping epigenetic modifications by sequencing technologies

X Chen, H Xu, X Shu, CX Song - Cell Death & Differentiation, 2023 - nature.com
The “epigenetics” concept was first described in 1942. Thus far, chemical modifications on
histones, DNA, and RNA have emerged as three important building blocks of epigenetic …

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

A Dorey, S Howorka - Nature chemistry, 2024 - nature.com
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid
readout, high accuracy, low cost and portability. This label-free method for sequencing at the …

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

EB Fabyanic, P Hu, Q Qiu, KN Berríos… - Nature …, 2024 - nature.com
Abstract Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET)
DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of …

TET Enzymes in the Immune system: from DNA demethylation to immunotherapy, inflammation, and cancer

IF López-Moyado, M Ko, PG Hogan… - Annual Review of …, 2024 - annualreviews.org
Ten-eleven translocation (TET) proteins are iron-dependent and α-ketoglutarate-dependent
dioxygenases that sequentially oxidize the methyl group of 5-methylcytosine (5mC) to 5 …

Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability

Y Cao, Y Bai, T Yuan, L Song, Y Fan… - Proceedings of the …, 2023 - National Acad Sciences
Existing single-cell bisulfite-based DNA methylation analysis is limited by low DNA recovery,
and the measurement of 5hmC at single-base resolution remains challenging. Here, we …

Epigenomic heterogeneity as a source of tumour evolution

M Laisné, M Lupien, C Vallot - Nature Reviews Cancer, 2024 - nature.com
In the past decade, remarkable progress in cancer medicine has been achieved by the
development of treatments that target DNA sequence variants. However, a purely genetic …

Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq

D Bai, X Zhang, H Xiang, Z Guo, C Zhu, C Yi - Nature Biotechnology, 2024 - nature.com
Abstract Dynamic 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC)
modifications to DNA regulate gene expression in a cell-type-specific manner and are …

BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies

W Zhou, BK Johnson, J Morrison… - Nucleic Acids …, 2024 - academic.oup.com
Data from both bulk and single-cell whole-genome DNA methylation experiments are under-
utilized in many ways. This is attributable to inefficient mapping of methylation sequencing …

Population epigenetics: DNA methylation in the plant omics era

J Liu, X Zhong - Plant Physiology, 2024 - academic.oup.com
DNA methylation plays an important role in many biological processes. The mechanisms
underlying the establishment and maintenance of DNA methylation are well understood …

5-Hydroxymethylcytosine: The many faces of the sixth base of mammalian DNA

E Kriukienė, M Tomkuvienė… - Chemical Society …, 2024 - pubs.rsc.org
Epigenetic phenomena play a central role in cell regulatory processes and are important
factors for understanding complex human disease. One of the best understood epigenetic …