Regulation of transposable elements by DNA modifications

Ö Deniz, JM Frost, MR Branco - Nature Reviews Genetics, 2019 - nature.com
Maintenance of genome stability requires control over the expression of transposable
elements (TEs), whose activity can have substantial deleterious effects on the host …

Means, mechanisms and consequences of adenine methylation in DNA

K Boulias, EL Greer - Nature Reviews Genetics, 2022 - nature.com
Abstract N 6-methyl-2′-deoxyadenosine (6mA or m6dA) has been reported in the DNA of
prokaryotes and eukaryotes ranging from unicellular protozoa and algae to multicellular …

Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution

Y Kong, L Cao, G Deikus, Y Fan, EA Mead, W Lai… - Science, 2022 - science.org
The discovery of N6-methyldeoxyadenine (6mA) across eukaryotes led to a search for
additional epigenetic mechanisms. However, some studies have highlighted confounding …

[HTML][HTML] N6-methyladenine DNA modification in glioblastoma

Q Xie, TP Wu, RC Gimple, Z Li, BC Prager, Q Wu, Y Yu… - Cell, 2018 - cell.com
Genetic drivers of cancer can be dysregulated through epigenetic modifications of DNA.
Although the critical role of DNA 5-methylcytosine (5mC) in the regulation of transcription is …

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

P Ni, N Huang, Z Zhang, DP Wang, F Liang… - …, 2019 - academic.oup.com
Abstract Motivation The Oxford Nanopore sequencing enables to directly detect methylation
states of bases in DNA from reads without extra laboratory techniques. Novel computational …

Deciphering bacterial epigenomes using modern sequencing technologies

J Beaulaurier, EE Schadt, G Fang - Nature Reviews Genetics, 2019 - nature.com
Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine
and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of …

[HTML][HTML] Epigenetic modifications of mRNA and DNA in plants

Z Liang, A Riaz, S Chachar, Y Ding, H Du, X Gu - Molecular Plant, 2020 - cell.com
Advances in the detection and mapping of messenger RNA (mRNA) N 6-methyladenosine
(m 6 A) and 5-methylcytosine (m 5 C), and DNA N 6-methyldeoxyadenosine (6mA) …

No evidence for DNA N6-methyladenine in mammals

K Douvlataniotis, M Bensberg, A Lentini, B Gylemo… - Science …, 2020 - science.org
N 6-methyladenine (6mdA) is a widespread DNA modification in bacteria. More recently,
6mdA has also been characterized in mammalian DNA. However, measurements of 6mdA …

Machine learning: its challenges and opportunities in plant system biology

M Hesami, M Alizadeh, AMP Jones… - Applied Microbiology and …, 2022 - Springer
Sequencing technologies are evolving at a rapid pace, enabling the generation of massive
amounts of data in multiple dimensions (eg, genomics, epigenomics, transcriptomic …

Navigating the pitfalls of mapping DNA and RNA modifications

Y Kong, EA Mead, G Fang - Nature Reviews Genetics, 2023 - nature.com
Chemical modifications to nucleic acids occur across the kingdoms of life and carry
important regulatory information. Reliable high-resolution mapping of these modifications is …