Type II restriction endonucleases—a historical perspective and more

A Pingoud, GG Wilson, W Wende - Nucleic acids research, 2014 - academic.oup.com
This article continues the series of Surveys and Summaries on restriction endonucleases
(REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II'REases, the …

Biosynthesis and function of modified bases in bacteria and their viruses

P Weigele, EA Raleigh - Chemical reviews, 2016 - ACS Publications
Naturally occurring modification of the canonical A, G, C, and T bases can be found in the
DNA of cellular organisms and viruses from all domains of life. Bacterial viruses …

[HTML][HTML] Single-cell dynamics of genome-nuclear lamina interactions

J Kind, L Pagie, H Ortabozkoyun, S Boyle, SS De Vries… - Cell, 2013 - cell.com
The nuclear lamina (NL) interacts with hundreds of large genomic regions termed lamina
associated domains (LADs). The dynamics of these interactions and the relation to …

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 …

The other face of restriction: modification-dependent enzymes

WAM Loenen, EA Raleigh - Nucleic acids research, 2014 - academic.oup.com
The 1952 observation of host-induced non-hereditary variation in bacteriophages by
Salvador Luria and Mary Human led to the discovery in the 1960s of modifying enzymes that …

Microbial arsenal of antiviral defenses–part I

AB Isaev, OS Musharova, KV Severinov - Biochemistry (Moscow), 2021 - Springer
Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review
we will also consider viruses that infect Archaea). Constant threat of phage infection is a …

Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing

GZ Luo, F Wang, X Weng, K Chen, Z Hao, M Yu… - Nature …, 2016 - nature.com
Although extensively studied in prokaryotes, the prevalence and significance of DNA N 6-
methyladenine (6mA or m6dA) in eukaryotes had been underappreciated until recent …

[HTML][HTML] DNA N6-methyladenine involvement and regulation of hepatocellular carcinoma development

Q Lin, J Chen, H Yin, M Li, C Zhou, T Hao, T Pan, C Wu… - Genomics, 2022 - Elsevier
Abstract DNA N6-methyladenine (6 mA) is a new type of DNA methylation identified in
various eukaryotic cells. However, its alteration and genomic distribution features in …

From keys to bulldozers: expanding roles for winged helix domains in nucleic-acid-binding proteins

GM Harami, M Gyimesi, M Kovács - Trends in biochemical sciences, 2013 - cell.com
The winged helix domain (WHD) is a widespread nucleic-acid-binding protein structural
element found in all kingdoms of life. Although the overall structure of the WHD is conserved …

[PDF][PDF] Engineering epigenetic regulation using synthetic read-write modules

M Park, N Patel, AJ Keung, AS Khalil - Cell, 2019 - cell.com
Chemical modifications to DNA and histone proteins are involved in epigenetic programs
underlying cellular differentiation and development. Regulatory networks involving …