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 …

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 …

Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA

F Rodriguez, IA Yushenova, D DiCorpo… - Nature …, 2022 - nature.com
DNA modifications are used to regulate gene expression and defend against invading
genetic elements. In eukaryotes, modifications predominantly involve C5-methylcytosine …

Fundamental characteristics of AAA+ protein family structure and function

JM Miller, EJ Enemark - Archaea, 2016 - Wiley Online Library
Many complex cellular events depend on multiprotein complexes known as molecular
machines to efficiently couple the energy derived from adenosine triphosphate hydrolysis to …

A structural perspective on readout of epigenetic histone and DNA methylation marks

DJ Patel - Cold Spring Harbor perspectives in biology, 2016 - cshperspectives.cshlp.org
This article outlines the protein modules that target methylated lysine histone marks and
5mC DNA marks, and the molecular principles underlying recognition. The article focuses …

Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA

CB Woodcock, JR Horton, J Zhou… - Nucleic acids …, 2020 - academic.oup.com
The recently characterized mammalian writer (methyltransferase) and eraser (demethylase)
of the DNA N6-methyladenine (N6mA) methyl mark act on single-stranded (ss) and …

Upregulated UHRF1 promotes bladder cancer cell invasion by epigenetic silencing of KiSS1

Y Zhang, Z Huang, Z Zhu, X Zheng, J Liu, Z Han, X Ma… - PloS one, 2014 - journals.plos.org
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1), as an epigenetic regulator,
plays important roles in the tumorigenesis and cancer progression. KiSS1 functions as a …

DNA base flipping: a general mechanism for writing, reading, and erasing DNA modifications

S Hong, X Cheng - DNA methyltransferases-role and function, 2016 - Springer
The modification of DNA bases is a classic hallmark of epigenetics. Four forms of modified
cytosine—5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5 …

Structural basis of the methylation specificity of R. DpnI

K Mierzejewska, W Siwek, H Czapinska… - Nucleic acids …, 2014 - academic.oup.com
R. DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are
separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a …

Structural basis for the recognition of sulfur in phosphorothioated DNA

G Liu, W Fu, Z Zhang, Y He, H Yu, Y Wang… - Nature …, 2018 - nature.com
There have been very few reports on protein domains that specifically recognize sulfur. Here
we present the crystal structure of the sulfur-binding domain (SBD) from the DNA …