DNAmod: the DNA modification database [PDF]
Journal of Cheminformatics, 2019 Covalent DNA modifications, such as 5-methylcytosine (5mC), are increasingly the focus of numerous research programs. In eukaryotes, both 5mC and 5-hydroxymethylcytosine (5hmC) are now recognized as stable epigenetic marks, with diverse functions ...
Ankur Jai Sood +2 more
doaj +5 more sources
Context-dependent DNA polymerization effects can masquerade as DNA modification signals [PDF]
BMC Genomics, 2022 Background Single molecule measurements of DNA polymerization kinetics provide a sensitive means to detect both secondary structures in DNA and deviations from primary chemical structure as a result of modified bases.
Yusuke Takahashi +3 more
doaj +2 more sources
In vivo mutational characterization of DndE involved in DNA phosphorothioate modification. [PDF]
PLoS ONE, 2014 DNA phosphorothioate (PT) modification is a recently identified epigenetic modification that occurs in the sugar-phosphate backbone of prokaryotic DNA. Previous studies have demonstrated that DNA PT modification is governed by the five DndABCDE proteins ...
Chongde Lai +10 more
doaj +3 more sources
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information [PDF]
BMC Genomics, 2011 Background In parallel with the quick development of high-throughput technologies, in vivo (vitro) experiments for genome-wide identification of protein-DNA interactions have been developed.
Wang Junbai
doaj +3 more sources
N6-Methyladenine DNA Modification in the Woodland Strawberry (Fragaria vesca) Genome Reveals a Positive Relationship With Gene Transcription [PDF]
Frontiers in Genetics, 2020 N6-methyladenine (6mA) DNA modification has been detected in several eukaryotic organisms, where it plays important roles in gene regulation and epigenetic memory maintenance.
Shang-Qian Xie +11 more
doaj +2 more sources
TET3-mediated accumulation of DNA hydroxymethylation contributes to the activity-dependent gene expression of Rab3a in post-mitotic neurons [PDF]
Journal of Integrative Neuroscience, 2021 Rab3a, a subtype protein in the Rab3 family amongst the small G proteins, is closely associated with the learning and memory formation process. Various neuronal stimuli can induce the expression of Rab3a; however, how DNA modification is involved in ...
Kun Luo +5 more
doaj +1 more source
Open Biology, 2022 The formation of three oxidative DNA 5-methylcytosine (5mC) modifications (oxi-mCs)—5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)—by the TET/JBP family of dioxygenases prompted intensive studies of their functional ...
Janina Ličytė +9 more
doaj +1 more source
Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations
Frontiers in Cell and Developmental Biology, 2021 Neuroblastoma (NB) is a pediatric cancer of the developing sympathetic nervous system that exhibits significant variation in the stage of differentiation and cell composition of tumors.
Milda Narmontė +5 more
doaj +1 more source
mBio, 2022 Phosphorothioate (PT) modification, a sequence-specific modification that replaces the nonbridging oxygen atom with sulfur in a DNA phosphodiester through the gene products of dndABCDE or sspABCD, is widely distributed in prokaryotes. DNA PT modification
Wei He +9 more
doaj +1 more source
Traditional Chinese Medicine: A Class of Potentially Reliable Epigenetic Drugs
Frontiers in Pharmacology, 2022 Epigenetic modification, especially DNA methylation, plays a nonnegligible role in the occurrence and development of tumors. Increasing studies are indicating that traditional Chinese medicine (TCM) plays a considerable anti-tumor role by regulating the ...
Daoqi Zhu, Aiwu Li, Ying Lv, Qin Fan
doaj +1 more source