DNA methylation markers for kidney function and progression of diabetic kidney disease Article Open access 15 May 2023 Introduction Chronic kidney disease (CKD) ranks as the tenth leading cause of death globally, accounting for approximately one million deaths each year1. CKD is a complex disease ...
which include the colon, intestine, stomach, pancreas, liver, lung, esophagus, pharynx, and thyroid1. The primitive gut tube forms at embryonic day (E) 8.5 as the left and right sides merge. This tube is mainly derived from two primary germ layers, with most of the cells being...
The BIND&MODIFY method is based on the indirect labeling of DNA regions bound to the protein of interest using an engineered recombinant fusion protein, protein A-M.EcoGII (pA-M.EcoGII), whose methyltransferase activity can be locally controlled (Fig.1a). The recently characterized adenosine met...
We experimentally validated one of the previously unreported interactions, MYC–HCFC1. An interactive visualization tool is available at http://chromnet.cs.washington.edu.Introduction Regulatory factors—such as transcription factors, histone modifications, and other DNA-associated proteins—co-localize in...
The probability of the result (p), assuming a hypergeometric distribution, is also indicated. (J) Gene Ontology (GO) biological process categories enriched in the downregulated (left) and upregulated (right) differentially expressed genes following a 30-h BRM014 treatment. FDR, false discovery ...
genomes including yeast, Drosophila and mammal genomes (see review, for example, [14]). These methods rely on precise alignment of regulatory elements across multiple genomes which is not necessarily true for all elements, or prior knowledge of a set of cooperative TFs which is not always ...
RNA polymerase (pol) III transcribes a unique class of genes with intra-genic promoters and high transcriptional activity. The major contributors to the pol III transcriptome, tRNAs genes are found scattered on all chromosomes of yeast. A prototype tDNA of <150 bp length, is generally considered...
Molecular Probes, Eugene, OR, USA) is a DNA dye that, upon oxidation, binds to DNA with a signal localized primarily in the nucleus and mitochondria. In contrast, the signal from CellROX©Deep Red Reagent (C10443, Life technologies, Molecular Probes, Eugene, OR, USA) is localized in the...
In senescent cells, H4K20me3 is especially enriched at DNA sequences contained within specialized domains of senescence-associated heterochromatin foci (SAHF), as well as specific families of non-genic and genic repeats. Altered H4K20me3 does not correlate strongly with changes in gene expression...
Chromatin immunoprecipitation (ChIP) with DNA sequencing is a widely applied chromatin profiling method for genome-wide mapping of DNA–protein interactions. However, the strategy suffers from its high background signal and false-positive artifacts caused by formaldehyde cross-linking and solubilization of...