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| http://dx.doi.org/10.3324/haematol.2019.224030 | DOI Listing |
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Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING.
Nat Protoc
September 2024
Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'An, P. R. China.
Epigenetic modifications and spatial proximities of nucleic acids and proteins play important roles in regulating physiological processes and disease progression. Currently available cell imaging methods, such as fluorescence in situ hybridization (FISH) and immunofluorescence, struggle to detect low-abundance modifications and their spatial proximities. Here we describe a step-by-step protocol for three DNA-encoded amplifying FISH-based imaging strategies to overcome these challenges for varying applications: base-encoded amplifying FISH (BEA-FISH), pairwise proximity-differentiated amplifying FISH (PPDA-FISH) and cellular macromolecules-tethered DNA walking indexing (Cell-TALKING).
View Article and Find Full Text PDFβ-Aminobutyric acid promotes stress tolerance, physiological adjustments, as well as broad epigenetic changes at DNA and RNA nucleobases in field elms (Ulmus minor).
BMC Plant Biol
August 2024
Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, Bydgoszcz, 85-095, Poland.
Background: β-Aminobutyric acid (BABA) has been successfully used to prime stress resistance in numerous plant species; however, its effectiveness in forest trees has been poorly explored thus far. This study aimed to investigate the influence of BABA on morphological, physiological, and epigenetic parameters in field elms under various growth conditions. Epigenetic changes were assessed in both DNA and RNA through the use of reversed-phase ultra-performance liquid chromatography (UPLC) coupled with sensitive mass spectrometry.
View Article and Find Full Text PDFUncovering plant epigenetics: new insights into cytosine methylation in rye genomes.
J Exp Bot
June 2023
Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
This article comments on: 2023. Global DNA 5-hydroxymethylcytosine level and its chromosomal distribution in four rye species. Journal of Experimental Botany , 3488–3502.
View Article and Find Full Text PDFGlobal DNA 5-hydroxymethylcytosine level and its chromosomal distribution in four rye species.
J Exp Bot
June 2023
Institute of Biology, University of Szczecin, 71-415 Szczecin, Poland.
The rye genome has a large size with a high level of cytosine methylation, which makes it particularly convenient for studying the occurrence of potential cytosine demethylation intermediates. Levels of global 5-hydroxymethylcytosine (5hmC) were analysed by enzyme-linked immunosorbent assay (ELISA) and mass spectrometry in four rye species: Secale cereale, Secale strictum, Secale sylvestre, and Secale vavilovii. The amount of 5hmC showed interspecific variation, and was also variable among organs, i.
View Article and Find Full Text PDFUrinary Measurement of Epigenetic DNA Modifications and 8-oxodG as Possible Noninvasive Markers of Colon Cancer Evolution.
Int J Mol Sci
November 2022
Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland.
The active DNA demethylation mechanism involves 5-methylcytosine (5-mCyt) enzymatic oxidation with the subsequent formation of 5-hydroxymethylcytosine (5-hmCyt), which can be further oxidized to 5-formylcytosine (5-fCyt) and 5-carboxylcytosine (5-caCyt). The products of active DNA demethylation are released into the bloodstream and eventually also appear in urine. We used online two-dimensional ultraperformance liquid chromatography with tandem mass spectrometry (2D-UPLC-MS/MS) to compare DNA methylation marks and 8-oxo-2'-deoxyguanosine (8-oxodG) in colorectal cancer and pre-cancerous condition in urine.
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