J 2021

Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations

FRANEK, Michal, Agata Magdalena KILAR, Petr FOJTÍK, Marie OLSINOVA, Ales BENDA et. al.

Basic information

Original name

Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations

Authors

FRANEK, Michal (703 Slovakia, guarantor, belonging to the institution), Agata Magdalena KILAR (616 Poland, belonging to the institution), Petr FOJTÍK (203 Czech Republic, belonging to the institution), Marie OLSINOVA (203 Czech Republic), Ales BENDA (203 Czech Republic), Vladimír ROTREKL (203 Czech Republic, belonging to the institution), Martina DVOŘÁČKOVÁ (203 Czech Republic, belonging to the institution) and Jiří FAJKUS (203 Czech Republic, belonging to the institution)

Edition

Journal of Cell Science, Cambridge, Company of Biologists Ltd. 2021, 0021-9533

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10601 Cell biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 5.235

RIV identification code

RIV/00216224:14740/21:00119668

Organization unit

Central European Institute of Technology

DOI

UT WoS

000686349300013

Keywords in English

DNA; Fiber; Chromatin; Methylation; Microscopy

Tags

Tags

International impact, Reviewed
Změněno: 8/10/2024 10:09, Ing. Martina Blahová

Abstract

V originále

Analysis of histone variants and epigenetic marks is dominated by genome-wide approaches in the form of chromatin immunoprecipitation-sequencing (ChIP-seq) and related methods. Although uncontested in their value for single-copy genes, mapping the chromatin of DNA repeats is problematic for biochemical techniques that involve averaging of cell populations or analysis of clusters of tandem repeats in a single-cell analysis. Extending chromatin and DNA fibers allows us to study the epigenetics of individual repeats in their specific chromosomal context, and thus constitutes an important tool for gaining a complete understanding of the epigenetic organization of genomes. We report that using an optimized fiber extension protocol is essential in order to obtain more reproducible data and to minimize the clustering of fibers. We also demonstrate that the use of super-resolution microscopy is important for reliable evaluation of the distribution of histone modifications on individual fibers. Furthermore, we introduce a custom script for the analysis of methylation levels on DNA fibers and apply it to map the methylation of telomeres, ribosomal genes and centromeres.

Links

EF16_013/0001775, research and development project
Name: Modernizace a podpora výzkumných aktivit národní infrastruktury pro biologické a medicínské zobrazování Czech-BioImaging
EF16_026/0008446, research and development project
Name: Integrace signálu a epigenetické reprogramování pro produktivitu rostlin
GJ19-11880Y, research and development project
Name: Chromatinové prostředí indukované genotoxickými látkami
Investor: Czech Science Foundation, Chromatin environment induced by genotoxic agents
LTC18048, research and development project
Name: Prostorové uspořádání významných jaderných domén a jejich proteinových složek
Investor: Ministry of Education, Youth and Sports of the CR, Spatial organisation of key nuclear domains and their protein components, INTER-COST
LTC20003, research and development project
Name: Dynamics of telomeres and rDNA loci in plant cell nuclei
Investor: Ministry of Education, Youth and Sports of the CR, INTER-COST
NU20-06-00156, research and development project
Name: Vliv pneumologické medikace na funkce lidských kardiomyocytů.
Investor: Ministry of Health of the CR, Subprogram 1 - standard
90129, large research infrastructures
Name: Czech-BioImaging II