4.5 Article

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

期刊

JOURNAL OF CELL SCIENCE
卷 134, 期 15, 页码 -

出版社

COMPANY BIOLOGISTS LTD
DOI: 10.1242/jcs.258374

关键词

DNA; Fiber; Chromatin; Methylation; Microscopy

资金

  1. Grantova Agentura Ceske Republiky [19-11880Y]
  2. Ministerstvo Skolstvi, Mladeze a Telovychovy (projects INTER-COST) [LTC18048, LTC20003]
  3. European Regional Development Fund (project SINGING PLANT) [CZ.02.1.01/0.0/0.0/16_026/0008446]
  4. European Regional Development Fund [CZ.02.1.01/0.0/0.0/16_013/0001775]
  5. Ministerstvo Skolstvi, Mladeze a Telovychovy
  6. European Regional Development Fund (project ENOCH) [CZ.02.1.01/0.0/0.0/16_019/0000868]
  7. National Program of Sustainability II (Ministerstvo Skolstvi, Mladeze a Telovychovy) [LQ1605]
  8. Ministerstvo Zdravotnictvi Ceske Republiky [NU20-06-00156]

向作者/读者索取更多资源

The analysis of histone variants and epigenetic marks is mainly conducted through genome-wide approaches, such as ChIP-seq, to study the chromatin organization. Extending chromatin and DNA fibers allows for the study of individual DNA repeats in their specific chromosomal context, providing valuable insights into the epigenetic organization of genomes. It is essential to use optimized fiber extension protocols and super-resolution microscopy for reproducible data and accurate evaluation of histone modifications.
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.

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