Biopolym. Cell. 2019; 35(3):209-210.
Chronicle and Information
Probing the chromatin structure of ribosomal DNA using extended chromatin fibers
1Franek M., 1Kutashev K., 1, 2Fajkus J., 1, 2Dvořáčková M.
  1. Central European Institute of Technology (CEITEC) and Faculty of Science of Masaryk University
    Kamenice 5, 62500 Brno, CZ
  2. Institute of Biophysics, The Czech Academy of Sciences
    Královopolská 135, 612 65 Brno, CZ


The chromatin organization of ribosomal genes, which encode essential 25S, 18S and 5.8S ribosomal RNA, remains unresolved to this day in many biological models. Hundreds of rDNA copies exist in the genome in a mostly tandem, head-to-tail arrangement. Nucleoli, the main transcription factories of the cell, are known to assemble around actively transcribed rDNA copies. Evidence from electron microscopy studies shows a subset of actively transcribed genes which appear mostly nucleosome-free [1], but this represents only a small fraction of rDNA units. Our understanding of the epigenetic state of the remaining copies is still incomplete [2]. Our main goal was to identify individual rDNA chromatin fibers and probe their chromatin structure. Methods We prepared chromatin fibers from the plant model Arabidopsis thaliana in combination with immunofluorescence and FISH detection of histone marks in rDNA loci. Results We show the presence of histones and histone modifications in rDNA clusters, even in plants with a reduced number of rDNA copies [3]. This indicates that a subset of rDNA copies exists in a poised state for transcription, marked by the presence of H3K4me3 and H3K27me3 modifications. Furthermore, these histone modifications are found intermingling or colocalizing on individual chromatin fibers in plants, reinforcing the notion that as opposed to mammalian models, H3K27me3 is not a marker of compact heterochromatin in plants. Conclusions: Microscopy of chromatin fibers has been used previously to study the structure of centromeres. We show that it is possible to adapt this strategy to study the epigenetic structure of rDNA. Once optimized, this method can be used to study repetitive genomic regions, telomeres and satellites included, and fill the gaps in knowledge in genomic regions hard to analyze by ChIP-seq. Fundings: This project was supported by The Czech Science Foundation, grant number 19-11880Y and Ministry of education, youth and sports INTER-COST LTC18048. References: 1)Miller OL, Beatty BR. 1969. Visualization of Nucleolar Genes. Science, 164: 955-957. 2)Dvořáčková M, Fojtová M, Fajkus J. 2015. Chromatin dynamics of plant telomeres and ribosomal genes. Plant J. 83:18-37. 3)Pavlištová V, Dvořáčková M, Jež M, Mozgová I, Mokroš P, Fajkus J. 2016. Phenotypic reversion in fas mutants of Arabidopsis thaliana by reintroduction of FAS genes: variable recovery of telomeres with major spatial rearrangements and transcriptional reprogramming of 45S rDNA genes. Plant J. 88: 411-424.