Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes)

@article{1557842,
   author = {Matyášek, Roman and Krumpolcová, Alice and Lunerová, Jana and Mikulášková, Eva and Rossello, Josep A. and Kovařík, Aleš},
   article_location = {Lausanne (Switzerland)},
   article_number = {SEP 5 2019},
   doi = {http://dx.doi.org/10.3389/fpls.2019.01066},
   keywords = {rDNA; cytosine methylation; bryophytes; epigenetics; histone marks; genome evolution},
   language = {eng},
   issn = {1664-462X},
   journal = {Frontiers in Plant Science},
   title = {Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes)},
   url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739443/},
   volume = {10},
   year = {2019}
}

TY  - JOUR
ID  - 1557842
AU  - Matyášek, Roman - Krumpolcová, Alice - Lunerová, Jana - Mikulášková, Eva - Rossello, Josep A. - Kovařík, Aleš
PY  - 2019
TI  - Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes)
JF  - Frontiers in Plant Science
VL  - 10
IS  - SEP 5 2019
SP  - 1-13
EP  - 1-13
PB  - Frontiers Media SA
SN  - 1664462X
KW  - rDNA
KW  - cytosine methylation
KW  - bryophytes
KW  - epigenetics
KW  - histone marks
KW  - genome evolution
UR  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739443/
L2  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739443/
N2  - Introduction: In plants, the multicopy genes encoding ribosomal RNA (rDNA) typically exhibit heterochromatic features and high level of DNA methylation. Here, we explored rDNA methylation in early diverging land plants from Bryophyta (15 species, 14 families) and Marchantiophyta (4 species, 4 families). DNA methylation was investigated by methylation-sensitive Southern blot hybridization in all species. We also carried out whole genomic bisulfite sequencing in Polytrichum formosum (Polytrichaceae) and Dicranum scoparium (Dicranaceae) and used available model plant methyloms (Physcomitrella patents and Marchantia polymorpha) to determine rDNA unit-wide methylation patterns. Chromatin structure was analyzed using fluorescence in situ hybridization (FISH) and immunoprecipitation (CHIP) assays. Results: In contrast to seed plants, bryophyte rDNAs were efficiently digested with methylation-sensitive enzymes indicating no or low levels of CG and CHG methylation in these loci. The rDNA methylom analyses revealed variation between species ranging from negligible (<3%, P formosum, P patens) to moderate (7 and 17% in M. polymorpha and D. scoparium, respectively) methylation levels. There were no differences between coding and noncoding parts of rDNA units and between gametophyte and sporophyte tissues. However, major satellite repeat and transposable elements were heavily methylated in P formosum and a scoparium. In P formosum rDNA, the euchromatic H3K4m3 and heterochromatic H3K9m2 histone marks were nearly balanced contrasting the angiosperms data where H3K9m2 typically dominates rDNA chromatin. In moss interphase nuclei, rDNA was localized at the nucleolar periphery and its condensation level was high. Conclusions: Unlike seed plants, the rRNA genes seem to escape global methylation machinery in bryophytes. Distinct epigenetic features may be related to rDNA expression and the physiology of these early diverging plants that exist in haploid state for most of their life cycles.
ER  - 

MATYÁŠEK, Roman, Alice KRUMPOLCOVÁ, Jana LUNEROVÁ, Eva MIKULÁŠKOVÁ, Josep A. ROSSELLO and Aleš KOVAŘÍK. Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes). \textit{Frontiers in Plant Science}. Lausanne (Switzerland): Frontiers Media SA, 2019, vol.~10, SEP 5 2019, p.~1-13. ISSN~1664-462X. Available from: https://dx.doi.org/10.3389/fpls.2019.01066.