Transcriptional Silencing of 35S RDNA in Correlates with Cytosine Methylation in Sequence-Specific Manner

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2024 Jul 27

PMID 39062783

Authors

Roman Matyasek

Radka Kalfusova

Alena Kuderova

Katerina rehurkova

Jana Sochorova

Ales Kovarik

Affiliations

Soon will be listed here.

Abstract

Despite the widely accepted involvement of DNA methylation in the regulation of rDNA transcription, the relative participation of different cytosine methylation pathways is currently described only for a few model plants. Using PacBio, Bisulfite, and RNA sequencing; PCR; Southern hybridizations; and FISH, the epigenetic consequences of rDNA copy number variation were estimated in two lineages, por1 and por2, the latter with more than twice the rDNA copy numbers distributed approximately equally between NORs on chromosomes A and D. The lower rDNA content in por1 correlated with significantly reduced (>90%) sizes of both D-NORs. Moreover, two (L and S) prominent rDNA variants, differing in the repetitive organization of intergenic spacers, were detected in por2, while only the S-rDNA variant was detected in por1. Transcriptional activity of S-rDNA in por1 was associated with secondary constriction of both A-NORs. In contrast, silencing of S-rDNA in por2 was accompanied by condensation of A-NORs, secondary constriction on D-NORs, and L-rDNA transcriptional activity, suggesting (i) bidirectional nucleolar dominance and (ii) association of S-rDNAs with A-NORs and L-rDNAs with D-NORs in Each S- and L-rDNA array was formed of several sub-variants differentiating both genetically (specific SNPs) and epigenetically (transcriptional efficiency and cytosine methylation). The most significant correlations between rDNA silencing and methylation were detected for symmetric CWG motifs followed by CG motifs. No correlations were detected for external cytosine in CCGs or asymmetric CHHs, where methylation was rather position-dependent, particularly for AT-rich variants. We conclude that variations in rDNA copy numbers in plant diploids can be accompanied by prompt epigenetic responses to maintain an appropriate number of active rDNAs. The methylation dynamics of CWGs are likely to be the most responsible for regulating silent and active rDNA states.

References

Kobayashi T . A new role of the rDNA and nucleolus in the nucleus--rDNA instability maintains genome integrity. Bioessays. 2008; 30(3):267-72. DOI: 10.1002/bies.20723. View

Hemleben V, Zentgraf U . Structural organization and regulation of transcription by RNA polymerase I of plant nuclear ribosomal RNA genes. Results Probl Cell Differ. 1994; 20:3-24. DOI: 10.1007/978-3-540-48037-2_1. View

Manelyte L, Strohner R, Gross T, Langst G . Chromatin targeting signals, nucleosome positioning mechanism and non-coding RNA-mediated regulation of the chromatin remodeling complex NoRC. PLoS Genet. 2014; 10(3):e1004157. PMC: 3961174. DOI: 10.1371/journal.pgen.1004157. View

Kobayashi T . Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast. Cell Mol Life Sci. 2011; 68(8):1395-403. PMC: 3064901. DOI: 10.1007/s00018-010-0613-2. View

Gouil Q, Baulcombe D . DNA Methylation Signatures of the Plant Chromomethyltransferases. PLoS Genet. 2016; 12(12):e1006526. PMC: 5221884. DOI: 10.1371/journal.pgen.1006526. View

Matyasek R, Tate J, Lim Y, Srubarova H, Koh J, Leitch A . Concerted evolution of rDNA in recently formed Tragopogon allotetraploids is typically associated with an inverse correlation between gene copy number and expression. Genetics. 2007; 176(4):2509-19. PMC: 1950650. DOI: 10.1534/genetics.107.072751. View

Galian J, Rosato M, Rossello J . Incomplete sequence homogenization in 45S rDNA multigene families: intermixed IGS heterogeneity within the single NOR locus of the polyploid species Medicago arborea (Fabaceae). Ann Bot. 2014; 114(2):243-51. PMC: 4111382. DOI: 10.1093/aob/mcu115. View

Yaari R, Noy-Malka C, Wiedemann G, Auerbach Gershovitz N, Reski R, Katz A . DNA METHYLTRANSFERASE 1 is involved in (m)CG and (m)CCG DNA methylation and is essential for sporophyte development in Physcomitrella patens. Plant Mol Biol. 2015; 88(4-5):387-400. DOI: 10.1007/s11103-015-0328-8. View

Caudy A, Pikaard C . Xenopus ribosomal RNA gene intergenic spacer elements conferring transcriptional enhancement and nucleolar dominance-like competition in oocytes. J Biol Chem. 2002; 277(35):31577-84. DOI: 10.1074/jbc.M202737200. View

10.

Shiba H, Takayama S . RNA silencing systems and their relevance to allele-specific DNA methylation in plants. Biosci Biotechnol Biochem. 2007; 71(11):2632-46. DOI: 10.1271/bbb.70339. View

11.

Komarova N, Grabe T, Huigen D, Hemleben V, Volkov R . Organization, differential expression and methylation of rDNA in artificial Solanum allopolyploids. Plant Mol Biol. 2004; 56(3):439-63. DOI: 10.1007/s11103-004-4678-x. View

12.

Du J, Johnson L, Jacobsen S, Patel D . DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol. 2015; 16(9):519-32. PMC: 4672940. DOI: 10.1038/nrm4043. View

13.

Matyasek R, Kuderova A, Kutilkova E, Kucera M, Kovarik A . Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations. DNA Res. 2019; 26(3):273-286. PMC: 6589552. DOI: 10.1093/dnares/dsz008. View

14.

Fultz D, McKinlay A, Enganti R, Pikaard C . Sequence and epigenetic landscapes of active and silent nucleolus organizer regions in . Sci Adv. 2023; 9(44):eadj4509. PMC: 10619934. DOI: 10.1126/sciadv.adj4509. View

15.

Pikaard C, Chandrasekhara C, McKinlay A, Enganti R, Fultz D . Reaching for the off switch in nucleolar dominance. Plant J. 2023; 115(5):1185-1192. PMC: 10524600. DOI: 10.1111/tpj.16318. View

16.

Law J, Jacobsen S . Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010; 11(3):204-20. PMC: 3034103. DOI: 10.1038/nrg2719. View

17.

Chen Z, Pikaard C . Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proc Natl Acad Sci U S A. 1997; 94(7):3442-7. PMC: 20389. DOI: 10.1073/pnas.94.7.3442. View

18.

Sims J, Sestini G, Elgert C, von Haeseler A, Schlogelhofer P . Sequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants. Nat Commun. 2021; 12(1):387. PMC: 7810690. DOI: 10.1038/s41467-020-20728-6. View

19.

Matyasek R, Dobesova E, Huska D, Jezkova I, Soltis P, Soltis D . Interpopulation hybridization generates meiotically stable rDNA epigenetic variants in allotetraploid Tragopogon mirus. Plant J. 2015; 85(3):362-77. DOI: 10.1111/tpj.13110. View

20.

Pikaard C . Ribosomal gene promoter domains can function as artificial enhancers of RNA polymerase I transcription, supporting a promoter origin for natural enhancers in Xenopus. Proc Natl Acad Sci U S A. 1994; 91(2):464-8. PMC: 42969. DOI: 10.1073/pnas.91.2.464. View