Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells.
Ribosomal DNA (rDNA) genes encode the structural RNAs of the ribosome and are present in hundreds of copies in mammalian genomes. Age-linked DNA hypermethylation throughout the rDNA constitutes a robust "methylation clock" that accurately reports age, yet the consequences of hypermethylati...
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Public Library of Science (PLoS)
2024-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0310626 |
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| author | Yana Blokhina Abigail Buchwalter |
| author_facet | Yana Blokhina Abigail Buchwalter |
| author_sort | Yana Blokhina |
| collection | DOAJ |
| description | Ribosomal DNA (rDNA) genes encode the structural RNAs of the ribosome and are present in hundreds of copies in mammalian genomes. Age-linked DNA hypermethylation throughout the rDNA constitutes a robust "methylation clock" that accurately reports age, yet the consequences of hypermethylation on rDNA function are unknown. We confirmed that pervasive hypermethylation of rDNA occurs during mammalian aging and senescence while rDNA copy number remains stable. We found that DNA methylation is exclusively found on the promoters and gene bodies of inactive rDNA. To model the effects of age-linked methylation on rDNA function, we directed de novo DNA methylation to the rDNA promoter or gene body with a nuclease-dead Cas9 (dCas9)-DNA methyltransferase fusion enzyme in human cells. Hypermethylation at each target site had no detectable effect on rRNA transcription, nucleolar morphology, or cellular growth rate. Instead, human UBF and Pol I remain bound to rDNA promoters in the presence of increased DNA methylation. These data suggest that promoter methylation is not sufficient to impair transcription of the human rDNA and imply that the human rDNA transcription machinery may be resilient to age-linked rDNA hypermethylation. |
| format | Article |
| id | doaj-art-fedca42368a648ba887ae04d79a662ac |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-fedca42368a648ba887ae04d79a662ac2025-01-08T05:33:23ZengPublic Library of Science (PLoS)PLoS ONE1932-62032024-01-011912e031062610.1371/journal.pone.0310626Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells.Yana BlokhinaAbigail BuchwalterRibosomal DNA (rDNA) genes encode the structural RNAs of the ribosome and are present in hundreds of copies in mammalian genomes. Age-linked DNA hypermethylation throughout the rDNA constitutes a robust "methylation clock" that accurately reports age, yet the consequences of hypermethylation on rDNA function are unknown. We confirmed that pervasive hypermethylation of rDNA occurs during mammalian aging and senescence while rDNA copy number remains stable. We found that DNA methylation is exclusively found on the promoters and gene bodies of inactive rDNA. To model the effects of age-linked methylation on rDNA function, we directed de novo DNA methylation to the rDNA promoter or gene body with a nuclease-dead Cas9 (dCas9)-DNA methyltransferase fusion enzyme in human cells. Hypermethylation at each target site had no detectable effect on rRNA transcription, nucleolar morphology, or cellular growth rate. Instead, human UBF and Pol I remain bound to rDNA promoters in the presence of increased DNA methylation. These data suggest that promoter methylation is not sufficient to impair transcription of the human rDNA and imply that the human rDNA transcription machinery may be resilient to age-linked rDNA hypermethylation.https://doi.org/10.1371/journal.pone.0310626 |
| spellingShingle | Yana Blokhina Abigail Buchwalter Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells. PLoS ONE |
| title | Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells. |
| title_full | Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells. |
| title_fullStr | Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells. |
| title_full_unstemmed | Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells. |
| title_short | Modeling the consequences of age-linked rDNA hypermethylation with dCas9-directed DNA methylation in human cells. |
| title_sort | modeling the consequences of age linked rdna hypermethylation with dcas9 directed dna methylation in human cells |
| url | https://doi.org/10.1371/journal.pone.0310626 |
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