Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy
The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and lat...
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eLife Sciences Publications Ltd
2025-01-01
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| Online Access: | https://elifesciences.org/articles/97438 |
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| author | Carmina Lichauco Eric J Foss Tonibelle Gatbonton-Schwager Nelson F Athow Brandon Lofts Robin Acob Erin Taylor James J Marquez Uyen Lao Shawna Miles Antonio Bedalov |
| author_facet | Carmina Lichauco Eric J Foss Tonibelle Gatbonton-Schwager Nelson F Athow Brandon Lofts Robin Acob Erin Taylor James J Marquez Uyen Lao Shawna Miles Antonio Bedalov |
| author_sort | Carmina Lichauco |
| collection | DOAJ |
| description | The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA (rDNA) arrays. We have previously reported that in the absence of SIR2, a de-repressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the nondisplaced MCMs. Furthermore, we found that both activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity of FUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication origin in vivo relies on the nucleosome context shaped by a single chromatin remodeler. |
| format | Article |
| id | doaj-art-c92cbb0c5c37496baa50bd72afc6599d |
| institution | Kabale University |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | eLife Sciences Publications Ltd |
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| series | eLife |
| spelling | doaj-art-c92cbb0c5c37496baa50bd72afc6599d2025-01-20T11:17:34ZengeLife Sciences Publications LtdeLife2050-084X2025-01-011310.7554/eLife.97438Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancyCarmina Lichauco0Eric J Foss1https://orcid.org/0000-0002-5553-9412Tonibelle Gatbonton-Schwager2Nelson F Athow3Brandon Lofts4Robin Acob5Erin Taylor6James J Marquez7Uyen Lao8Shawna Miles9Antonio Bedalov10https://orcid.org/0000-0002-7373-8255Translational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United StatesTranslational Science and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, United States; Department of Biochemistry and Department of Medicine, University of Washington, Seattle, United StatesThe association between late replication timing and low transcription rates in eukaryotic heterochromatin is well known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA (rDNA) arrays. We have previously reported that in the absence of SIR2, a de-repressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the nondisplaced MCMs. Furthermore, we found that both activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity of FUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication origin in vivo relies on the nucleosome context shaped by a single chromatin remodeler.https://elifesciences.org/articles/97438Sir2DNA replicationchromatinchromatin remodeling enzymeFun30silencing |
| spellingShingle | Carmina Lichauco Eric J Foss Tonibelle Gatbonton-Schwager Nelson F Athow Brandon Lofts Robin Acob Erin Taylor James J Marquez Uyen Lao Shawna Miles Antonio Bedalov Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy eLife Sir2 DNA replication chromatin chromatin remodeling enzyme Fun30 silencing |
| title | Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy |
| title_full | Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy |
| title_fullStr | Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy |
| title_full_unstemmed | Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy |
| title_short | Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy |
| title_sort | sir2 and fun30 regulate ribosomal dna replication timing via mcm helicase positioning and nucleosome occupancy |
| topic | Sir2 DNA replication chromatin chromatin remodeling enzyme Fun30 silencing |
| url | https://elifesciences.org/articles/97438 |
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