Cell-Cycle–Dependent Chromatin Dynamics at Replication Origins
Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle–dependent manner. The assembly of the pre-replicative complex in G1 and the pre-initiation complex prior to activation in S phase are well characterized; however, the interplay between the asse...
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| Format: | Article |
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MDPI AG
2021-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/12/1998 |
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| author | Yulong Li Alexander J. Hartemink David M. MacAlpine |
| author_facet | Yulong Li Alexander J. Hartemink David M. MacAlpine |
| author_sort | Yulong Li |
| collection | DOAJ |
| description | Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle–dependent manner. The assembly of the pre-replicative complex in G1 and the pre-initiation complex prior to activation in S phase are well characterized; however, the interplay between the assembly of these complexes and the local chromatin environment is less well understood. To investigate the dynamic changes in chromatin organization at and surrounding replication origins, we used micrococcal nuclease (MNase) to generate genome-wide chromatin occupancy profiles of nucleosomes, transcription factors, and replication proteins through consecutive cell cycles in <i>Saccharomyces cerevisiae</i>. During each G1 phase of two consecutive cell cycles, we observed the downstream repositioning of the origin-proximal +1 nucleosome and an increase in protected DNA fragments spanning the ARS consensus sequence (ACS) indicative of pre-RC assembly. We also found that the strongest correlation between chromatin occupancy at the ACS and origin efficiency occurred in early S phase, consistent with the rate-limiting formation of the Cdc45–Mcm2-7–GINS (CMG) complex being a determinant of origin activity. Finally, we observed nucleosome disruption and disorganization emanating from replication origins and traveling with the elongating replication forks across the genome in S phase, likely reflecting the disassembly and assembly of chromatin ahead of and behind the replication fork, respectively. These results provide insights into cell-cycle–regulated chromatin dynamics and how they relate to the regulation of origin activity. |
| first_indexed | 2024-03-10T04:02:02Z |
| format | Article |
| id | doaj.art-11df2267e3eb49688c5a5e8cb6a707a0 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T04:02:02Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-11df2267e3eb49688c5a5e8cb6a707a02023-11-23T08:31:28ZengMDPI AGGenes2073-44252021-12-011212199810.3390/genes12121998Cell-Cycle–Dependent Chromatin Dynamics at Replication OriginsYulong Li0Alexander J. Hartemink1David M. MacAlpine2Department of Computer Science, Duke University, Durham, NC 27708, USADepartment of Computer Science, Duke University, Durham, NC 27708, USADepartment of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USAOrigins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle–dependent manner. The assembly of the pre-replicative complex in G1 and the pre-initiation complex prior to activation in S phase are well characterized; however, the interplay between the assembly of these complexes and the local chromatin environment is less well understood. To investigate the dynamic changes in chromatin organization at and surrounding replication origins, we used micrococcal nuclease (MNase) to generate genome-wide chromatin occupancy profiles of nucleosomes, transcription factors, and replication proteins through consecutive cell cycles in <i>Saccharomyces cerevisiae</i>. During each G1 phase of two consecutive cell cycles, we observed the downstream repositioning of the origin-proximal +1 nucleosome and an increase in protected DNA fragments spanning the ARS consensus sequence (ACS) indicative of pre-RC assembly. We also found that the strongest correlation between chromatin occupancy at the ACS and origin efficiency occurred in early S phase, consistent with the rate-limiting formation of the Cdc45–Mcm2-7–GINS (CMG) complex being a determinant of origin activity. Finally, we observed nucleosome disruption and disorganization emanating from replication origins and traveling with the elongating replication forks across the genome in S phase, likely reflecting the disassembly and assembly of chromatin ahead of and behind the replication fork, respectively. These results provide insights into cell-cycle–regulated chromatin dynamics and how they relate to the regulation of origin activity.https://www.mdpi.com/2073-4425/12/12/1998chromatincell cycleDNA replicationreplication origins |
| spellingShingle | Yulong Li Alexander J. Hartemink David M. MacAlpine Cell-Cycle–Dependent Chromatin Dynamics at Replication Origins Genes chromatin cell cycle DNA replication replication origins |
| title | Cell-Cycle–Dependent Chromatin Dynamics at Replication Origins |
| title_full | Cell-Cycle–Dependent Chromatin Dynamics at Replication Origins |
| title_fullStr | Cell-Cycle–Dependent Chromatin Dynamics at Replication Origins |
| title_full_unstemmed | Cell-Cycle–Dependent Chromatin Dynamics at Replication Origins |
| title_short | Cell-Cycle–Dependent Chromatin Dynamics at Replication Origins |
| title_sort | cell cycle dependent chromatin dynamics at replication origins |
| topic | chromatin cell cycle DNA replication replication origins |
| url | https://www.mdpi.com/2073-4425/12/12/1998 |
| work_keys_str_mv | AT yulongli cellcycledependentchromatindynamicsatreplicationorigins AT alexanderjhartemink cellcycledependentchromatindynamicsatreplicationorigins AT davidmmacalpine cellcycledependentchromatindynamicsatreplicationorigins |