Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information
DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication. Here, we design a computational approach named iOR...
| Main Authors: | , , , |
|---|---|
| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2023
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/168771 |
| _version_ | 1811678015922372608 |
|---|---|
| author | Dao, Fu-Ying Lv, Hao Fullwood, Melissa Jane Lin, Hao |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Dao, Fu-Ying Lv, Hao Fullwood, Melissa Jane Lin, Hao |
| author_sort | Dao, Fu-Ying |
| collection | NTU |
| description | DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication. Here, we design a computational approach named iORI-Epi to recognize ORIs by incorporating epigenome-based features, sequence-based features, and 3D genome-based features. The iORI-Epi displays excellent robustness and generalization ability on both training datasets and independent datasets of K562 cell line. Further experiments confirm that iORI-Epi is highly scalable in other cell lines (MCF7 and HCT116). We also analyze and clarify the regulatory role of epigenomic marks, DNA motifs, and chromatin interaction in DNA replication initiation of eukaryotic genomes. Finally, we discuss gene enrichment pathways from the perspective of ORIs in different replication timing states and heuristically dissect the effect of promoters on replication initiation. Our computational methodology is worth extending to ORI identification in other eukaryotic species. |
| first_indexed | 2024-10-01T02:46:33Z |
| format | Journal Article |
| id | ntu-10356/168771 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T02:46:33Z |
| publishDate | 2023 |
| record_format | dspace |
| spelling | ntu-10356/1687712023-06-19T15:32:05Z Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information Dao, Fu-Ying Lv, Hao Fullwood, Melissa Jane Lin, Hao School of Biological Sciences Institute of Molecular and Cell Biology, A∗STAR Science::Biological sciences DNA Cell Lines DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication. Here, we design a computational approach named iORI-Epi to recognize ORIs by incorporating epigenome-based features, sequence-based features, and 3D genome-based features. The iORI-Epi displays excellent robustness and generalization ability on both training datasets and independent datasets of K562 cell line. Further experiments confirm that iORI-Epi is highly scalable in other cell lines (MCF7 and HCT116). We also analyze and clarify the regulatory role of epigenomic marks, DNA motifs, and chromatin interaction in DNA replication initiation of eukaryotic genomes. Finally, we discuss gene enrichment pathways from the perspective of ORIs in different replication timing states and heuristically dissect the effect of promoters on replication initiation. Our computational methodology is worth extending to ORI identification in other eukaryotic species. Published version 2023-06-19T05:02:57Z 2023-06-19T05:02:57Z 2022 Journal Article Dao, F., Lv, H., Fullwood, M. J. & Lin, H. (2022). Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information. Research, 2022, 9780293-. https://dx.doi.org/10.34133/2022/9780293 2096-5168 https://hdl.handle.net/10356/168771 10.34133/2022/9780293 36405252 2-s2.0-85145740579 2022 9780293 en Research © 2022 Fu-Ying Dao et al. Exclusive Licensee Science and Technology Review Publishing House. Distributed under a Creative Commons Attribution License (CCBY4.0). application/pdf |
| spellingShingle | Science::Biological sciences DNA Cell Lines Dao, Fu-Ying Lv, Hao Fullwood, Melissa Jane Lin, Hao Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information |
| title | Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information |
| title_full | Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information |
| title_fullStr | Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information |
| title_full_unstemmed | Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information |
| title_short | Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information |
| title_sort | accurate identification of dna replication origin by fusing epigenomics and chromatin interaction information |
| topic | Science::Biological sciences DNA Cell Lines |
| url | https://hdl.handle.net/10356/168771 |
| work_keys_str_mv | AT daofuying accurateidentificationofdnareplicationoriginbyfusingepigenomicsandchromatininteractioninformation AT lvhao accurateidentificationofdnareplicationoriginbyfusingepigenomicsandchromatininteractioninformation AT fullwoodmelissajane accurateidentificationofdnareplicationoriginbyfusingepigenomicsandchromatininteractioninformation AT linhao accurateidentificationofdnareplicationoriginbyfusingepigenomicsandchromatininteractioninformation |