1
|
da Costa-Nunes JA, Gierlinski M, Sasaki T, Haagensen EJ, Gilbert DM, Blow JJ. The location and development of Replicon Cluster Domains in early replicating DNA. Wellcome Open Res 2023; 8:158. [PMID: 37766844 PMCID: PMC10521077 DOI: 10.12688/wellcomeopenres.18742.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Background: It has been known for many years that in metazoan cells, replication origins are organised into clusters where origins within each cluster fire near-synchronously. Despite clusters being a fundamental organising principle of metazoan DNA replication, the genomic location of origin clusters has not been documented. Methods: We synchronised human U2OS by thymidine block and release followed by L-mimosine block and release to create a population of cells progressing into S phase with a high degree of synchrony. At different times after release into S phase, cells were pulsed with EdU; the EdU-labelled DNA was then pulled down, sequenced and mapped onto the human genome. Results: The early replicating DNA showed features at a range of scales. Wavelet analysis showed that the major feature of the early replicating DNA was at a size of 500 kb, consistent with clusters of replication origins. Over the first two hours of S phase, these Replicon Cluster Domains broadened in width, consistent with their being enlarged by the progression of replication forks at their outer boundaries. The total replication signal associated with each Replicon Cluster Domain varied considerably, and this variation was reproducible and conserved over time. We provide evidence that this variability in replication signal was at least in part caused by Replicon Cluster Domains being activated at different times in different cells in the population. We also provide evidence that adjacent clusters had a statistical preference for being activated in sequence across a group, consistent with the 'domino' model of replication focus activation order observed by microscopy. Conclusions: We show that early replicating DNA is organised into Replicon Cluster Domains that behave as expected of replicon clusters observed by DNA fibre analysis. The coordinated activation of different Replicon Cluster Domains can generate the replication timing programme by which the genome is duplicated.
Collapse
Affiliation(s)
- José A. da Costa-Nunes
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marek Gierlinski
- Data Analysis Group, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, California, CA 92121, USA
| | - Emma J. Haagensen
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Present address: School of Medical Education, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David M. Gilbert
- San Diego Biomedical Research Institute, San Diego, California, CA 92121, USA
| | - J. Julian Blow
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| |
Collapse
|
2
|
da Costa-Nunes JA, Noordermeer D. TADs: Dynamic structures to create stable regulatory functions. Curr Opin Struct Biol 2023; 81:102622. [PMID: 37302180 DOI: 10.1016/j.sbi.2023.102622] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023]
Abstract
Mammalian chromosomes are organized at different length scales within the cell nucleus. Topologically Associating Domains (TADs) are structural units of 3D genome organization with functions in gene regulation, DNA replication, recombination and repair. Whereas TADs were initially interpreted as insulated domains, recent studies are revealing that these domains should be interpreted as dynamic collections of actively extruding loops. This process of loop extrusion is subsequently blocked at dedicated TAD boundaries, thereby promoting intra-domain interactions over their surroundings. In this review, we discuss how mammalian TAD structure can emerge from this dynamic process and we discuss recent evidence that TAD boundaries can have regulatory functions.
Collapse
Affiliation(s)
- José A da Costa-Nunes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| |
Collapse
|
3
|
da Costa-Nunes JA, Capitão C, Kozak J, Costa-Nunes P, Ducasa GM, Pontes O, Angelis KJ. The AtRAD21.1 and AtRAD21.3 Arabidopsis cohesins play a synergistic role in somatic DNA double strand break damage repair. BMC Plant Biol 2014; 14:353. [PMID: 25511710 PMCID: PMC4273318 DOI: 10.1186/s12870-014-0353-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 11/26/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND The RAD21 cohesin plays, besides its well-recognised role in chromatid cohesion, a role in DNA double strand break (dsb) repair. In Arabidopsis there are three RAD21 paralog genes (AtRAD21.1, AtRAD21.2 and AtRAD21.3), yet only AtRAD21.1 has been shown to be required for DNA dsb damage repair. Further investigation of the role of cohesins in DNA dsb repair was carried out and is here reported. RESULTS We show for the first time that not only AtRAD21.1 but also AtRAD21.3 play a role in somatic DNA dsb repair. Comet data shows that the lack of either cohesins induces a similar high basal level of DNA dsb in the nuclei and a slower DNA dsb repair kinetics in both cohesin mutants. The observed AtRAD21.3 transcriptional response to DNA dsb induction reinforces further the role of this cohesin in DNA dsb repair. The importance of AtRAD21.3 in DNA dsb damage repair, after exposure to DNA dsb damage inducing agents, is notorious and recognisably evident at the phenotypical level, particularly when the AtRAD21.1 gene is also disrupted. CONCLUSIONS Our data demonstrates that both Arabidopsis cohesin (AtRAD21.1 and AtRAD21.3) play a role in somatic DNA dsb repair. Furthermore, the phenotypical data from the atrad21.1 atrad21.3 double mutant indicates that these two cohesins function synergistically in DNA dsb repair. The implications of this data are discussed.
Collapse
Affiliation(s)
- José A da Costa-Nunes
- />Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa (UNL), Av. República, Apartado 127, 2781-901 Oeiras, Portugal
| | - Cláudio Capitão
- />Laboratório de Biotecnologia de Células Vegetais, ITQB, UNL, Av. República, Apartado 127, 2781-901 Oeiras, Portugal
- />Current address: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Jaroslav Kozak
- />Molecular Farming Lab., Institute of Experimental Botany AS CR, Na Karlovce 1, 160 00 Praha 6, Czech Republic
| | - Pedro Costa-Nunes
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
- />Current address: Nuclear Organization and Epigenetics Lab., Shanghai Center for Plant Stress Biology (PSC), No. 3888 Chenhua Road, Shanghai, 201602 P. R. China
| | - Gloria M Ducasa
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
| | - Olga Pontes
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
- />Current address: Nuclear Organization and Epigenetics Lab., Shanghai Center for Plant Stress Biology (PSC), No. 3888 Chenhua Road, Shanghai, 201602 P. R. China
| | - Karel J Angelis
- />Molecular Farming Lab., Institute of Experimental Botany AS CR, Na Karlovce 1, 160 00 Praha 6, Czech Republic
| |
Collapse
|
4
|
Kozak J, West CE, White C, da Costa-Nunes JA, Angelis KJ. Rapid repair of DNA double strand breaks in Arabidopsis thaliana is dependent on proteins involved in chromosome structure maintenance. DNA Repair (Amst) 2008; 8:413-9. [PMID: 19070688 DOI: 10.1016/j.dnarep.2008.11.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 11/05/2008] [Accepted: 11/09/2008] [Indexed: 10/21/2022]
Abstract
DNA double strand breaks (DSBs) are one of the most cytotoxic forms of DNA damage and must be repaired by recombination, predominantly via non-homologous joining of DNA ends (NHEJ) in higher eukaryotes. However, analysis of DSB repair kinetics of plant NHEJ mutants atlig4-4 and atku80 with the neutral comet assay shows that alternative DSB repair pathways are active. Surprisingly, these kinetic measurements show that DSB repair was faster in the NHEJ mutant lines than in wild-type Arabidopsis. Here we provide the first characterization of this KU-independent, rapid DSB repair pathway operating in Arabidopsis. The alternate pathway that rapidly removes the majority of DSBs present in nuclear DNA depends upon structural maintenance of chromosomes (SMC) complex proteins, namely MIM/AtRAD18 and AtRAD21.1. An absolute requirement for SMC proteins and kleisin for rapid repair of DSBs in Arabidopsis opens new insight into the mechanism of DSB removal in plants.
Collapse
Affiliation(s)
- Jaroslav Kozak
- Institute of Experimental Botany AS CR, Praha 6, Czech Republic
| | | | | | | | | |
Collapse
|