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Louzada S, Lopes M, Ferreira D, Adega F, Escudeiro A, Gama-Carvalho M, Chaves R. Decoding the Role of Satellite DNA in Genome Architecture and Plasticity-An Evolutionary and Clinical Affair. Genes (Basel) 2020; 11:E72. [PMID: 31936645 PMCID: PMC7017282 DOI: 10.3390/genes11010072] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/29/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.
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Affiliation(s)
- Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
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Louzada S, Vieira-da-Silva A, Mendes-da-Silva A, Kubickova S, Rubes J, Adega F, Chaves R. A novel satellite DNA sequence in the Peromyscus genome (PMSat): Evolution via copy number fluctuation. Mol Phylogenet Evol 2015; 92:193-203. [PMID: 26103000 DOI: 10.1016/j.ympev.2015.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 06/11/2015] [Accepted: 06/12/2015] [Indexed: 12/16/2022]
Abstract
Satellite DNAs (satDNA) are tandemly arrayed repeated sequences largely present in eukaryotic genomes, which play important roles in genome evolution and function, and therefore, their analysis is vital. Here, we describe the isolation of a novel satellite DNA family (PMSat) from the rodent Peromyscus eremicus (Cricetidae, Rodentia), which is located in pericentromeric regions and exhibits a typical satellite DNA genome organization. Orthologous PMSat sequences were isolated and characterized from three species belonging to Cricetidae: Cricetus cricetus, Phodopus sungorus and Microtus arvalis. In these species, PMSat is highly conserved, with the absence of fixed species-specific mutations. Strikingly, different numbers of copies of this sequence were found among the species, suggesting evolution by copy number fluctuation. Repeat units of PMSat were also found in the Peromyscus maniculatus bairdii BioProject, but our results suggest that these repeat units are from genome regions outside the pericentromere. The remarkably high evolutionary sequence conservation along with the preservation of a few numbers of copies of this sequence in the analyzed genomes may suggest functional significance but a different sequence nature/organization. Our data highlight that repeats are difficult to analyze due to the limited tools available to dissect genomes and the fact that assemblies do not cover regions of constitutive heterochromatin.
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Affiliation(s)
- Sandra Louzada
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal
| | - Ana Vieira-da-Silva
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Ana Mendes-da-Silva
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | | | - Jiri Rubes
- Veterinary Research Institute, Brno, Czech Republic
| | - Filomena Adega
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Raquel Chaves
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal.
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Vieira-da-Silva A, Louzada S, Adega F, Chaves R. A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions. Cytogenet Genome Res 2015; 145:59-67. [PMID: 25999143 DOI: 10.1159/000381840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 11/19/2022] Open
Abstract
Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes.
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Affiliation(s)
- Ana Vieira-da-Silva
- Center of Agricultural and Genomics Biotechnology (CGBA), University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
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LINE-1 retrotransposons: from 'parasite' sequences to functional elements. J Appl Genet 2014; 56:133-45. [PMID: 25106509 DOI: 10.1007/s13353-014-0241-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 10/24/2022]
Abstract
Long interspersed nuclear elements-1 (LINE-1) are the most abundant and active retrotransposons in the mammalian genomes. Traditionally, the occurrence of LINE-1 sequences in the genome of mammals has been explained by the selfish DNA hypothesis. Nevertheless, recently, it has also been argued that these sequences could play important roles in these genomes, as in the regulation of gene expression, genome modelling and X-chromosome inactivation. The non-random chromosomal distribution is a striking feature of these retroelements that somehow reflects its functionality. In the present study, we have isolated and analysed a fraction of the open reading frame 2 (ORF2) LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus and Praomys tullbergi. Physical mapping of the isolated sequences revealed an interspersed longitudinal AT pattern of distribution along all the chromosomes of the complement in the three genomes. A detailed analysis shows that these sequences are preferentially located in the euchromatic regions, although some signals could be detected in the heterochromatin. In addition, a coincidence between the location of imprinted gene regions (as Xist and Tsix gene regions) and the LINE-1 retroelements was also observed. According to these results, we propose an involvement of LINE-1 sequences in different genomic events as gene imprinting, X-chromosome inactivation and evolution of repetitive sequences located at the heterochromatic regions (e.g. satellite DNA sequences) of the rodents' genomes analysed.
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The involvement of repetitive sequences in the remodelling of karyotypes: The Phodopus genomes (Rodentia, Cricetidae). Micron 2013; 46:27-34. [DOI: 10.1016/j.micron.2012.11.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 02/08/2023]
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Chaves R, Louzada S, Meles S, Wienberg J, Adega F. Praomys tullbergi (Muridae, Rodentia) genome architecture decoded by comparative chromosome painting with Mus and Rattus. Chromosome Res 2012; 20:673-83. [PMID: 22847644 DOI: 10.1007/s10577-012-9304-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 11/25/2022]
Abstract
The order Rodentia and in particular the Muridae are characterised by extremely high rates of chromosome evolution and remarkable chromosome diversity. The Praomys group (Murinae, Muridae and Rodentia) constitutes a diverse and abundant group divided into two complexes, the jacksoni complex and the tullbergi complex which includes the species Praomys tullbergi. Comparative chromosome painting using the two index genomes, Mus musculus and Rattus norvegicus, was performed resulting in a high resolution chromosome map for P. tullbergi. The combined use of rat and mouse probes and the assistance of the assembly of all the available sequencing data from Ensembl genome browser allowed a great dissection of P. tullbergi genome, the detection of inversion events and ultimately the refinement of P. tullbergi comparative map. A key achievement was the reconstruction of a high precision Muroidea ancestral karyotype (Muridae/Cricetidae and Murine) based in a broad species analysis combining previous reported comparative maps together with the presented data. This permitted the reconstruction of the evolutionary history of chromosome changes since the ancestral Muroidea genome and enlightened the phylogenetic relationships with the related species mouse and rat. The analysis of constitutive heterochromatin and its co-localisation with the identified evolutionary breakpoints regions was performed suggesting the involvement of repetitive sequences in the chromosome rearrangements that originated the present P. tullbergi genome architecture.
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Affiliation(s)
- Raquel Chaves
- Centre of Genomics and Biotechnology, Institute for Biotechnology and Bioengineering, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD), Vila Real, Portugal.
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Karamysheva TV, Bogdanov AS, Kartavtseva IV, Likhoshvay TV, Bochkarev MN, Kolcheva NE, Marochkina VV, Rubtsov NB. Comparative FISH analysis of C-positive blocks of centromeric chromosomal regions of pygmy wood mice Sylvaemus uralensis (Rodentia, Muridae). RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410060128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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