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Convergent evolution of a genomic rearrangement may explain cancer resistance in hystrico- and sciuromorpha rodents. NPJ Aging Mech Dis 2021; 7:20. [PMID: 34471123 PMCID: PMC8410860 DOI: 10.1038/s41514-021-00072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/21/2021] [Indexed: 11/09/2022] Open
Abstract
The rodents of hystricomorpha and sciuromorpha suborders exhibit remarkably lower incidence of cancer. The underlying genetic basis remains obscure. We report a convergent evolutionary split of human 3p21.31, a locus hosting a large number of tumour-suppressor genes (TSGs) and frequently deleted in several tumour types, in hystrico- and sciuromorphs. Analysis of 34 vertebrate genomes revealed that the synteny of 3p21.31 cluster is functionally and evolutionarily constrained in most placental mammals, but exhibit large genomic interruptions independently in hystricomorphs and sciuromorphs, owing to relaxation of underlying constraints. Hystrico- and sciuromorphs, therefore, escape from pro-tumorigenic co-deletion of several TSGs in cis. The split 3p21.31 sub-clusters gained proximity to proto-oncogene clusters from elsewhere, which might further nullify pro-tumorigenic impact of copy number variations due to co-deletion or co-amplification of genes with opposing effects. The split of 3p21.31 locus coincided with the accelerated rate of its gene expression and the body mass evolution of ancestral hystrico- and sciuromorphs. The genes near breakpoints were associated with the traits specific to hystrico- and sciuromorphs, implying adaptive significance. We conclude that the convergently evolved chromosomal interruptions of evolutionarily constrained 3p21.31 cluster might have impacted evolution of cancer resistance, body mass variation and ecological adaptations in hystrico- and sciuromorphs.
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Guimarães AR, Correia I, Sousa I, Oliveira C, Moura G, Bezerra AR, Santos MAS. tRNAs as a Driving Force of Genome Evolution in Yeast. Front Microbiol 2021; 12:634004. [PMID: 33776966 PMCID: PMC7990762 DOI: 10.3389/fmicb.2021.634004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/01/2021] [Indexed: 11/29/2022] Open
Abstract
Transfer RNAs (tRNAs) are widely known for their roles in the decoding of the linear mRNA information into amino acid sequences of proteins. They are also multifunctional platforms in the translation process and have other roles beyond translation, including sensing amino acid abundance, interacting with the general stress response machinery, and modulating cellular adaptation, survival, and death. In this mini-review, we focus on the emerging role of tRNA genes in the organization and modification of the genomic architecture of yeast and the role of tRNA misexpression and decoding infidelity in genome stability, evolution, and adaption. We discuss published work showing how quickly tRNA genes can mutate to meet novel translational demands, how tRNAs speed up genome evolution, and how tRNA genes can be sites of genomic instability. We highlight recent works showing that loss of tRNA decoding fidelity and small alterations in tRNA expression have unexpected and profound impacts on genome stability. By dissecting these recent evidence, we hope to lay the groundwork that prompts future investigations on the mechanistic interplay between tRNAs and genome modification that likely triggers genome evolution.
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Affiliation(s)
- Ana Rita Guimarães
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Inês Correia
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Inês Sousa
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela Moura
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Rita Bezerra
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Manuel A S Santos
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
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Ghosh SK, Jost D. Genome organization via loop extrusion, insights from polymer physics models. Brief Funct Genomics 2020; 19:119-127. [PMID: 31711163 DOI: 10.1093/bfgp/elz023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/26/2019] [Accepted: 08/31/2019] [Indexed: 12/12/2022] Open
Abstract
Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.
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Affiliation(s)
- Surya K Ghosh
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - Daniel Jost
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, Inserm U1210, F-69007 Lyon, France
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Evolutionary Loss of Genomic Proximity to Conserved Noncoding Elements Impacted the Gene Expression Dynamics During Mammalian Brain Development. Genetics 2019; 211:1239-1254. [PMID: 30796012 DOI: 10.1534/genetics.119.301973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/14/2019] [Indexed: 01/05/2023] Open
Abstract
Conserved noncoding elements (CNEs) have a significant regulatory influence on their neighboring genes. Loss of proximity to CNEs through genomic rearrangements can, therefore, impact the transcriptional states of the cognate genes. Yet, the evolutionary implications of such chromosomal alterations have not been studied. Through genome-wide analysis of CNEs and the cognate genes of representative species from five different mammalian orders, we observed a significant loss of genes' linear proximity to CNEs in the rat lineage. The CNEs and the genes losing proximity had a significant association with fetal, but not postnatal, brain development as assessed through ontology terms, developmental gene expression, chromatin marks, and genetic mutations. The loss of proximity to CNEs correlated with the independent evolutionary loss of fetus-specific upregulation of nearby genes in the rat brain. DNA breakpoints implicated in brain abnormalities of germline origin had significant representation between a CNE and the gene that exhibited loss of proximity, signifying the underlying developmental tolerance of genomic rearrangements that allowed the evolutionary splits of CNEs and the cognate genes in the rodent lineage. Our observations highlighted a nontrivial impact of chromosomal rearrangements in shaping the evolutionary dynamics of mammalian brain development and might explain the loss of brain traits, like cerebral folding of the cortex, in the rodent lineage.
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Moretti AIS, Pavanelli JC, Nolasco P, Leisegang MS, Tanaka LY, Fernandes CG, Wosniak J, Kajihara D, Dias MH, Fernandes DC, Jo H, Tran NV, Ebersberger I, Brandes RP, Bonatto D, Laurindo FRM. Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families. Sci Rep 2017; 7:17262. [PMID: 29222525 PMCID: PMC5722932 DOI: 10.1038/s41598-017-16947-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/21/2017] [Indexed: 02/07/2023] Open
Abstract
Protein disulfide isomerases (PDIs) support endoplasmic reticulum redox protein folding and cell-surface thiol-redox control of thrombosis and vascular remodeling. The family prototype PDIA1 regulates NADPH oxidase signaling and cytoskeleton organization, however the related underlying mechanisms are unclear. Here we show that genes encoding human PDIA1 and its two paralogs PDIA8 and PDIA2 are each flanked by genes encoding Rho guanine-dissociation inhibitors (GDI), known regulators of RhoGTPases/cytoskeleton. Evolutionary histories of these three microsyntenic regions reveal their emergence by two successive duplication events of a primordial gene pair in the last common vertebrate ancestor. The arrangement, however, is substantially older, detectable in echinoderms, nematodes, and cnidarians. Thus, PDI/RhoGDI pairing in the same transcription orientation emerged early in animal evolution and has been largely maintained. PDI/RhoGDI pairs are embedded into conserved genomic regions displaying common cis-regulatory elements. Analysis of gene expression datasets supports evidence for PDI/RhoGDI coexpression in developmental/inflammatory contexts. PDIA1/RhoGDIα were co-induced in endothelial cells upon CRISP-R-promoted transcription activation of each pair component, and also in mouse arterial intima during flow-induced remodeling. We provide evidence for physical interaction between both proteins. These data support strong functional links between PDI and RhoGDI families, which likely maintained PDI/RhoGDI microsynteny along > 800-million years of evolution.
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Affiliation(s)
- Ana I S Moretti
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Jessyca C Pavanelli
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Patrícia Nolasco
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | | | - Leonardo Y Tanaka
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Carolina G Fernandes
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - João Wosniak
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Daniela Kajihara
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Matheus H Dias
- Special Laboratory for Cell Cycle, Center of Toxins, Immune-Response and Cell Signaling - CeTICS-Cepid, Butantan Institute, São Paulo, Brazil
| | - Denise C Fernandes
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Hanjoong Jo
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, USA
| | - Ngoc-Vinh Tran
- Applied Bioinformatics Group, Institute of Cell Biology & Neuroscience, Goethe University, Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology & Neuroscience, Goethe University, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Center (BiK-F), Frankfurt, Germany
| | - Ralf P Brandes
- Institut für Kardiovaskuläre Physiologie, Goethe University, Frankfurt, Germany
| | - Diego Bonatto
- Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Francisco R M Laurindo
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil.
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Tsochatzidou M, Malliarou M, Papanikolaou N, Roca J, Nikolaou C. Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae. Nucleic Acids Res 2017; 45:5818-5828. [PMID: 28369650 PMCID: PMC5449599 DOI: 10.1093/nar/gkx198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/15/2017] [Indexed: 02/01/2023] Open
Abstract
The eukaryotic genome evolves under the dual constraint of maintaining coordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through the function of DNA topoisomerases, as has been shown in the concurrent transcriptional activation and suppression of genes upon transient deactivation of topoisomerase II (topoII). By analyzing a genome-wide transcription run-on experiment upon thermal inactivation of topoII in Saccharomyces cerevisiae we were able to define 116 gene clusters of consistent response (either positive or negative) to topological stress. A comprehensive analysis of these topologically co-regulated gene clusters reveals pronounced preferences regarding their functional, regulatory and structural attributes. Genes that negatively respond to topological stress, are positioned in gene-dense pericentromeric regions, are more conserved and associated to essential functions, while upregulated gene clusters are preferentially located in the gene-sparse nuclear periphery, associated with secondary functions and under complex regulatory control. We propose that genome architecture evolves with a core of essential genes occupying a compact genomic ‘old town’, whereas more recently acquired, condition-specific genes tend to be located in a more spacious ‘suburban’ genomic periphery.
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Affiliation(s)
- Maria Tsochatzidou
- Computational Genomics Group, Department of Biology, University of Crete, Herakleion 70013, Greece
| | - Maria Malliarou
- Computational Genomics Group, Department of Biology, University of Crete, Herakleion 70013, Greece
| | - Nikolas Papanikolaou
- Computational Genomics Group, Department of Biology, University of Crete, Herakleion 70013, Greece
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Christoforos Nikolaou
- Computational Genomics Group, Department of Biology, University of Crete, Herakleion 70013, Greece
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Kjer K, Borowiec ML, Frandsen PB, Ware J, Wiegmann BM. Advances using molecular data in insect systematics. CURRENT OPINION IN INSECT SCIENCE 2016; 18:40-47. [PMID: 27939709 DOI: 10.1016/j.cois.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
The size of molecular datasets has been growing exponentially since the mid 1980s, and new technologies have now dramatically increased the slope of this increase. New datasets include genomes, transcriptomes, and hybrid capture data, producing hundreds or thousands of loci. With these datasets, we are approaching a consensus on the higher level insect phylogeny. Huge datasets can produce new challenges in interpreting branch support, and new opportunities in developing better models and more sophisticated partitioning schemes. Dating analyses are improving as we recognize the importance of careful fossil calibration selection. With thousands of genes now available, coalescent methods have come of age. Barcode libraries continue to expand, and new methods are being developed for incorporating them into phylogenies with tens of thousands of individuals.
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Affiliation(s)
- Karl Kjer
- Rutgers University, Department of Biological Sciences, 415 Boyden Hall, Newark, NJ 07012, USA
| | - Marek L Borowiec
- University of Rochester, 226 Hutchison Hall, Rochester, NY 14627, USA
| | - Paul B Frandsen
- Smithsonian Institution, Office of Research Information Services, Office of the Chief Information Officer, Washington, D.C. 20024, USA
| | - Jessica Ware
- Rutgers University, Department of Biological Sciences, 415 Boyden Hall, Newark, NJ 07012, USA
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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