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Huttener R, Thorrez L, Veld TI, Potter B, Baele G, Granvik M, Van Lommel L, Schuit F. Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes. BMC Ecol Evol 2021; 21:153. [PMID: 34348656 PMCID: PMC8336415 DOI: 10.1186/s12862-021-01882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/22/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. RESULTS We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. CONCLUSIONS A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.
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Affiliation(s)
- Raf Huttener
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Lieven Thorrez
- Tissue Engineering Laboratory, Department of Development and Regeneration, KU Leuven, Kortrijk, Belgium
| | - Thomas In't Veld
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Barney Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mikaela Granvik
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Leentje Van Lommel
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Frans Schuit
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium.
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HoxA Genes and the Fin-to-Limb Transition in Vertebrates. J Dev Biol 2016; 4:jdb4010010. [PMID: 29615578 PMCID: PMC5831813 DOI: 10.3390/jdb4010010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/27/2016] [Accepted: 02/04/2016] [Indexed: 12/12/2022] Open
Abstract
HoxA genes encode for important DNA-binding transcription factors that act during limb development, regulating primarily gene expression and, consequently, morphogenesis and skeletal differentiation. Within these genes, HoxA11 and HoxA13 were proposed to have played an essential role in the enigmatic evolutionary transition from fish fins to tetrapod limbs. Indeed, comparative gene expression analyses led to the suggestion that changes in their regulation might have been essential for the diversification of vertebrates' appendages. In this review, we highlight three potential modifications in the regulation and function of these genes that may have boosted appendage evolution: (1) the expansion of polyalanine repeats in the HoxA11 and HoxA13 proteins; (2) the origin of +a novel long-non-coding RNA with a possible inhibitory function on HoxA11; and (3) the acquisition of cis-regulatory elements modulating 5' HoxA transcription. We discuss the relevance of these mechanisms for appendage diversification reviewing the current state of the art and performing additional comparative analyses to characterize, in a phylogenetic framework, HoxA11 and HoxA13 expression, alanine composition within the encoded proteins, long-non-coding RNAs and cis-regulatory elements.
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Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system. Cell Tissue Res 2015; 363:267-278. [DOI: 10.1007/s00441-015-2257-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/05/2015] [Indexed: 12/30/2022]
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Owens KM, Quinonez SC, Thomas PE, Keegan CE, Lefebvre N, Roulston D, Larsen CA, Stadler HS, Innis JW. Analysis of De NovoHOXA13Polyalanine Expansions Supports Replication Slippage Without Repair in Their Generation. Am J Med Genet A 2013; 161A:1019-27. [DOI: 10.1002/ajmg.a.35843] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/12/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Kailey M. Owens
- Department of Pediatrics and Communicable Diseases; University of Michigan; Ann Arbor, Michigan
| | - Shane C. Quinonez
- Department of Pediatrics and Communicable Diseases; University of Michigan; Ann Arbor, Michigan
| | | | | | - Nanci Lefebvre
- Department of Pathology; Cytogenetics Laboratory, University of Michigan; Ann Arbor; Michigan
| | - Diane Roulston
- Department of Pathology; Cytogenetics Laboratory, University of Michigan; Ann Arbor; Michigan
| | - Christine A. Larsen
- Department of Molecular and Medical Genetics; Oregon Health Sciences University and Shriners Hospital for Children; Portland, Oregon
| | - H. Scott Stadler
- Department of Molecular and Medical Genetics; Oregon Health Sciences University and Shriners Hospital for Children; Portland, Oregon
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