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Rogers TF, Simakov O. Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. Brief Funct Genomics 2023; 22:533-542. [PMID: 37815133 PMCID: PMC10658181 DOI: 10.1093/bfgp/elad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/17/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Information on how 3D genome topology emerged in animal evolution, how stable it is during development, its role in the evolution of phenotypic novelties and how exactly it affects gene expression is highly debated. So far, data to address these questions are lacking with the exception of a few key model species. Several gene regulatory mechanisms have been proposed, including scenarios where genome topology has little to no impact on gene expression, and vice versa. The ancient and diverse clade of spiralians may provide a crucial testing ground for such mechanisms. Sprialians have followed distinct evolutionary trajectories, with some clades experiencing genome expansions and/or large-scale genome rearrangements, and others undergoing genome contraction, substantially impacting their size and organisation. These changes have been associated with many phenotypic innovations in this clade. In this review, we describe how emerging genome topology data, along with functional tools, allow for testing these scenarios and discuss their predicted outcomes.
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Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
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Hehmeyer J, Spitz F, Marlow H. Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies. Curr Opin Genet Dev 2023; 81:102064. [PMID: 37390583 PMCID: PMC10547022 DOI: 10.1016/j.gde.2023.102064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 07/02/2023]
Abstract
3D genome folding enables the physical storage of chromosomes into the compact volume of a cell's nucleus, allows for the accurate segregation of chromatin to daughter cells, and has been shown to be tightly coupled to the way in which genetic information is converted into transcriptional programs [1-3]. Importantly, this link between chromatin architecture and gene regulation is a selectable feature in which modifications to chromatin organization accompany, or perhaps even drive the establishment of new regulatory strategies with enduring impacts on animal body plan complexity. Here, we discuss the nature of different 3D genome folding systems found across the tree of life, with particular emphasis on metazoans, and the relative influence of these systems on gene regulation. We suggest how the properties of these folding systems have influenced regulatory strategies employed by different lineages and may have catalyzed the partitioning and specialization of genetic programs that enabled multicellularity and organ-grade body plan complexity.
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Affiliation(s)
- Jenks Hehmeyer
- Department of Organismal Biology and Anatomy, The University of Chicago, USA
| | - François Spitz
- Department of Human Genetics, The University of Chicago, USA
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, USA.
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Rouressol L, Briseno J, Vijayan N, Chen GY, Ritschard EA, Sanchez G, Nyholm SV, McFall-Ngai MJ, Simakov O. Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid. iScience 2023; 26:107091. [PMID: 37426346 PMCID: PMC10329180 DOI: 10.1016/j.isci.2023.107091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Light organs (LO) with symbiotic bioluminescent bacteria are hallmarks of many bobtail squid species. These organs possess structural and functional features to modulate light, analogous to those found in coleoid eyes. Previous studies identified four transcription factors and modulators (SIX, EYA, PAX6, DAC) associated with both eyes and light organ development, suggesting co-option of a highly conserved gene regulatory network. Using available topological, open chromatin, and transcriptomic data, we explore the regulatory landscape around the four transcription factors as well as genes associated with LO and shared LO/eye expression. This analysis revealed several closely associated and putatively co-regulated genes. Comparative genomic analyses identified distinct evolutionary origins of these putative regulatory associations, with the DAC locus showing a unique topological and evolutionarily recent organization. We discuss different scenarios of modifications to genome topology and how these changes may have contributed to the evolutionary emergence of the light organ.
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Affiliation(s)
- Lisa Rouressol
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - John Briseno
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Grischa Y. Chen
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - Elena A. Ritschard
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, NA, Italy
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Margaret J. McFall-Ngai
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Pasadena, CA 91125, USA
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna 1030, Austria
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Robert NSM, Sarigol F, Zieger E, Simakov O. SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes. Bioinformatics 2022; 38:5434-5436. [PMID: 36269177 PMCID: PMC9750109 DOI: 10.1093/bioinformatics/btac695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/24/2022] [Accepted: 10/19/2022] [Indexed: 12/25/2022] Open
Abstract
SUMMARY Current approaches detect conserved genomic order either at chromosomal (macrosynteny) or at subchromosomal scales (microsynteny). The latter generally requires collinearity and hard thresholds on syntenic region size, thus excluding a major proportion of syntenies with recent expansions or minor rearrangements. 'SYNPHONI' bridges the gap between micro- and macrosynteny detection, providing detailed information on both synteny conservation and transformation throughout the evolutionary history of animal genomes. AVAILABILITY AND IMPLEMENTATION Source code is freely available at https://github.com/nsmro/SYNPHONI, implemented in Python 3.9. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Fatih Sarigol
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna A-1030, Austria
| | - Elisabeth Zieger
- Department of Evolutionary Biology, University of Vienna, Vienna A-1030, Austria
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