A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

Acemel, Rafael D.; Tena, Juan J.; Irastorza-Azcárate, Ibai; Marlétaz, Ferdinand; Gómez-Marín, Carlos; Calle‐Mustienes, Elisa de la; Bertrand, Stéphanie; Díaz, Sergio González; Aldea, Daniel; Aury, Jean‐Marc; Mangenot, Sophie; Holland, Peter W.H.; Devos, Damien P.; Maeso, Ignacio; Escrivà, Héctor; Gómez-Skármeta, José Luis

doi:10.1038/ng.3497

Cited by 120 publications

(123 citation statements)

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“…The physiology and phototransduction cascade in isolated DO and JCs has been investigated in several studies (Acemel et al, 2016;Angueyra et al, 2012;Ferrer et al, 2012;Gomez Mdel et al, 2009;Nasi and del Pilar Gomez, 2009;Peinado et al, 2015;Pulido et al, 2012). These seminal studies not only confirmed that JCs and DO indeed function as photoreceptors, but also provided comparative data with respect to invertebrate rhabdomeric photoreceptors and ipRGCs.…”

Section: Rhabdomeric Photoreceptorsmentioning

confidence: 58%

Amphioxus photoreceptors - insights into the evolution of vertebrate opsins, vision and circadian rhythmicity

Pergner

Kozmík²

2017

Int. J. Dev. Biol.

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Studies on amphioxus, representing the most basal group of chordates, can give insights into the evolution of vertebrate traits. The present review of amphioxus research is focused on the physiology of light-guided behavior as well as on the fine structure, molecular biology, and electrophysiology of the nervous system, with special attention being given to the photoreceptive organs. The amphioxus visual system is especially interesting because four types of receptors are involved in light detection -dorsal ocelli and Joseph cells (both rhabdomeric photoreceptors) and the frontal eye and lamellar body (both ciliary photoreceptors). Here, we consider how the available information on photoreceptive organs and light-guided behavior in amphioxus helps generate hypotheses about the history of these features during chordate and subsequently vertebrate evolution.

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Section: Rhabdomeric Photoreceptorsmentioning

confidence: 58%

Amphioxus photoreceptors - insights into the evolution of vertebrate opsins, vision and circadian rhythmicity

Pergner

Kozmík²

2017

Int. J. Dev. Biol.

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“…However, regulatory interactions across TAD boundaries seem inhibited, underlining their importance in maintaining proper genome organization and gene regulation [79,80]. Cross-species comparisons of TADs have revealed both deeply conserved, as well as step-wise evolutionary dynamic assembly of such regulatory domains [81,82]. TAD conservation could thus reveal deep homology of entire regulatory landscapes, just as deep conservation of enhancer activities might inform us about evolutionary relationships of different morphological structures that they help to pattern [76].…”

Section: Homology Assessment: Gene Expression and Regulatory Strategiesmentioning

confidence: 99%

Deep homology in the age of next-generation sequencing

Tschopp

Tabin

2017

Phil. Trans. R. Soc. B

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One contribution of 17 to a theme issue 'Evodevo in the genomics era, and the origins of morphological diversity'. The principle of homology is central to conceptualizing the comparative aspects of morphological evolution. The distinctions between homologous or non-homologous structures have become blurred, however, as modern evolutionary developmental biology (evo-devo) has shown that novel features often result from modification of pre-existing developmental modules, rather than arising completely de novo. With this realization in mind, the term 'deep homology' was coined, in recognition of the remarkably conserved gene expression during the development of certain animal structures that would not be considered homologous by previous strict definitions. At its core, it can help to formulate an understanding of deeper layers of ontogenetic conservation for anatomical features that lack any clear phylogenetic continuity. Here, we review deep homology and related concepts in the context of a gene expression-based homology discussion. We then focus on how these conceptual frameworks have profited from the recent rise of high-throughput nextgeneration sequencing. These techniques have greatly expanded the range of organisms amenable to such studies. Moreover, they helped to elevate the traditional gene-by-gene comparison to a transcriptome-wide level. We will end with an outlook on the next challenges in the field and how technological advances might provide exciting new strategies to tackle these questions.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

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“…This position has recently been affirmed especially thanks to the access to genome sequence data (Holland et al, 2008;Huang et al, 2014;Putnam et al, 2008), introduction of novel techniques (Acemel et al, 2016;Kozmikova and Kozmik, 2015;Li et al, 2017;Yue et al, 2016), and establishment of amphioxus as a model species for evolutionary developmental studies (for review see Bertrand and Escriva (2011)). Cephalochordates include three genera, namely Branchiostoma, Asymmetron and Epigonychtys.…”

Section: Abstract: Branchiostoma Amphioxus Antibody Expression Pamentioning

confidence: 99%

Novel polyclonal antibodies as a useful tool for expression studies in amphioxus embryos

Bozzo¹,

Pergner²,

Kozmík³

et al. 2017

Int. J. Dev. Biol.

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Cephalochordates, commonly called amphioxus or lancelets, are widely regarded as a useful proxy for the chordate ancestor. In recent decades, expression patterns of important developmental genes have been used extensively to infer homologies between cephalochordate and vertebrate embryos. Such comparisons provided important insight into cephalochordate biology and the origin of vertebrate traits. Most of the developmental expression data are collected using whole-mount in situ hybridization that allows the distributions of specific transcripts to be detected in fixed embryos. Here, we describe an experimental pipeline for production of small amounts of functional antibodies directed against amphioxus antigens for use in immunohistochemical labelling. In this pilot study, we generated antibodies against b-catenin and the transcription factors FoxA, Lhx1, Lhx3 and Pax6. We demonstrate the usefulness of antibodies by performing immunostainings on fixed specimens of B. lanceolatum and B. floridae. We anticipate that amphioxus-specific antibodies will provide a useful tool for high-resolution labelling of individual cells within the embryo and for determining the subcellular localization of the corresponding proteins. KEY WORDS: Branchiostoma, amphioxus, antibody, expression patternCephalochordates, commonly called amphioxus or lancelets, are regarded as a key animal group for understanding the origin of vertebrates, and a useful proxy to the ancestral chordate condition. This position has recently been affirmed especially thanks to the access to genome sequence data (Holland et al., 2008;Huang et al., 2014;Putnam et al., 2008), introduction of novel techniques (Acemel et al., 2016;Kozmikova and Kozmik, 2015;Li et al., 2017;Yue et al., 2016), and establishment of amphioxus as a model species for evolutionary developmental studies (for review see Bertrand and Escriva (2011)). Cephalochordates include three genera, namely Branchiostoma, Asymmetron and Epigonychtys. The phylogenetic relationships within the extant amphioxus lineage were recently investigated providing divergence time estimates and suggesting a rather recent diversification (Igawa et al., 2017). For example, the estimated divergence times among species within the Branchiostoma genus (22.6 +/-2.3 Mya for B.lanceolatum -B. floridae split) are comparable to those among rodents belonging to Muridae family (such as mouse and rat). Close phylogenetic relationship is mirrored by a high degree of coding sequence , which permits you to Share (copy and redistribute the material in any medium or format) and Adapt (remix, transform, and build upon the material for any purpose, even commercially), providing you give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. Printed in Spain Abbreviations used in this paper: TH, tyrosine hydroxylase; WMISH, whole mount in situ hybridization.identity (Holland et al., 2008;H...

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A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

Cited by 120 publications

References 53 publications

Amphioxus photoreceptors - insights into the evolution of vertebrate opsins, vision and circadian rhythmicity

Amphioxus photoreceptors - insights into the evolution of vertebrate opsins, vision and circadian rhythmicity

Deep homology in the age of next-generation sequencing

Novel polyclonal antibodies as a useful tool for expression studies in amphioxus embryos

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