The evolution of cell types in animals: emerging principles from molecular studies

Arendt, Detlev

doi:10.1038/nrg2416

Cited by 453 publications

(493 citation statements)

References 114 publications

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“…The exact fraction of tetrads with tree structure varies between data sets, most probably reflecting differences in celltype sampling. Overall, these results support the notion that the transcriptomes of normal human and mouse cells have substantial tree structure, consistent with the sister cell-type model 4 ( Supplementary Fig. 1a,b).…”

Section: Resultssupporting

confidence: 86%

“…For one, it supports the sister cell-type model of cell origination in evolution 4 , and the second is that the analysis of cell-type trees can yield mechanistic insights. Here we briefly discuss these two points in turn.…”

Section: Discussionmentioning

confidence: 54%

“…We also note that the sister cell-type model predicts that closely related cell types have similar gene expression patterns, because they share the developmental trajectory that they inherited from their ancestral cell type. Hence, the sister cell-type model also predicts a degree of congruence between the similarity of transcriptomes (interpreted here as a phylogenetic signal) and the ontogenetic cell lineage relationships 4 . In our analysis, this is reflected in the transcriptomic similarity between macrophages and dendritic cells, which are both derived from monocytes, as well as the separation between lymphoid and myeloid cells, which represent separate ontogenetic cell lineages ( Supplementary Fig.…”

Section: Discussionmentioning

confidence: 99%

“…The processes that create this diversity, however, are not well understood. The only published model for cell-type origination we are aware of is the so-called sister celltype model 4 . The model suggests that novel cell types arise through sub-specialization of an ancestral cell type.…”

mentioning

confidence: 99%

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The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Liang

Forrest²,

Wagner

2015

Nat Commun

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In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination.

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 54%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Liang

Forrest²,

Wagner

2015

Nat Commun

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“…According to Detlev Arendt (Arendt 2008), homology hypotheses are based on the comparison of genes, cytological features and ontological location in the body of the embryo. Functional experiments with genome editing in model organisms will add extremely important cues to this domain.…”

Section: A Short Natural History Of the Nervous System: Several Questmentioning

confidence: 99%

Aquatic Model Organisms in Neurosciences: The Genome-Editing Revolution

Joly¹

2017

Research and Perspectives in Neurosciences

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The use of aquatic model organisms has been greatly diversified in laboratories. Zebrafish is the most advanced aquatic species for the use of Crispr-Cas9 in laboratories. Because of the simplicity and broad applicability of this later system, knock-out is now efficiently performed at medium scale. Forward genetics in zebrafish can now be performed by CRISPR-based F0 screening using high speed and high content phenotyping for example by confocal imaging. As zebrafish, marine model organisms have the prominent advantage to be transparent, all the more at young stages (embryos and larvae) or when fixed samples are cleared by novel methods. The Cripsr-Cas9 system is routinely used in the ascidian Ciona intestinalis. It also starts to be used in many other marine models, such as the medusa Clythia hemispherica. We provide at the end of this review a list of aquatic model species and some examples of questions on the origin of our nervous system that can be coped with these models, where the possibility to perform genome editing would constitute a major advance.

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Phox2b expression in the taste centers of fish

Coppola

D’Autréaux

Nomaksteinsky

et al. 2012

J of Comparative Neurology

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The homeodomain transcription factor Phox2b controls the formation of the sensory-motor reflex circuits of the viscera in vertebrates. Among Phox2b-dependent structures characterized in rodents is the nucleus of the solitary tract, the first relay for visceral sensory input, including taste. Here we show that Phox2b is expressed throughout the primary taste centers of two cyprinid fish, Danio rerio and Carassius auratus, i.e., in their vagal, glossopharyngeal, and facial lobes, providing the first molecular evidence for their homology with the nucleus of the solitary tract of mammals and suggesting that a single ancestral Phox2b-positive neuronal type evolved to give rise to both fish and mammalian structures. In zebrafish larvae, the distribution of Phox2b²⁺ neurons, combined with the expression pattern of Olig4 (a homologue of Olig3, determinant of the nucleus of the solitary tract in mice), reveals that the superficial position and sheet-like architecture of the viscerosensory column in cyprinid fish, ideally suited for the somatotopic representation of oropharyngeal and bodily surfaces, arise by radial migration from a dorsal progenitor domain, in contrast to the tangential migration observed in amniotes.

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The evolution of cell types in animals: emerging principles from molecular studies

Cited by 453 publications

References 114 publications

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Aquatic Model Organisms in Neurosciences: The Genome-Editing Revolution

Phox2b expression in the taste centers of fish

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