Cis-regulatory landscapes in development and evolution

Maeso, Ignacio; Acemel, Rafael D.; Gómez-Skármeta, José Luis

doi:10.1016/j.gde.2016.10.004

Cited by 15 publications

(9 citation statements)

References 49 publications

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“…The association between TAD co-localisation and both distance to TSS and conservation depth cannot be explained by chance alone (Supplementary Figure 7). In line with previous observations 42 , our results therefore support the existence of a link 170 between the control of gene expression and 3D chromatin organisation. …”

Section: Cc-by-nc-nd 40 International License Not Peer-reviewed) Is supporting

confidence: 92%

Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation

Clément

Torbey

Gilardi-Hebenstreit

et al. 2018

Preprint

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Gene regulation by enhancer sequences controls the spatiotemporal expression of target genes, often over long genomic distances. Current methods used to identify these interactions in the human genome require complex experimental setups and are restricted to specific cell types. Here we use PEGASUS, an approach that captures evolutionary signals 5 of synteny conservation to predict such interaction potentially in any biological context. We apply it to the human and zebrafish genomes and exploit the 1.3 million human and 55,000 zebrafish enhancers that we predicted to uncover fundamental principles of gene enhancer function in vertebrates. We show that the number of enhancers linked to a gene positively correlates with expression breadth in space and time and that the enhancer-target distance 10 is evolutionarily neutral. We uncover almost 2000 regulatory interactions ancestral to vertebrates, which are strongly enriched in core developmental processes. Using PEGASUS and its evolutionary view of enhancer-gene interactions, we provide a highly complementary resource to functional assays which uncovers key principles of enhancer biology.

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Section: Cc-by-nc-nd 40 International License Not Peer-reviewed) Is supporting

confidence: 92%

Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation

Clément

Torbey

Gilardi-Hebenstreit

et al. 2018

Preprint

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“…SVs have immense potential to alter regulatory elements and their interactions with target genes. For example, inserting or deleting topologically associating domain (TAD) boundaries, which are often conserved across cell types and species [ 84 ], can associate regulatory elements with new genes (termed ‘enhancer hijacking’) or insulate them from their ancestral gene targets [ 85 , 86 ]. It will be exciting to explore the evolution of human gene expression in terms of 3D genome organization and its effects on regulatory interactions.…”

Section: Thinking Again: What Are We Missing In the Study Of Genetic mentioning

confidence: 99%

Human evolution: the non-coding revolution

Franchini

Pollard

2017

BMC Biol

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What made us human? Gene expression changes clearly played a significant part in human evolution, but pinpointing the causal regulatory mutations is hard. Comparative genomics enabled the identification of human accelerated regions (HARs) and other human-specific genome sequences. The major challenge in the past decade has been to link diverged sequences to uniquely human biology. This review discusses approaches to this problem, progress made at the molecular level, and prospects for moving towards genetic causes for uniquely human biology.

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“…For example, the exaptation or overprinting of ancestral enhancer regions is a common phenomenon in the evolution of cis- regulatory novelties [8–13]. Numerous variations to this pattern exist in nature however, indicating that precise modes of cis- regulatory evolution are more complex than is currently understood [14, 15]. Pathway-specific investigations of selection at CREs founded in the evolution of distinctive and derived traits, particularly in non-model systems, can provide valuable insight into the diversity of evolutionary mechanisms acting on gene regulatory networks in nature [16, 17].…”

Section: Introductionmentioning

confidence: 99%

Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

Bogan

Place

2019

BMC Evol Biol

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BackgroundAntarctic fishes of the Notothenioidei suborder constitutively upregulate multiple inducible chaperones, a highly derived adaptation that preserves proteostasis in extreme cold, and represent a system for studying the evolution of gene frontloading. We screened for Hsf1-binding sites, as Hsf1 is a master transcription factor of the heat shock response, and highly-conserved non-coding elements within proximal promoters of chaperone genes across 10 Antarctic notothens, 2 subpolar notothens, and 17 perciform fishes. We employed phylogenetic models of molecular evolution to determine whether (i) changes in motifs associated with Hsf1-binding and/or (ii) relaxed purifying selection or exaptation at ancestral cis-regulatory elements coincided with the evolution of chaperone frontloading in Antarctic notothens.ResultsAntarctic notothens exhibited significantly fewer Hsf1-binding sites per bp at chaperone promoters than subpolar notothens and Serranoidei, the most closely-related suborder to Notothenioidei included in this study. 90% of chaperone promoters exhibited accelerated substitution rates among Antarctic notothens relative to other perciformes. The proportion of bases undergoing accelerated evolution (i) was significantly greater in Antarctic notothens than in subpolar notothens and Perciformes in 70% of chaperone genes and (ii) increased among bases that were more conserved among perciformes. Lastly, we detected evidence of relaxed purifying selection and exaptation acting on ancestrally conserved cis-regulatory elements in the Antarctic notothen lineage and its major branches.ConclusionA large degree of turnover has occurred in Notothenioidei at chaperone promoter regions that are conserved among perciform fishes following adaptation to the cooling of the Southern Ocean. Additionally, derived reductions in Hsf1-binding site frequency suggest cis-regulatory modifications to the classical heat shock response. Of note, turnover events within chaperone promoters were less frequent in the ancestral node of Antarctic notothens relative to younger Antarctic lineages. This suggests that cis-regulatory divergence at chaperone promoters may be greater between Antarctic notothen lineages than between subpolar and Antarctic clades. These findings demonstrate that strong selective forces have acted upon cis-regulatory elements of chaperone genes among Antarctic notothens.

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Cis-regulatory landscapes in development and evolution

Cited by 15 publications

References 49 publications

Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation

Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation

Human evolution: the non-coding revolution

Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

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