Functional conserved non-coding elements among tunicates and chordates

Ambrosino, Luca; Vassalli, Quirino Attilio; D’Agostino, Ylenia; Esposito, Riccardo; Cetrangolo, Viviana; Caputi, Luigi; Amoroso, Alessandro; Aniello, Francesco; D’Aniello, Salvatore; Chatzigeorgiou, Marios; Chiusano, Maria Luisa; Locascio, Annamaria

doi:10.1016/j.ydbio.2018.12.012

Cited by 7 publications

(6 citation statements)

References 65 publications

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“…InterProScan analysis predicted domains within the salp lipase (Lu et al 2020) based on conserved molecular functions (Figure 2). They included the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) and LH2 (Lipoxygenase homology) domains that are found within membrane or lipid associated proteins (Bateman and Sandford 1999).…”

Section: Resultsmentioning

confidence: 99%

“…These domains were identified from Superfamily (Gough et al 2001; Wilson et al 2009) and Pfam (Mistry et al 2021) databases. Lipase domains were also identified through PRINTS (Attwood et al 2003), Pfam (Mistry et al 2021) and CDD (Lu et al 2020) protein prediction software databases.…”

Section: Resultsmentioning

confidence: 99%

“…Salpa thompsoni is a marine animal found in the Southern Ocean surrounding Antarctica (Figure 1). Commonly referred to as a salp, it is a zooplankton from the tunicate group, which is an early diverging lineage of chordates (Ambrosino et al 2019). In contrast to the vast majority of salp species that occur in tropical to temperate waters, S. thompsoni appears to have evolved as a low temperature adapted species (Goodall-Copestake 2018).…”

Section: Introductionmentioning

confidence: 99%

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Recombinant expression and characterisation of a lipase from the Antarctic zooplanktonSalpa thompsoni

Rayani

Cotton

Roberts

et al. 2022

Preprint

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Cold marine environments are abundant on earth and represent a rich resource for low-temperature enzymes. Here we apply in silico bioprospecting methods followed by in vitro expression and biochemical analyses to characterise a novel low-temperature lipase from the Antarctic tunicate Salpa thompsoni. A 586 amino acid pancreatic lipase-like gene was identified from S. thompsoni transcriptomic data, expressed as a hexahistidine fusion protein in Escherichia coli at 10 °C and purified by affinity chromatography. Hydrolysis of the synthetic substrate p-nitrophenyl butyrate (PNPB) showed that this recombinant protein has optimal activity at 20 °C and pH 7, and specific activity of 3.16 U/mg under this condition. Over 60% of enzyme activity was maintained between 15 to 25 °C, with a sharp decrease outside this range. These results are indicative of cold-active psychrophilic enzyme activity. A meta-analysis of lipase activities towards PNPB showed that the novel S. thompsoni lipase displays a higher activity at lower temperatures relative to previously characterised enzymes. The work demonstrates a methodology for the conversion of transcriptomic to in vitro expression data for the discovery of new cold-active biocatalysts from marine organisms.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Recombinant expression and characterisation of a lipase from the Antarctic zooplanktonSalpa thompsoni

Rayani

Cotton

Roberts

et al. 2022

Preprint

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“…Owing to their functional relevance in the regulation of gene expression, CREs tend to be evolutionarily conserved across species ( Sandelin et al, 2004 ; Sanges et al, 2013 ; 2006 ). However, several studies have shown that enhancers controlling developmental gene expression can be functionally conserved even across distant phylogenetic lineages, despite a strong divergence in their DNA sequences ( Ambrosino et al, 2019 ; Berthelot et al, 2018 ; Wong et al, 2020 ; Eichenlaub and Ettwiller, 2011 ; Schmidt et al, 2010 ; Villar et al, 2015 ). Our inter-species comparison of CNEs enriched in H3K27ac across different embryonic structures revealed that a considerable portion of evolutionarily conserved CREs diverged in their patterns of activity between the two species analysed, in agreement with previous observations ( Dermitzakis and Clark, 2002 ; Schmidt et al, 2010 ; Vierstra et al, 2014 ; Villar et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken

et al. 2022

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Modifications in gene regulation are driving forces in the evolution of organisms. Part of these changes involve cis-regulatory elements (CREs), which contact their target genes through higher-order chromatin structures. However, how such architectures and variations in CREs contribute to transcriptional evolvability remains elusive. We use Hoxd genes as a paradigm for the emergence of regulatory innovations, as many relevant enhancers are located in a regulatory landscape highly conserved in amniotes. Here, we analysed their regulation in murine vibrissae and chicken feather primordia, two skin appendages expressing different Hoxd gene subsets, and compared the regulation of these genes in these appendages with that in the elongation of the posterior trunk. In the two former structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, probably as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the gene regulation that occurs in the mouse and chicken embryonic trunk partially relies on conserved CREs. A high proportion of these non-coding sequences active in the trunk have functionally diverged between species, suggesting that transcriptional robustness is maintained, despite considerable divergence in enhancer sequences.

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“…Due to their functional relevance in the regulation of gene expression, CREs tend to be evolutionarily conserved across species (Sandelin et al, 2004;Sanges et al, 2013Sanges et al, , 2006. However, several studies have shown that enhancers controlling developmental gene expression can be functionally conserved even across distant phylogenetic lineages despite a strong divergence in their DNA sequences (Ambrosino et al, 2019;Berthelot et al, 2018;Wong et al, 2020) (Eichenlaub and Ettwiller, 2011;Schmidt et al, 2010;Villar et al, 2015). Our inter-species comparison of CNEs enriched in H3K27ac across different embryonic structures revealed that a considerable portion of evolutionary conserved CREs diverged in their patterns of activity between the two species analyzed, in agreement with previous observations (Dermitzakis and Clark, 2002;Schmidt et al, 2010;Vierstra et al, 2014;Villar et al, 2015).…”

Section: Plasticity Of the Cis-regulatory Code Versus Conservation In Tad Organizationmentioning

confidence: 99%

Developmental and Evolutionary Comparative Analysis of a Regulatory Landscape in Mammals and Birds

Hintermann

Guerreiro

Bolt

et al. 2021

Preprint

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Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. During vertebrate evolution, Hox genes were redeployed in different organs in a class-specific manner, while maintaining the same basic function in organizing the primary body axis. Since a large part of the relevant enhancers are located in a conserved regulatory landscape, this gene cluster represents an interesting paradigm to study the emergence of regulatory innovations. In this work, we analyzed Hoxd gene regulation in both murine vibrissae and chicken feather primordia, two mammalian- and avian-specific skin appendages which express different subsets of Hoxd genes, and compared their regulatory modalities with the regulations at work during the elongation of the posterior trunk, a mechanism highly conserved in amniotes. We show that in the former two structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, likely as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the regulations implemented in the mouse and chicken embryonic trunk rely more on conserved CREs. Nevertheless, a high proportion of these non-coding sequences active in the trunk appear to have functionally diverged between the two species, suggesting that transcriptional robustness is maintained despite a considerable divergence in CRE sequences, an observation supported by a genome-wide comparative approach.

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Functional conserved non-coding elements among tunicates and chordates

Cited by 7 publications

References 65 publications

Recombinant expression and characterisation of a lipase from the Antarctic zooplanktonSalpa thompsoni

Recombinant expression and characterisation of a lipase from the Antarctic zooplanktonSalpa thompsoni

Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken

Developmental and Evolutionary Comparative Analysis of a Regulatory Landscape in Mammals and Birds

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