Rapid divergence of histones in Hydrozoa (Cnidaria) and evolution of a novel histone involved in DNA damage response in hydra.
TL;DR: In this paper, the complete repertoire of histone-coding genes in the Hydra magnipapillata genome was identified based on their copy numbers, gene structure and other characteristic features.
About: This article is published in Zoology.The article was published on 2017-08-01. It has received 16 citations till now. The article focuses on the topics: Histone-modifying enzymes & Histone code.
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TL;DR: This comprehensive review of marine environmental epigenetics guides the recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, and the evolutionary implications of the interaction of genetic and epigenetic features.
Abstract: Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.
145 citations
Cites background from "Rapid divergence of histones in Hyd..."
...X is another variant intensively studied due to its involvement in the maintenance of genome integrity, as shown by its study in molluscs (González-Romero et al. 2017) and cnidarians (Reddy et al. 2017)....
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TL;DR: Monitoring two types of epigenetic mechanisms, namely histone modifications and DNA methylation, during a 7‐week‐long experiment in which staghorn coral fragments were exposed to nutrient stress (nitrogen, nitrogen + phosphorus) in the presence of thermal stress provides new insights into the role of epigenetics during coral responses to global change.
Abstract: Nutrient pollution and thermal stress constitute two of the main drivers of global change in the coastal oceans. While different studies have addressed the physiological effects and ecological consequences of these stressors in corals, the role of acquired modifications in the coral epigenome during acclimatory and adaptive responses remains unknown. The present work aims to address that gap by monitoring two types of epigenetic mechanisms, namely histone modifications and DNA methylation, during a 7-week-long experiment in which staghorn coral fragments (Acropora cervicornis) were exposed to nutrient stress (nitrogen, nitrogen + phosphorus) in the presence of thermal stress. The major conclusion of this experiment can be summarized by two main results: First, coral holobiont responses to the combined effects of nutrient enrichment and thermal stress involve the post-translational phosphorylation of the histone variant H2A.X (involved in responses to DNA damage), as well as nonsignificant modifications in DNA methylation trends. Second, the reduction in H2A.X phosphorylation (and the subsequent potential impairment of DNA repair mechanisms) observed after prolonged coral exposure to nitrogen enrichment and thermal stress is consistent with the symbiont-driven phosphorus limitation previously observed in corals subject to nitrogen enrichment. The alteration of this epigenetic mechanism could help to explain the synergistic effects of nutrient imbalance and thermal stress on coral fitness (i.e., increased bleaching and mortality) while supporting the positive effect of phosphorus addition to improving coral resilience to thermal stress. Overall, this work provides new insights into the role of epigenetic mechanisms during coral responses to global change, discussing future research directions and the potential benefits for improving restoration, management and conservation of coral reef ecosystems worldwide.
34 citations
Cites background from "Rapid divergence of histones in Hyd..."
...X.2 mRNA levels were found in Hydra exposed to the genotoxic agent bleomycin (Reddy et al., 2017)....
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...X levels upon expo‐ sure to environmental stress (Gonzalez‐Romero et al., 2017; Reddy et al., 2017), supporting that the main functional role of this variant during DNA repair is regulated at a post‐translational level....
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01 Jan 2018
TL;DR: The present contribution underscores the importance of environmental epigenetic studies in marine organisms to better understand how organisms respond to their surrounding environment, fostering the development of a new generation of biomarkers enhancing restoration, conservation, and management efforts.
Abstract: Although epigenetics is still a relatively new discipline, its development during the last 10 years has revolutionized the current understanding of genome structure and function. The present chapter provides an insight on the exciting field of environmental epigenetics (i.e., the cause-effect relationships between environmental signals and epigenetic modifications altering phenotypes) and its potential applications for different types of studies in the marine environment. In the first part of this chapter, this work focuses on defining epigenetics, the different mechanisms involved in the epigenetic regulation of gene expression, as well as their potential role during the evolution of life on Earth. In the second part, this chapter moves into the potential applications of epigenetics in marine organisms, using current research projects on model species ranging from marine invertebrates to large marine megafauna as references. Overall, the present contribution underscores the importance of environmental epigenetic studies in marine organisms to better understand how organisms respond to their surrounding environment, fostering the development of a new generation of biomarkers enhancing restoration, conservation, and management efforts.
20 citations
Cites background from "Rapid divergence of histones in Hyd..."
...This constitutes a research priority based on the very promising results obtained on related species and other marine invertebrates (Moran et al. 2014; Rivera-Casas et al. 2016a, b; Fraune et al. 2016; Reddy et al. 2017) and the implication these mechanisms can have on “preconditioning” of corals....
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...ising results obtained on related species and other marine invertebrates (Moran et al. 2014; Rivera-Casas et al. 2016a, b; Fraune et al. 2016; Reddy et al. 2017) and the implication these mechanisms can have on “preconditioning” of corals....
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TL;DR: A review of the existing literature on Hydra regeneration biology and the future perspectives is presented and further research on cross communication among extracellular, cellular, and molecular signalling in Hydra will advance the field of regeneration biology.
Abstract: Regeneration of lost body parts is essential to regain the fitness of the organism for successful living. In the animal kingdom, organisms from different clades exhibit varied regeneration abilities. Hydra is one of the few organisms that possess tremendous regeneration potential, capable of regenerating complete organism from small tissue fragments or even from dissociated cells. This peculiar property has made this genus one of the most invaluable model organisms for understanding the process of regeneration. Multiple studies in Hydra led to the current understanding of gross morphological changes, basic cellular dynamics, and the role of molecular signalling such as the Wnt signalling pathway. However, cell-to-cell communication by cell adhesion, role of extracellular components such as extracellular matrix (ECM), and nature of cell types that contribute to the regeneration process need to be explored in depth. Additionally, roles of developmental signalling pathways need to be elucidated to enable more comprehensive understanding of regeneration in Hydra. Further research on cross communication among extracellular, cellular, and molecular signalling in Hydra will advance the field of regeneration biology. Here, we present a review of the existing literature on Hydra regeneration biology and outline the future perspectives.
19 citations
TL;DR: The ability to differentially modify the H3K27 residue is critical for the patterning of Hydra axis revealing a dynamic acetylation/methylation switch to regulate gene expression and chromatin architecture.
Abstract: Axis patterning during development is accompanied by large-scale gene expression changes. These are brought about by changes in the histone modifications leading to dynamic alterations in chromatin architecture. The cis regulatory DNA elements also play an important role towards modulating gene expression in a context-dependent manner. Hydra belongs to the phylum Cnidaria where the first asymmetry in the body plan was observed and the oral-aboral axis originated. Wnt signaling has been shown to determine the head organizer function in the basal metazoan Hydra. To gain insights into the evolution of cis regulatory elements and associated chromatin signatures, we ectopically activated the Wnt signaling pathway in Hydra and monitored the genome-wide alterations in key histone modifications. Motif analysis of putative intergenic enhancer elements from Hydra revealed the conservation of bilaterian cis regulatory elements that play critical roles in development. Differentially regulated enhancer elements were identified upon ectopic activation of Wnt signaling and found to regulate many head organizer specific genes. Enhancer activity of many of the identified cis regulatory elements was confirmed by luciferase reporter assay. Quantitative chromatin immunoprecipitation analysis upon activation of Wnt signaling further confirmed the enrichment of H3K27ac on the enhancer elements of Hv_Wnt5a, Hv_Wnt11 and head organizer genes Hv_Bra1, CnGsc and Hv_Pitx1. Additionally, perturbation of the putative H3K27me3 eraser activity using a specific inhibitor affected the ectopic activation of Wnt signaling indicating the importance of the dynamic changes in the H3K27 modifications towards regulation of the genes involved in the head organizer activity. The activation-associated histone marks H3K4me3, H3K27ac and H3K9ac mark chromatin in a similar manner as seen in bilaterians. We identified intergenic cis regulatory elements which harbor sites for key transcription factors involved in developmental processes. Differentially regulated enhancers exhibited motifs for many zinc-finger, T-box and ETS related TFs whose homologs have a head specific expression in Hydra and could be a part of the pioneer TF network in the patterning of the head. The ability to differentially modify the H3K27 residue is critical for the patterning of Hydra axis revealing a dynamic acetylation/methylation switch to regulate gene expression and chromatin architecture.
17 citations
References
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TL;DR: The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.
Abstract: For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
44,587 citations
"Rapid divergence of histones in Hyd..." refers methods in this paper
...Images were processed using the ImageJ software (Schneider et al., 2012)....
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TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
Abstract: Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein— and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
25,931 citations
"Rapid divergence of histones in Hyd..." refers methods in this paper
...Bayesian analysis was carried out by MrBayes version 3.2.2 program (Ronquist and Huelsenbeck, 2003) by running 1x105 generations of searches with four chains using the Dayhoff substitution matrix, 25% burn-in....
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...2 program (Ronquist and Huelsenbeck, 2003) by running 1x10(5) generations of searches with four chains using the Dayhoff substitution matrix, 25% burn-in....
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TL;DR: This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
Abstract: Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting postanalyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU
23,838 citations
"Rapid divergence of histones in Hyd..." refers methods in this paper
...Phylogenetic trees were computed using version 8 of the randomized accelerated maximum likelihood (RAxML) method (Stamatakis, 2014) using the CIPRES Science Gateway (Miller et al., 2010)....
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...Phylogenetic trees were computed using version 8 of the randomized accelerated maximum likelihood (RAxML) method (Stamatakis, 2014) using the CIPRES Science Gateway (Miller et al....
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23 Dec 2010
TL;DR: Development of the CIPRES Science Gateway is described, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources.
Abstract: Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
9,117 citations
TL;DR: Jalview 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.
Abstract: Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.
Availability: The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org
Contact: g.j.barton@dundee.ac.uk
7,926 citations
"Rapid divergence of histones in Hyd..." refers methods in this paper
...Alignments were manually curated in Jalview version 2 and used for phylogenetic analysis (Waterhouse et al., 2009)....
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