共查询到20条相似文献，搜索用时 15 毫秒
1.
2.
3.
4.
5.
Rocío Prez‐Portela Ana Riesgo Owen S. Wangensteen Cruz Palacín Xavier Turon 《Molecular ecology》2020,29(17):3299-3315
6.
Bernard Angers Maëva Perez Tatiana Menicucci Christelle Leung 《Evolutionary Applications》2020,13(6):1262-1278
Epigenetic processes manage gene expression and products in a real‐time manner, allowing a single genome to display different phenotypes. In this paper, we discussed the relevance of assessing the different sources of epigenetic variation in natural populations. For a given genotype, the epigenetic variation could be environmentally induced or occur randomly. Strategies developed by organisms to face environmental fluctuations such as phenotypic plasticity and diversified bet‐hedging rely, respectively, on these different sources. Random variation can also represent a proxy of developmental stability and can be used to assess how organisms deal with stressful environmental conditions. We then proposed the microbiome as an extension of the epigenotype of the host to assess the factors determining the establishment of the community of microorganisms. Finally, we discussed these perspectives in the applied context of conservation. 相似文献
7.
水域是地球环境的重要组成部分,也是最易受污染的生态系统之一。水生态系统中不同营养级别的水生生物可通过摄食、接触等多种途径摄入水体中的污染物。因此,监测水域污染物对水生生物和生态系统的影响,解析污染物对不同水生生物的毒性机制,筛选敏感、有效的生物标志物对生态毒理学研究和环境风险评价具有重要意义。RNA测序（RNA sequencing,RNA?seq）技术因所需样品量少,且不需参考序列,可在整体水平上鉴定基因差异表达,成为水生生物生态毒理学研究的最佳方法之一。基于此,介绍了RNA?seq技术的基本流程与数据分析过程,对该技术在不同生态位的水生生物（如鱼类、两栖类、贝类、甲壳类等）生态毒理学中的应用展开综述,并对RNA?seq技术面临的不足、挑战及发展趋势进行探讨,以期为该技术在水生生物生态毒理学研究中的应用,尤其是水生态环境中污染物胁迫水生生物机制的阐明及污染水域生态环境恢复提供参考。 相似文献
8.
9.
Daniel Hebenstreit Miaoqing Fang Muxin Gu Varodom Charoensawan Alexander van Oudenaarden Sarah A Teichmann 《Molecular systems biology》2011,7(1)
The expression level of a gene is often used as a proxy for determining whether the protein or RNA product is functional in a cell or tissue. Therefore, it is of fundamental importance to understand the global distribution of gene expression levels, and to be able to interpret it mechanistically and functionally. Here we use RNA sequencing (RNA‐seq) of mouse Th2 cells, coupled with a range of other techniques, to show that all genes can be separated, based on their expression abundance, into two distinct groups: one group comprised of lowly expressed and putatively non‐functional mRNAs, and the other of highly expressed mRNAs with active chromatin marks at their promoters. These observations are confirmed in many other microarray and RNA‐seq data sets of metazoan cell types. 相似文献
10.
Allison Bailey Pierre De Wit Peter Thor Howard I. Browman Reidun Bjelland Steven Shema David M. Fields Jeffrey A. Runge Cameron Thompson Haakon Hop 《Ecology and evolution》2017,7(18):7145-7160
Ocean acidification is the increase in seawater pCO2 due to the uptake of atmospheric anthropogenic CO2, with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in pCO2, and associated decrease in pH, represents a climate change‐related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal‐level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular‐level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild‐caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA‐seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms. 相似文献
11.
12.
Nicole R. Hales Drew R. Schield Audra L. Andrew Daren C. Card Matthew R. Walsh Todd A. Castoe 《Molecular ecology》2017,26(19):5003-5015
Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., “within‐generation phenotypic plasticity”) as well as induce heritable phenotypic responses that persist for multiple generations (i.e., “transgenerational plasticity”, TGP). It has long been assumed that shifts in gene expression are tightly linked to observed trait responses at the phenotypic level. Yet, the manner in which organisms couple within‐ and TGP at the molecular level is unclear. Here we tested the influence of fish predator chemical cues on patterns of gene expression within‐ and across generations using a clone of Daphnia ambigua that is known to exhibit strong TGP but weak within‐generation plasticity. Daphnia were reared in the presence of predator cues in generation 1, and shifts in gene expression were tracked across two additional asexual experimental generations that lacked exposure to predator cues. Initial exposure to predator cues in generation 1 was linked to ~50 responsive genes, but such shifts were 3–4× larger in later generations. Differentially expressed genes included those involved in reproduction, exoskeleton structure and digestion; major shifts in expression of genes encoding ribosomal proteins were also identified. Furthermore, shifts within the first‐generation and transgenerational shifts in gene expression were largely distinct in terms of the genes that were differentially expressed. Such results argue that the gene expression programmes involved in within‐ vs. transgeneration plasticity are fundamentally different. Our study provides new key insights into the plasticity of gene expression and how it relates to phenotypic plasticity in nature. 相似文献
13.
14.
Avril M. Harder Janna R. Willoughby William R. Ardren Mark R. Christie 《Molecular ecology》2020,29(6):1035-1049
15.
16.
Suda Parimala Ravindran Maike Herrmann Mathilde Cordellier 《Ecology and evolution》2019,9(5):2487-2504
17.
As coral reefs continue to decline due to climate change, the role of coral epigenetics (specifically, gene body methylation, GBM) in coral acclimatization warrants investigation. The evidence is currently conflicting. In diverse animal phyla, the baseline GBM level is associated with gene function: continuously expressed “housekeeping” genes are typically highly methylated, while inducible context-dependent genes have low or no methylation at all. Some authors report an association between GBM and the environment and interpret this observation as evidence of the GBM's role in acclimatization. Yet, others argue that the correlation between GBM change and gene expression change is typically absent or negligible. Here, we used the reef-building coral, Acropora millepora, to test whether environmentally driven changes in GBM are associated with a gene's ability to respond to environmental changes (plasticity) rather than expression level. We analyzed two cases of modified gene expression plasticity observed in a 3-week-long heat acclimatization experiment. The first one was a group of heat-induced genes that failed to revert their expression after the coral was translocated back to the control tank. The second case involved genes that changed the magnitude of their response to the daily temperature fluctuations over the course of the experiment. In both cases, we found negligible or no association with GBM change. We conclude that although both gene expression plasticity and GBM can change during acclimatization, there is no direct association between the two. This adds to the increasing volume of evidence that the function of GBM in invertebrates is unrelated to acclimatization on physiological timescales. 相似文献
18.
Profiling multiple omic layers in a single cell enables the discovery and analysis of biological phenomena that are not apparent from analysis of mono‐omic data. While methods for multiomic profiling have been reported, their adoption has been limited due to high cost and complex workflows. Here, a simple method for joint profiling of gene expression and chromatin accessibility in tens to hundreds of single cells is presented. Assessed herein is the quality of resulting single cell ATAC‐ and RNA‐seq data across three cell types, examining the link between accessibility and expression at the CD3G and FTH1 loci in human primary T cells and monocytes, and comparing the accuracy of clustering solutions for mono‐omic and combined data. The new method allows biological laboratories to perform simultaneous profiling of gene expression and chromatin accessibility using standard reagents and instrumentation. This technique, in conjunction with other advances in multiomic profiling, will enable highly resolved cell state classification and more specific mechanistic hypothesis generation than is possible with mono‐omic analysis. 相似文献
19.
Fan Qiu Seton Bachle Jesse B. Nippert Mark C. Ungerer 《Molecular ecology resources》2020,20(3):681-691
20.