Selection of suitable reference genes for gene expression analysis in gills and liver of fish under field pollution conditions

Rojas‐Hernández, Noemí; Véliz, David; Vega‐Retter, Caren

doi:10.1038/s41598-019-40196-3

Cited by 22 publications

(19 citation statements)

References 30 publications

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“…Reference genes are fundamental to the exact determination of changes in gene expression [ 52 , 55 ]. These are usually chosen based on previous studies, but only a limited number of these have selected reference genes according to their stable expression pattern in distinct tissues [ 56 , 57 ]. Typical reference genes are related to maintenance of cell structures and metabolism.…”

Section: Discussionmentioning

confidence: 99%

Distress Regulates Different Pathways in the Brain of Common Carp: A Preliminary Study

Burren

Pietsch

2021

Animals

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In this study, a stress trial was conducted with common carp, one of the most important species in aquaculture worldwide, to identify relevant gene regulation pathways in different areas of the brain. Acute distress due to exposure to air significantly activated the expression of the immediate early gene c-fos in the telencephalon. In addition, evidence for regulation of the two corticotropin-releasing factor (crf) genes in relation to their binding protein (corticotropin-releasing hormone-binding protein, crh-bp) is presented in this preliminary study. Inferences on the effects of due to exposure to air were obtained by using point estimation, which allows the prediction of a single value. This constitutes the best description to date of the previously generally unknown effects of stress in different brain regions in carp. Furthermore, principal component analyses were performed to reveal possible regulation patterns in the different regions of the fish brain. In conclusion, these preliminary studies on gene regulation in the carp brain that has been influenced by exposure to a stressor reveal that a number of genes may be successfully used as markers for exposure to unfavourable conditions.

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Section: Discussionmentioning

confidence: 99%

Distress Regulates Different Pathways in the Brain of Common Carp: A Preliminary Study

Burren

Pietsch

2021

Animals

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“…Phenotypic and physiological changes that develop as adaptations to toxic pressure have a confirmed or inferred genetic basis [7], but so far the processes are well understood in a handful of species for a few chemicals only [3]. Most of the studies on dynamics of gene expression are focused on organisms under controlled laboratory conditions, while data on expression variations in organisms under natural conditions are scarce [8]. Typically, laboratory species are aquarium or farm-reared fish, chosen for practical reasons (e.g., short generation time, small size, easy maintenance in aquaria), but their lower level of genetic diversity in comparison to wild populations can alter responses to anthropogenic chemicals [4].…”

Section: Introductionmentioning

confidence: 99%

Fish biomarkers from a different perspective: evidence of adaptive strategy of Abramis brama (L.) to chemical stress

et al. 2020

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Background: A prerequisite for long-term survival of populations under multi-stress conditions is their capacity to set up efficient adaptive strategies. However, changes in the activity of molecular biomarkers have been for decades considered as early signals of the deterioration of the fish health and evidence of stress-related adverse biological effects. The aim of this study was to show that such changes actually represent adaptive response of fish to chemical stress. Gene expression and enzyme activity level in liver and brain of specimens from two populations of Abramis brama from contrasted habitats (nature reserve and urban) were examined. Selected parameters included biomarkers of general stress, antioxidative defence, xenobiotic metabolism, endocrine disruption, glucose homeostasis, iron homeostasis, and neurotoxicity. Results: Exposure of A. brama population from urban area to chemical stress was confirmed by assessment of chronic toxic pressure at fish habitats using Toxic Unit approach. The most pronounced response to chemical stress is observed through the activation of antioxidative defence mechanisms in brain and liver at gene and enzyme activity level, high biotransformation capacity of liver, and activation of mechanisms that will meet energy demands and compensate for the metabolic costs of the response to toxicants (higher expression of genes related to glucose homeostasis in the exposed population). Higher hepatosomatic index in the exposed population implies liver hypertrophy due to increased functional load caused by pollution. Body condition factors indicate good overall condition of both fish populations and confirm high efficacy of mobilized adaptation mechanisms in the exposed population. Conclusions: The study provided the first data on basal expression of a number of genes in A. brama, potentially valuable for biomonitoring studies in absence of clear pollution gradient and/or reference sites (conditions). The study highlights importance of newly identified roles of various genes and proteins, typically considered as biomarkers of effects, and shows that changes in these parameters do not necessarily indicate the deterioration of the fish health. Such changes should be considered as adaptive response to chemical stress, rather than direct proof of ecological impact of pollution in situ.

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“…Several authors noticed that the River Ganga (Habitat B) is one of the highly polluted river systems in India [81,82], and this might impose extreme selection pressure on the fish. As evidenced in this study, in this habitat the promoter region has undergone functional changes which may be related to this pressure [83]. In comparison, the β actin promoter architecture of fish from habitat "C" was found to be less complex (S3 Fig).…”

Section: Comparison Of 5' Regulatory Region Among the Species Belong mentioning

confidence: 70%

The 5’ regulatory region of the β actin gene inClariasspecies is complex and variable in relation to ecological needs

Sangale

Tiknaik

Khedkar³

et al. 2020

Preprint

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22The β actin gene is involved in various cellular housekeeping processes 23 including transcription, mRNA processing, cell signaling and chromosome 24 remodeling. For regulating the expression of this gene under different 25 environmental conditions, the promoter region of the β actin gene is 26 structurally dynamic with multiple regulatory features in the upstream region.27 Most previous information about the 5' regulatory region of the β actin gene 28 has been limited to in vitro laboratory experiments. Considering the need for 29 functional versatility of expression of this gene in the Catfish Clarias batrachus 30 in different environments, here we have analyzed the 5' regulatory region of β 31 actin and identified numerous elements that are variable. We have made 2 32 comparisons of individuals from three populations found in three different 33 diverse ecological systems, as well as in three sister species, to elucidate its 34 structural diversity. Our results show that the 5' regulatory region has 35 considerable diversity and changes in architecture with respect Cis-acting 36 regulatory elements. These changes may be linked to positive selection in 37 combating pollution or disease like conditions encountered by the organism.38 These observations leads to the conclusion that 5' regulatory region of a 39 housekeeping gene like β actin, modify its architecture as per the 40 environmental conditions. These modifications specifically includes diversity of 41 TF binding sites indicating the assortment of environmental variables and only 42 one third region of 5' regulatory region is conserved which was yet not 43 highlighted. 44 45 Author summary 46 47 Promoter is a regulatory region where the basal transcription machinery 48 assembles to initiate the process of transcription. It plays crucial role in 49 controlling the gene expression. The 5' regulatory region includes TATA box, 50 CAAT box, GC box and Cis -acting regulatory elements. Most previous 51 information about the 5' regulatory region of the β actin gene has been limited 52 to in vitro laboratory experiments. Our study results show that the 5' 53 regulatory region has considerable diversity and changes in architecture with 54 respect Cis-acting regulatory elements. These changes may be linked to 55 positive selection in combating pollution or disease like conditions encountered 56 by the organism. These observations leads to the conclusion that 5' regulatory 3 57 region of a housekeeping gene like β actin, modify its architecture as per the 58 environmental requirements. These modifications precisely includes diversity of 59 TF binding sites indicating the assortment of environmental variables and only 60 one third region of 5' regulatory region is conserved. These findings clearly 61 define a novel role of promotor of β actin gene which was yet not highlighted. 62 These findings can broaden our understanding in linking TF in 5' regulatory 63 regions to a specific environmental variable/disease conditions. This may 64 become a simple strategy in under...

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Selection of suitable reference genes for gene expression analysis in gills and liver of fish under field pollution conditions

Cited by 22 publications

References 30 publications

Distress Regulates Different Pathways in the Brain of Common Carp: A Preliminary Study

Distress Regulates Different Pathways in the Brain of Common Carp: A Preliminary Study

Fish biomarkers from a different perspective: evidence of adaptive strategy of Abramis brama (L.) to chemical stress

The 5’ regulatory region of the β actin gene inClariasspecies is complex and variable in relation to ecological needs

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