Figure - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
Cell-to-cell interactions and ECM. A: numbers of genes by functional groups and pathways involved in regulation of communication and contacts between cells. B: expression patterns of genes coding for proteins involved in cell adhesion and cell-to-ECM interactions.
Source publication
Background
Regulation of gene expression plays a central role in embryonic development. Early stages are controlled by gametic transcripts, which are subsequently substituted with transcripts from the genome of the zygote. Transcriptomic analyses provide an efficient approach to explore the temporal gene expression profiles in embryos and to search...
Similar publications
The canonical Wnt/ β-catenin pathway is activated in triple-negative breast cancer (TNBC). The activation of this pathway leads to the expression of specific target genes depending on the cell/tissue context. Here, we analyzed the transcriptome of two different TNBC cell lines to define a comprehensive list of Wnt target genes. The treatment of cel...
Mammalian wounds typically heal by fibrotic repair without hair follicle (HF) regeneration. Fibrosis and regeneration are currently considered the opposite end of wound healing. This study sought to determine if scar could be remodeled to promote healing with HF regeneration. Here, we identify that activation of the Sonic hedgehog (Shh) pathway rei...
Heritability is one of the strongest risk factors of prostate cancer, emphasizing the importance of the genetic contribution towards prostate cancer risk. To date, 86 established prostate cancer risk variants have been identified by genome-wide association studies (GWAS). To determine if these risk variants are located near genes that interact toge...
The primary hurdle in the treatment of cancer is acquisition of resistance by the tumor cells toward multiple drugs and selectively targeting the cancer stem cells. This problem was overcome by the chemotherapeutic property of recently discovered drug salinomycin. Exact mechanism of action of salinomycin is not yet known, but there are multiple pat...
Citations
... GPL18775; Agilent, Santa Clara, CA, USA) using the Gene Expression Hybridization Kit (Agilent, Santa Clara, CA, USA), according to the manufacturer's protocol. This DNA oligonucleotide 4 × 44 k microarray includes 60 mer probes for unique transcripts from the Ensembl and Unigene databases [44]. The hybridized arrays were washed using the Agilent Gene Expression Wash Buffer Kit and scanned with an Agilent Technologies Scanner G2505C, according to the manufacturer's protocol (GE2_1010_Sep10). ...
Adaptation to environmental variation caused by global climate change is a significant aspect of fisheries management and ecology. A reduction in ocean salinity is visible in near-shore areas, especially in the Baltic Sea, where it is affecting the Atlantic cod population. Cod is one of the most significant teleost species, with high ecological and economical value worldwide. The population of cod in the Baltic Sea has been traditionally divided into two subpopulations (western and eastern) existing in higher- and lower-salinity waters, respectively. In recent decades, both Baltic cod subpopulations have declined massively. One of the reasons for the poor condition of cod in the Baltic Sea is environmental factors, including salinity. Thus, in this study, an oligonucleotide microarray was applied to explore differences between Baltic cod subpopulations in response to salinity fluctuations. For this purpose, an exposure experiment was conducted consisting of salinity elevation and reduction, and gene expression was measured in gill tissue. We found 400 differentially expressed genes (DEGs) involved in the immune response, metabolism, programmed cell death, cytoskeleton, and extracellular matrix that showed a subpopulation-dependent pattern. These findings indicate that osmoregulation in Baltic cod is a complex process, and that western and eastern Baltic cod subpopulations respond differently to salinity changes.
... Transcriptome analyses were performed using Nofima's 44k genome-wide oligonucleotide Atlantic cod microarray. Due to the high similarity of protein coding sequences, this platform works equally well with both species [8,69]. Microarrays were manufactured by Agilent Technologies, and all reagents and equipment were purchased from the same provider. ...
Fish skin is a multifunctional barrier tissue with high regeneration capacity that interacts with the surrounding environment and provides protection. Functional importance, high complexity and activity make skin an attractive tissue for studying the effects of environmental challenges and chemical stressors in fish. The aim of this work was to characterize skin from polar cod (Boreogadus saida) and Atlantic cod (Gadus morhua), and to test cod skin as an in vitro model in exposure studies. Both species have similar skin structures including epidermis, mucous cells, club cells and scales. However, microarchitectural differences were detected; Atlantic cod has a smooth epidermal surface and overlapping scales, whereas polar cod has a folded outer surface and discontinuous scales. Genome-wide microarray found 6.5k genes with expression differences, which suggested more active turnover of proteins, proliferation and motility of cells in skin of polar cod. Hydrogen peroxide (H2O2) was used to examine skin responses. Transcriptome response was stronger in the skin of polar cod, with 155 differentially expressed genes. The skin from Atlantic cod was further used to develop a cell culture. H2O2 decreased the cell migration rate in a dose-dependent manner, which could indicate reduced skin healing capacity. The results revealed novel skin structures and confirmed that the skin from cod is a promising tissue for evaluation of stressors.
... Studies of molecular ontogeny during early embryogenesis have documented a tight relationship between the abundance of specific maternal mRNA transcripts, egg quality, and embryonic developmental competence [18][19][20][21][22][23]. Embryogenesis is mainly governed by maternal transcripts until MZT, when embryonic mRNA transcripts take over accompanied by clearance of maternal RNA. ...
Low egg quality and embryonic survival are critical challenges in aquaculture, where assisted reproduction procedures and other factors may impact egg quality. This includes European eel (Anguilla anguilla), where pituitary extract from carp (CPE) or salmon (SPE) is applied to override a dopaminergic inhibition of the neuroendocrine system, preventing gonadotropin secretion and gonadal development. The present study used either CPE or SPE to induce vitellogenesis in female European eel and compared impacts on egg quality and offspring developmental competence with emphasis on the maternal-to-zygotic transition (MZT). Females treated with SPE produced significantly higher proportions of floating eggs with fewer cleavage abnormalities and higher embryonic survival. These findings related successful embryogenesis to higher abundance of mRNA transcripts of genes involved in cell adhesion, activation of MZT, and immune response (dcbld1, epcam, oct4, igm) throughout embryonic development. The abundance of mRNA transcripts of cldnd, foxr1, cea, ccna1, ccnb1, ccnb2, zar1, oct4, and npm2 was relatively stable during the first eight hours, followed by a drop during MZT and low levels thereafter, indicating transfer and subsequent clearance of maternal mRNA. mRNA abundance of zar1, epcam, and dicer1 was associated with cleavage abnormalities, while mRNA abundance of zar1, sox2, foxr1, cldnd, phb2, neurod4, and neurog1 (before MZT) was associated with subsequent embryonic survival. In a second pattern, low initial mRNA abundance with an increase during MZT and higher levels persisting thereafter indicating the activation of zygotic transcription. mRNA abundance of ccna1, npm2, oct4, neurod4, and neurog1 during later embryonic development was associated with hatch success. A deviating pattern was observed for dcbld1, which mRNA levels followed the maternal-effect gene pattern but only for embryos from SPE treated females. Together, the differences in offspring production and performance reported in this study show that PE composition impacts egg quality and embryogenesis and in particular, the transition from initial maternal transcripts to zygotic transcription.
... Until this point, maternal gene products are the most essential drivers for early embryonic development. Studies have shown essential impacts of the abundance of specific mRNA transcripts on egg quality and embryonic development Lanes et al., 2013;Rozenfeld et al., 2016;Škugor et al., 2014). The observed decline in survival of embryos from farm-raised females around this time in embryonic development indicates possible failure of the embryonic transcription as suggested by a previous study (Rozenfeld et al., 2016). ...
Production of high-quality offspring from farm-raised broodstock is fundamental to establish a closed-cycle hatchery production of European eel, Anguilla anguilla. While development of larval culture technologies progresses, the present study focused on effects of essential fatty acid (EFA) composition of eggs on offspring quality. Three reproduction experiments were conducted, two of which included farm-raised broodstock fed different diets for different periods of time and one wild-caught broodstock, using size-matched females. The formulated diets varied in levels and ratios of three essential fatty acids, arachidonic acid (20:4n-6; ARA), eicosapentaenoic acid (20:5n-3; EPA), and docosahexaenoic acid (22:6n-3; DHA), while feeding periods lasted either 55 or 79 weeks. Dietary influences on egg and offspring fatty acid composition and offspring quality were evaluated and results of the most successful dietary regime was compared to those of wild-caught females. Results showed that elevated dietary levels of ARA were reflected in unfertilized eggs, with high ARA diets significantly increasing the amounts of floating eggs, total lipid content in eggs, fertilization success, and embryonic survival. Further EFA enhancements and prolonged feeding resulted in higher ARA and lower EPA levels in the unfertilized eggs, while DHA levels did not change. Females with prolonged feeding produced offspring of higher quality, i.e. higher egg dry weight and larval survival. Overall, offspring of farm-raised females showed higher EFA levels than those of wild-caught females. However, while fertilization success was comparable, offspring of farm-raised females had significantly lower embryonic survival and hatch success as well as higher proportions of cleavage abnormalities. These results identified embryonic development as the main bottleneck in offspring production from farm-raised females. Once hatched, larval survival and quality was comparable between farm-raised and wild-caught females. Notably, enhancement of essential fatty acids in female broodstock diets in combination with a long feeding period improved the production of high quality offspring.
... With the decreasing cost of broad-scale gene expression studies, transcriptomic profiling of fish embryos is starting to receive increased attention. Recently, researchers have started to investigate how gene expression varies during embryonic development [28][29][30][31] and have attempted to identify transcripts and markers associated with embryo quality [31,32]. Renaut et al. [33] showed that gene expression in hybrid embryos is affected when divergent populations are crossed. ...
Background
Due to selective breeding, domesticated and wild Atlantic salmon are genetically diverged, which raises concerns about farmed escapees having the potential to alter the genetic composition of wild populations and thereby disrupting local adaptation. Documenting transcriptional differences between wild and domesticated stocks under controlled conditions is one way to explore the consequences of domestication and selection. We compared the transcriptomes of wild and domesticated Atlantic salmon embryos, by using a custom 44k oligonucleotide microarray to identify perturbed gene pathways between the two stocks, and to document the inheritance patterns of differentially-expressed genes by examining gene expression in their reciprocal hybrids.
Results
Data from 24 array interrogations were analysed: four reciprocal cross types (W♀ × W♂, D♀ × W♂; W♀ × D♂, D♀ × D♂) × six biological replicates. A common set of 31,491 features on the microarrays passed quality control, of which about 62 % were assigned a KEGG Orthology number. A total of 6037 distinct genes were identified for gene-set enrichment/pathway analysis. The most highly enriched functional groups that were perturbed between the two stocks were cellular signalling and immune system, ribosome and RNA transport, and focal adhesion and gap junction pathways, relating to cell communication and cell adhesion molecules. Most transcripts that were differentially expressed between the stocks were governed by additive gene interaction (33 to 42 %). Maternal dominance and over-dominance were also prevalent modes of inheritance, with no convincing evidence for a stock effect.
Conclusions
Our data indicate that even at this relatively early developmental stage, transcriptional differences exist between the two stocks and affect pathways that are relevant to wild versus domesticated environments. Many of the identified differentially perturbed pathways are involved in organogenesis, which is expected to be an active process at the eyed egg stage. The dominant effects are more largely due to the maternal line than to the origin of the stock. This finding is particularly relevant in the context of potential introgression between farmed and wild fish, since female escapees tend to have a higher spawning success rate compared to males.
Electronic supplementary material
The online version of this article (doi:10.1186/s12711-016-0200-6) contains supplementary material, which is available to authorized users.
... Until this point, development of the embryo has been driven by the aforementioned maternal gene products, which are vastly important for embryonic development. Likewise, mortality in early embryonic stages may be affected by differential transcription of specific maternal gene products either at the embryonic stages or earlier (Aegerter et al., 2005;Lanes et al., 2013;Skugor et al., 2014). For example, studies have shown that the quantity of specific maternal mRNA transcripts is related to the quality of eggs and/or larvae in several teleost species (Aegerter et al., 2004;Lanes et al., 2013;Skugor et al., 2014). ...
... Likewise, mortality in early embryonic stages may be affected by differential transcription of specific maternal gene products either at the embryonic stages or earlier (Aegerter et al., 2005;Lanes et al., 2013;Skugor et al., 2014). For example, studies have shown that the quantity of specific maternal mRNA transcripts is related to the quality of eggs and/or larvae in several teleost species (Aegerter et al., 2004;Lanes et al., 2013;Skugor et al., 2014). Previous studies have identified a large catalog of integral maternal mRNA transcripts coding for many different proteins (Howley and Ho, 2000;Suzuki et al., 2000;Aegerter et al., 2004). ...
Maternal mRNA governs early embryonic development in fish and variation in abundance of maternal transcripts may contribute to variation in embryonic survival and hatch success in European eel, Anguilla anguilla. Previous studies have shown that quantity of the maternal gene products β-tubulin, insulin-like growth factor 2 (igf2), nucleoplasmin (npm2), prohibitin 2 (phb2), phosphatidylinositol glycan biosynthesis class F protein 5 (pigf5), and carnitine O-palmitoyltransferase liver isoform-like 1 (cpt1) are associated with embryonic developmental competence in other teleosts. Here, the relations between relative mRNA abundance of these genes in eggs and/or embryos and egg quality, was studied and analyzed. We compared egg quality of the two groups: i) batches with hatching and ii) batches with no hatching. Results showed no significant differences in relative mRNA abundance between the hatch and no hatching groups for any of the selected genes at 0, 2.5, and 5 HPF. However, at 30 HPF the hatch group showed significantly higher abundance of cpt1a, cpt1b, β-tubulin, phb2, and pigf5 transcripts than the no hatch group. Therefore, these results indicate that up-regulation of the transcription of these genes in European eel after the mid-blastula transition, may be needed to sustain embryonic development and hatching success.
... During embryo and larval development, PyTollip mRNA appeared to be moderately abundant in the original egg, representing maternal expression. Subsequently, PyTollip expression decreased until the multiple cells phase, implying that the embryo relies on maternal PyTollip mRNA at the beginning of embryonic development and does not undertake new expression until the blastula stage (Zhang et al., 2013b;Garbarino et al., 2014;Škugor et al., 2014). The following stepwise increase of PyTollip expression is relevant to its involvement in protein trafficking and metabolic processes, which are physiologically required during the growth of scallops from blastula to the D-shaped larvae stage (Brissoni et al., 2006;Ciarrocchi et al., 2009;Capelluto, 2012;Zhu et al., 2012). ...
Toll-interacting protein (Tollip) is a critical regulator of Toll-like receptor (TLR)-mediated innate immune responses. However, the Tollip gene has not been systematically characterized in shellfish. In this study, we identified and characterized a Tollip gene, PyTollip, in Yesso scallop (Patinopecten yessoensis). Phylogenetic and protein structural analyses were conducted to determine its sequence identities and evolutionary relationships. Compared with Tollip genes from other invertebrate and vertebrate species, the PyTollip gene is highly conserved in its sequence and structural features, except that a unique asparagine residue was found at a conserved site in the C2 domain of PyTollip. Quantitative real-time PCR was used to investigate the expression profiles of PyTollip in different developmental stages, healthy adult tissues, and in hemolymph after Micrococcus luteus and Vibrio anguillarum bacterial infection. Real-time PCR analysis demonstrated differential expression of PyTollip at the acute phase (3 h) after infection with Gram-negative (V. anguillarum) and Gram-positive (M. luteus) bacteria. A second strong response of PyTollip expression was observed 24 h after challenge with V. anguillarum. Collectively, these results provide novel insights into the specific role and response of Tollip and TLR signaling pathways in host immune responses against different bacterial pathogens in bivalves.
... This and other unknown functions may explain a highest transcriptional level of apolipoproteins before hatching, e.g., trafficking of structural lipids for new cell membranes, or signaling among others. However, transcripts detected early in development may originate from maternal transfer (Skugor et al. 2014). ...
Growth and energy transfer are critically dependent on effective transport of lipid molecules between tissues and cellular compartments. This process is specific in egg and eleutheroembryos, when energetic and structural lipids, located at the yolk sac, need to be mobilized in order to be incorporated in the new forming embryo, or to produce energy. Here, we describe the transcriptional profile of 11 genes that codify for proteins involved in intercellular lipid transport and cholesterol metabolism during the early development of a marine teleost fish (Scophthalmus maximus), from notochord formation to the period beyond mouth opening. The mRNA expression pattern of genes (apoA1, apoB100, apoE, cetp, mtp, pltp, lipC, lpl, hmgcr1, soat1, lcat) is described and related to previously published lipid levels in larvae and PPARs—peroxisome proliferator-activated receptors—mRNA levels from the same experiment (Cunha et al. in Mar Genomics 10:17–25, 2013). Our findings show that the transcription of genes responsible for apolipoproteins production starts soon before hatching and that activities decline along the development. In contrast, genes responsible for cholesterol synthesis have a low transcription level early in the development and their activity increases later. Apolipoproteins and other genes related to reverse cholesterol transport are possibly under the control of Pparα2, while the expression of extracellular lipid transfer proteins and enzymes involved in cholesterol synthesis is possibly under the simultaneous control of Pparα1 and Pparγ. Generally, the observed transcription of genes involved in lipid transport is in accordance with the lipid composition of the larvae and transcription of master regulators of lipid metabolism such as the nuclear receptors—PPARs.
... The Baltic and Atlantic populations differ genetically (Nielsen et al., 2003;O'Leary et al., 2007;Poćwierz-Kotus et al., 2015), but current understanding of Baltic cod genetics is still limited. Several Atlantic cod transcriptomes obtained from eggs and embryos have been characterized with micro-arrays (Rise et al., 2014;Škugor et al., 2014). Furthermore, Roche GS-FLX 454 pyrosequencing based transcriptomes from different tissues (brain, gonad, head kidney, hindgut, liver, spleen) and eggs have been published (Star et al., 2011;Lanes et al., 2013). ...
The Atlantic cod (Gadus morhua L.) is one of the most ecologically and economically important marine fish species in the North Atlantic Ocean. Using Roche GS-FLX 454 pyrosequencing technique 962,516 reads, representing 379Mbp of the Baltic cod transcriptome, were obtained. Data was assembled into 14,029 contigs of which 100% displayed homology to the Atlantic cod transcriptome. Despite a high similarity between transcripts, evidence for significant differences between Baltic and Atlantic cod was found.
Copyright © 2015. Published by Elsevier B.V.
... During embryo and larval development, PyTollip mRNA appeared to be moderately abundant in the original egg, representing maternal expression. Subsequently, PyTollip expression decreased until the multiple cells phase, implying that the embryo relies on maternal PyTollip mRNA at the beginning of embryonic development and does not undertake new expression until the blastula stage (Zhang et al., 2013b;Garbarino et al., 2014;Škugor et al., 2014). The following stepwise increase of PyTollip expression is relevant to its involvement in protein trafficking and metabolic processes, which are physiologically required during the growth of scallops from blastula to the D-shaped larvae stage (Brissoni et al., 2006;Ciarrocchi et al., 2009;Capelluto, 2012;Zhu et al., 2012). ...
Toll-interacting protein (Tollip) is a critical regulator of Toll-like receptor (TLR)-mediated innate immune responses. However, the Tollip gene has not been systematically characterized in shellfish. In this study, we identified and characterized a Tollip gene, PyTollip, in Yesso scallop (Patinopecten yessoensis). Phylogenetic and protein structural analyses were conducted to determine its sequence identities and evolutionary relationships. Compared with Tollip genes from other invertebrate and vertebrate species, the PyTollip gene is highly conserved in its sequence and structural features, except that a unique asparagine residue was found at a conserved site in the C2 domain of PyTollip. Quantitative real-time PCR was used to investigate the expression profiles of PyTollip in different developmental stages, healthy adult tissues, and in hemolymph after Micrococcus luteus and Vibrio anguillarum bacterial infection. Real-time PCR analysis demonstrated differential expression of PyTollip at the acute phase (3 h) after infection with Gram-negative (V. anguillarum) and Gram-positive (M. luteus) bacteria. A second strong response of PyTollip expression was observed 24 h after challenge with V. anguillarum. Collectively, these results provide novel insights into the specific role and response of Tollip and TLR signaling pathways in host immune responses against different bacterial pathogens in bivalves.
