Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule

<p>Abstract</p> <p>Background</p> <p>Recovery growth is a phase of rapid growth that is triggered by adequate refeeding of animals following a period of weight loss caused by starvation. In this study, to obtain more information on the system-wide integration of recovery growth in muscle, we undertook a time-course analysis of transcript expression in trout subjected to a food deprivation-refeeding sequence. For this purpose complex targets produced from muscle of trout fasted for one month and from muscle of trout fasted for one month and then refed for 4, 7, 11 and 36 days were hybridized to cDNA microarrays containing 9023 clones.</p> <p>Results</p> <p>Significance analysis of microarrays (SAM) and temporal expression profiling led to the segregation of differentially expressed genes into four major clusters. One cluster comprising 1020 genes with high expression in muscle from fasted animals included a large set of genes involved in protein catabolism. A second cluster that included approximately 550 genes with transient induction 4 to 11 days post-refeeding was dominated by genes involved in transcription, ribosomal biogenesis, translation, chaperone activity, mitochondrial production of ATP and cell division. A third cluster that contained 480 genes that were up-regulated 7 to 36 days post-refeeding was enriched with genes involved in reticulum and Golgi dynamics and with genes indicative of myofiber and muscle remodelling such as genes encoding sarcomeric proteins and matrix compounds. Finally, a fourth cluster of 200 genes overexpressed only in 36-day refed trout muscle contained genes with function in carbohydrate metabolism and lipid biosynthesis. Remarkably, among the genes induced were several transcriptional regulators which might be important for the gene-specific transcriptional adaptations that underlie muscle recovery.</p> <p>Conclusion</p> <p>Our study is the first demonstration of a coordinated expression of functionally related genes during muscle recovery growth. Furthermore, the generation of a useful database of novel genes associated with muscle recovery growth will allow further investigations on particular genes, pathways or cellular process involved in muscle growth and regeneration.</p

Identification of gonadal miRNAs in zebrafish exposed to high temperature during early stages of development

IX Jornada de Cromatina i Epigenètica organizada por la Secció de Cromatina i Epigenètica de la Societat Catalana de Biologia (SCB) y el Barcelona Chromatin Club (BCC) y cebrada el 22 de marzo de 2019.-- 1 pageMicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression in a wide variety of physiological processes. In some fish species (e.g., rainbow trout and medaka), it has been shown that miRNAs play regulatory functions in the reproductive system and that some of them are specific to the fish gonads. However, how miRNAs change their gonadal dynamics in fish subjected to environmental factors (i.e., high-temperature) during early stages of life, has not been studied yet. In order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads, we exposed zebrafish (Danio rerio) to elevated temperatures during early development (18-32 days post fertilization, dpf), a treatment that is known to result in male-skewed sex ratios. Once the fish reached adulthood (90 dpf), 8 ovaries and 8 testes were dissected and kept at -80ºC. MiRNAs were isolated and specific small RNA libraries were prepared and sequenced by Illumina technology (50 bp 1x50, v4, HiSeq). About 8 million reads were obtained from gonadal samples. Sequencing results were analyzed by miRDeep2 software that allowed, with high accuracy, to trim the sequencing data, to detect known miRNA from several databases and to identify novel miRNAs. Analysis of the expression levels of the miRNA identified a total of 25 and 1 unique miRNAs in ovaries and testes, respectively. After retrieving UTR regions, we analyzed these 26 identified miRNA by Miranda software and after filtering, we obtained almost 400 potential RNA targets. Currently, validation of the differentially expressed miRNAs by qPCR analysis is being performed. This study will provide a catalogue of both sex-specific and thermosensitive miRNAs in the zebrafish gonads that might be used as potential molecular biomarkers of the effect of temperature during sex differentiatio

Identification of common ovarian and testicular miRNAs among cultured fish species

11th European Zebrafish Meeting, 26-27 October 2020MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression in a wide variety of physiological processes. In cul-tured fish, it has been shown that miRNAs play a role in the reproductive system, where gonad-specific miRNAs are involved. In order to identify common aquacultured markers for early sex-development and to improve reproduction of farmed fish, we compared our zebrafish data with published data of sex-specific gonadal miRNAs to four farmed fish species (i.e., Atlantic cod, catfish, Nile tilapia and European sea bass) together with available data for transgenic zebrafish. In our fish facilities, AB zebrafish were kept at standard husbandry conditions until adulthood when ovaries and testes were dissected. miRNAs were isolated and specific RNA libraries were prepared and sequenced by Illumina technology (50 bp 1 x 50 bp, v4, HiSeq). About 16 million clean reads were obtained from gonadal samples. After determining differentially expressed miRNAs in ovary versus testis, we found 18 significantly upregulated miRNAs specific for ovaries and 25 for testes. Comparing our data with transgenic zebrafish miRNAs, we found one common differentially expressed miRNA specific for each sex: dre-miR-146b-5p in the ovary and dre-miR-212-5p in the testis. FISH analysis revealed the expression of miR146 in the germ cells but not in supporting cells of the ovaries. Significantly expressed miRNAs (normalized reads >100) from the five teleost fish species showed 31 common miRNAs in the gonads, in which five miRNAs were specific for ovaries and other five for testes. Although fur 135research is needed, these common and sex-specific miRNAs in several cultured fish species reveal potential miRNA biomarkers for early development and sex differentiation. Functional studies will demonstrate the molecular mechanism behind these miRNAs and their role in sex differentiatio

Deciphering sex-specific miRNAs as heat-recorders in zebrafish

14 pages, 7 figures, supplementary information https://doi.org/10.1038/s41598-022-21864-3.-- Data availability: The datasets generated and analyzed during the current study are available in NCBI SRA repository with the accession number: PRJNA755482In the last decade, a plethora of microRNAs (miRNAs) has been reported in a wide variety of physiological processes, including reproduction, in many aquatic organisms. However, miRNAome alterations occurred by environmental cues due to water temperature increment have not yet been elucidated. With the aim to identify epigenetic regulations mediated by miRNAs in the gonads in a climate change scenario, the animal model zebrafish (Danio rerio) were subjected to high temperatures during sex differentiation, a treatment that results in male-skewed sex ratios in the adulthood. Once the fish reached adulthood, gonads were sequenced by high-throughput technologies and a total of 23 and 1 differentially expressed miRNAs in ovaries and testes, respectively, were identified two months after the heat treatment. Most of these heat-recorder miRNAs were involved in human sex-related cancer and about 400 predicted-target genes were obtained, some with reproduction-related functions. Their synteny in the zebrafish genome was, for more than half of the predicted target genes, in the chromosomes 7, 2, 4, 3 and 11 in the ovaries, chromosome 4 being the place where the sex-associated-region (sar) is localized in wild zebrafish. Further, spatial localization in the gonads of two selected heat-recorder miRNAs (miR-122-5p and miR-146-5p) showed exclusive expression in the ovarian germ cells. The present study expands the catalog of sex-specific miRNAs and deciphers, for the first time, thermosensitive miRNAs in the zebrafish gonads that might be used as potential epimarkers to predict environmental past eventsThis study was supported by the Spanish Ministry of Science and Innovation grant AGL2015-73864-JIN “Ambisex” and 2PID2020-113781RB-I00 “MicroMet” and by the Consejo Superior de Investigaciones Científicas (CSIC) grant 02030E004 “Interomics” to LR, by grant AEI grant PID2019-108888RB-I00 to FP and with funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation

Variable and low egg quality is a major limiting factor for the development of efficient aquaculture production. This stems from limited knowledge on the mechanisms underlying egg quality in cultured fish. Molecular analyses, such as transcriptomic studies, are valuable tools to identify the most important processes modulating egg quality. However, very few studies have been devoted to this aspect so far. Within this study, the microarray-based transcriptomic analysis of eggs (of different quality) of sea bass (Dicentrarchus labrax) was performed. An Agilent oligo microarray experiment was performed on labelled mRNA extracted from 16 batches of eggs (each batch obtained from a different female) of sea bass, in which over 24,000 published probe arrays were used. We identified 39 differentially expressed genes exhibiting a differential expression between the groups of low (fertilization rate 60 %) quality. The mRNA levels of eight genes were further analyzed by quantitative PCR. Seven genes were confirmed by qPCR to be differentially expressed in eggs of low and high quality. This study confirmed the importance of some of the genes already reported to be potential molecular quality indicators (mainly rnf213 and irf7), but we also found new genes (mainly usp5, mem-prot, plec, cenpf), which had not yet been reported to be quality-dependent in fish. These results suggest the importance of genes involved in several important processes, such as protein ubiquitination, translation, DNA repair, and cell structure and architecture; these probably being the mechanisms that contribute to egg developmental competence in sea bass

Permanent gonadal epigenetic changes in response to heat during early development in zebrafish.

6th International Symposium on Genomics in Aquaculture (GIA), 5-7 May 2021The environment can influence the epigenome through modifications that alter gene expression and, consequently, can produce the appearance of a new phenotype. DNA methylation and regulatory microRNAs (miRNAs) are two types of epigenetic mechanisms responsible to integrate environmental cues. In fish, epigenetic modifications can follow as result of external inputs, and some can affect sex determination and differentiation. However, the underlying molecular mechanisms remain poorly understood. Currently, the search for epigenetic biomarkers (epimarkers) to identify specific phenotypes is at the forefront of research. The present study aimed to find epimarkers (DNA methylation and miRNAs) in mature fish gonads linked to abnormal thermal conditions that these fish might have suffered during early gonadal development. Zebrafish (Danio rerio) larvae were exposed to either control or high temperature during sex differentiation (18¿32 days post fertilization). DNA methylation in the promoter region of a set of key genes related to sexual development was studied in adult gonads by a targeted sequencing approach (Multiplex Bisulfite Sequencing, MBS). miRNA expression was explored with RNA-seq using Illumina technology. Furthermore, the spatial distribution of a selection of miRNAs was studied in the ovaries and testes by fluorescent in situ hybridization (FISH). Results showed differences in the methylation level of the promoter of some genes between sexes and temperatures, thus allowing to predict, by machine-learning strategies, epimarkers associated with sex and previous thermal exposure. By biocomputational analysis, we identified 24 unique miRNAs targeting 402 RNA transcripts and that responded differentially to heat in the gonads. Some of these miRNAs were mostly located to germ cells. This study identified DNA methylation and miRNAs changes in the zebrafish adult gonads that can be considered permanent epimarkers of past thermal events. This work was supported by MINECO grants AGL2016-787107-R "Epimark" to FP, AGL2015-73864-JIN "Ambisex" to LR and scholarship BES-2014¿069051 to AV. This study identified DNA methylation and miRNAs changes in the zebrafish adult gonads that can be considered permanent epimarkers of past thermal events. This study identified DNA methylation and miRNAs changes in the zebrafish adult gonads that can be considered permanent epimarkers of past thermal events. Currently, the search for epigenetic biomarkers (epimarkers) to identify specific phenotypes at the forefront of researc

A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment

Background Propionibacterium freudenreichii is a food grade bacterium consumed both in cheeses and in probiotic preparations. Its promising probiotic potential, relying largely on the active release of beneficial metabolites within the gut as well as the expression of key surface proteins involved in immunomodulation, deserves to be explored more deeply. Adaptation to the colon environment is requisite for the active release of propionibacterial beneficial metabolites and constitutes a bottleneck for metabolic activity in vivo. Mechanisms allowing P. freudenreichii to adapt to digestive stresses have been only studied in vitro so far. Our aim was therefore to study P. freudenreichii metabolic adaptation to intra-colonic conditions in situ. Results We maintained a pure culture of the type strain P. freudenreichii CIRM BIA 1, contained in a dialysis bag, within the colon of vigilant piglets during 24 hours. A transcriptomic analysis compared gene expression to identify the metabolic pathways induced by this environment, versus control cultures maintained in spent culture medium. We observed drastic changes in the catabolism of sugars and amino-acids. Glycolysis, the Wood-Werkman cycle and the oxidative phosphorylation pathways were down-regulated but induction of specific carbohydrate catabolisms and alternative pathways were induced to produce NADH, NADPH, ATP and precursors (utilizing of propanediol, gluconate, lactate, purine and pyrimidine and amino-acids). Genes involved in stress response were down-regulated and genes specifically expressed during cell division were induced, suggesting that P. freudenreichii adapted its metabolism to the conditions encountered in the colon. Conclusions This study constitutes the first molecular demonstration of P. freudenreichii activity and physiological adaptation in vivo within the colon. Our data are likely specific to our pig microbiota composition but opens an avenue towards understanding probiotic action within the gut in further studies comparing bacterial adaptation to different microbiota

Additional file 5: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

List of probes in pathways significantly enriched based on early nutritional history in the brain. The list of differentially expressed mRNA probes comprising the pathways neurological system process; homocysteine and methionine metabolism; and neuroendocrine peptides that are significantly enriched based on early nutritional history in the brain are outlined in separate worksheets. Probe names highlighted in yellow were selected for RT-PCR confirmation. (XLSX 18 kb

Neurodevelopment vs. the immune system: Complementary contributions of maternally-inherited gene transcripts and proteins to successful embryonic development in fish

International audienceThe aim of this study was to investigate the respective contribution of maternally-inherited mRNAs and proteins to egg molecular cargo and to its developmental competence in fish using pikeperch as a model. Our study provides novel insights into the understanding of type-specific roles of maternally-inherited molecules in fish. Here we show, for the first time, that transcripts and proteins have distinct, yet complementary, functions in the egg of teleost fish. Maternally-inherited mRNAs would shape embryo neurodevelopment, while maternally-inherited proteins would rather be responsible for protecting the embryo against pathogens. Additionally, we observed that processes directly preceding ovulation may considerably affect the reproductive success by modifying expression level of genes crucial for proper embryonic development, being novel fish egg quality markers (e.g., smarca4 or h3f3a). These results are of major importance for understanding the influence of external factors on reproductive fitness in both captive and wild-type fish species