Transcriptomic analysis reveals potential mechanisms of toxicity in a combined exposure to dibutyl phthalate and diisobutyl phthalate in zebrafish (Danio rerio) ovary

Chen, Hui; Feng, Weiwei; Chen, Kun; Qiu, Xuchun; Xu, Hai; Mao, Guanghua; Zhao, Ting; Ding, Yangyang; Wu, Xiangyang

doi:10.1016/j.aquatox.2019.105290

Cited by 52 publications

(16 citation statements)

References 63 publications

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“…Subsequent analysis suggested that the neuroactive ligand-receptor interaction pathway was significantly enriched by both the DEGs and DE lncRNAs between SWG and LG at two ages. Transcriptome studies in poultry [7], pig [28], goat [29], and zebrafish [30] have also demonstrated the important role of this pathway in the control of reproductive activities. Furthermore, almost all DEGs enriched in this pathway, including OPRM1, F2RL2, GLRA2, HTR7, HTR2B, OPRK1, P2RY13, GRM4, LEPR, HTR1B, LPAR3, AVPR1A, and GABRP, were significantly upregulated in the ovarian stroma of SWG.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis Suggests Key Roles for 5-Hydroxytryptamlne Receptors in Control of Goose Egg Production

Ouyang

Wang

et al. 2020

Genes

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To date, research on poultry egg production performance has only been conducted within inter or intra-breed groups, while those combining both inter- and intra-breed groups are lacking. Egg production performance is known to differ markedly between Sichuan white goose (Anser cygnoides) and Landes goose (Anser anser). In order to understand the mechanism of egg production performance in geese, we undertook this study. Here, 18 ovarian stromal samples from both Sichuan white goose and Landes goose at the age of 145 days (3 individuals before egg production initiation for each breed) and 730 days (3 high- and low egg production individuals during non-laying periods for each breed) were collected to reveal the genome-wide expression profiles of ovarian mRNAs and lncRNAs between these two geese breeds at different physiological stages. Briefly, 58, 347, 797, 777, and 881 differentially expressed genes (DEGs) and 56, 24, 154, 105, and 224 differentially expressed long non-coding RNAs (DElncRNAs) were found in LLD vs. HLD (low egg production Landes goose vs. high egg production Landes goose), LSC vs. HSC (low egg production Sichuan White goose vs. high egg production Sichuan white goose), YLD vs. YSC (young Landes goose vs. young Sichuan white goose), HLD vs. HSC (high egg production Landes goose vs. high egg production Sichuan white goose), and LLD vs. LSC (low egg production Landes goose vs. low egg production Sichuan white goose) groups, respectively. Functional enrichment analysis of these DEGs and DElncRNAs suggest that the “neuroactive ligand–receptor interaction pathway” is crucial for egg production, and particularly, members of the 5-hydroxytryptamine receptor (HTR) family affect egg production by regulating ovarian metabolic function. Furthermore, the big differences in the secondary structures among HTR1F and HTR1B, HTR2B, and HTR7 may lead to their different expression patterns in goose ovaries of both inter- and intra-breed groups. These results provide novel insights into the mechanisms regulating poultry egg production performance.

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Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis Suggests Key Roles for 5-Hydroxytryptamlne Receptors in Control of Goose Egg Production

Ouyang

Wang

et al. 2020

Genes

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“…We generated 227,516 consensus isoforms with an average consensus isoform length of 2086 bp, including 148,836 high-quality isoforms (Table 1 ). We successfully obtained 80,654 non-redundant transcripts using CD-HIT [ 41 ] for caucasian clover rhizomes analysis.…”

Section: Resultsmentioning

confidence: 99%

“…The cDNA was purified by AMPure XP beads after synthesis of second cDNA strand (adding buffer, dNTPs, RNase H and DNA polymerase I). Then, double-stranded cDNA was end repaired, adding a tail and the sequencing linker, and the fragment size was determined by AMPure XP beads [ 41 ]. The final cDNA library was assessed by PCR, and the quality of the cDNA library was determined using an Agilent 2100 bioanalyzer.…”

Section: Methodsmentioning

confidence: 99%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

BMC Plant Biol

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Background Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result We adopted PacBio sequencing and Illumina sequencing to identify differentially expressed genes (DEGs) in five tissues, including taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) tissues, in the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6821 alternative splicing (AS) events, 2429 long noncoding RNAs (lncRNAs) and 4501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more DEGs, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) of transcription factors and physiological indicators were combined to reveal 11 hub genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 DEGs involved in hormone signalling and transduction, and the largest number of genes are associated with the auxin (IAA) signalling pathway, with significant up-regulation in T2 and T5. Conclusions This study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

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“…These authors also used R for data processing and essential statistics, plus gene enrichment and pathway analysis through DAVID and also the STRING and STICH databases and online tools for surveying gene and protein networks [49,50]. In another example with emerging pollutants, Chen et al [51] surveyed signaling pathways related to reproduction in female zebrafish recurring exposed to mixed phthalate plasticizers. The authors contrasted DEGs against the canonical pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG).…”

Section: Transcriptomicsmentioning

confidence: 99%

The State-of-the Art of Environmental Toxicogenomics: Challenges and Perspectives of “Omics” Approaches Directed to Toxicant Mixtures

Martins

Dreij

Costa

2019

IJERPH

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The last decade witnessed extraordinary advances in “omics” methods, particularly transcriptomics, proteomics and metabolomics, enabling toxicologists to integrate toxicokinetics and toxicodynamics with mechanistic insights on the mode-of-action of noxious chemicals, single or combined. The toxicology of mixtures is, nonetheless, a most challenging enterprise, especially for environmental toxicologists and ecotoxicologists, who invariably deal with chemical mixtures, many of which contain unknowns. Despite costs and demanding computations, the systems toxicology framework, of which “omics” is a major component, endeavors extracting adverse outcome pathways for complex mixtures. Still, the interplay between the multiple components of gene expression and cell metabolism tends to be overlooked. As an example, the proteome allocates DNA methyltransferases whose altered transcription or loss of function by action of chemicals can have a global impact on gene expression in the cell. On the other hand, chemical insult can produce reactive metabolites and radicals that can intercalate or bind to DNA as well as to enzymes and structural proteins, compromising their activity. These examples illustrate the importance of exploring multiple “omes” and the purpose of “omics” and multi-“omics” for building truly predictive models of hazard and risk. Here we will review the state-of-the-art of toxicogenomics highlighting successes, shortcomings and perspectives for next-generation environmental toxicologists.

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Transcriptomic analysis reveals potential mechanisms of toxicity in a combined exposure to dibutyl phthalate and diisobutyl phthalate in zebrafish (Danio rerio) ovary

Cited by 52 publications

References 63 publications

Comparative Transcriptome Analysis Suggests Key Roles for 5-Hydroxytryptamlne Receptors in Control of Goose Egg Production

Comparative Transcriptome Analysis Suggests Key Roles for 5-Hydroxytryptamlne Receptors in Control of Goose Egg Production

Revealing the full-length transcriptome of caucasian clover rhizome development

The State-of-the Art of Environmental Toxicogenomics: Challenges and Perspectives of “Omics” Approaches Directed to Toxicant Mixtures

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