Analysis of long non‐coding RNA involved in atrazine‐induced testicular degeneration of <scp><i>Xenopus laevis</i></scp>

Sai, Linlin; Qu, Binpeng; Zhang, Juan; Liu, Jian; Jia, Qiang; Bo, Cunxiang; Zhang, Yu; Yu, Gongchang; Han, Ru; Peng, Cheng

doi:10.1002/tox.22704

Cited by 20 publications

(10 citation statements)

References 28 publications

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“…The number of R. arenarum transcripts annotated as lncRNAs is higher than those reported for the amphibians Xenopus tropicalis, Xenopus laevis and Lithobates catesbeiana 6,[38][39][40] . In the case of the transcriptome studies in Xenopus, the number of lncRNAs defined depends on the temporal and spatial expression profiling of the samples.…”

Section: Resultscontrasting

confidence: 56%

The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction

Ceschin

Pires

Mardirosian

et al. 2020

Sci Rep

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the common toad Rhinella arenarum is widely distributed in Argentina, where it is utilised as an autochthonous model in ecotoxicological research and environmental toxicology. However, the lack of a reference genome makes molecular assays and gene expression studies difficult to carry out on this non-model species. to address this issue, we performed a genome-wide transcriptome analysis on R. arenarum larvae through massive RnA sequencing, followed by de novo assembly, annotation, and gene prediction. We obtained 57,407 well-annotated transcripts representing 99.4% of transcriptome completeness (available at http://rhinella.uncoma.edu.ar). We also defined a set of 52,800 highconfidence lncRNA transcripts and demonstrated the reliability of the transcriptome data to perform phylogenetic analysis. our comprehensive transcriptome analysis of R. arenarum represents a valuable resource to perform functional genomic studies and to identify potential molecular biomarkers in ecotoxicological research. Amphibians are poikilothermic vertebrates with morphological and ecological adaptations that allow them to occupy diverse terrestrial environments associated with humid ecosystems 1,2. They are the only terrestrial vertebrates that preserve free-living larvae and produce large oocytes with a transparent vitelline membrane that allows for the direct observation of the different stages of embryonic development. These characteristics have been exploited in various research areas such as toxicology, physiology, ecology, and evolution 3-7. The South American common toad Rhinella arenarum [ex. Bufo arenarum (Hensel, 1867)] is amply distributed in Argentina and breeds in shallow-water areas such as ponds and ditches 5,8,9. Amphibian research models can be easily and inexpensively established. However, only six anuran genomes are available to date: Pyxicephalus adspersus 10 , Nanorana parkeri 11 , Rana catesbeiana 6 , Rhinella marina (Bioproject: PRJEB24695, ID: 445546), Xenopus laevis 12 , and Xenopus tropicalis 13. Furthermore, several conserved morphological characteristics shared by anurans make both taxonomic classification and phylogenetic analysis difficult to perform 14. This stresses the need for combining novel genomic information with morphological and karyological data, as well as mitochondrial DNA sequencing, in order to improve accuracy in phylogenetic studies. Next Generation Sequencing (NGS) provides a cost-effective and rapid method to sequence and analyse complete genomes. However, amphibians have a very high DNA content and a large proportion of repetitive and non-coding sequences 15 ; thus, whole-genome assembly is still expensive and bioinformatically challenging. In contrast, high-throughput RNA-sequencing (RNA-Seq) is an affordable NGS technique that provides a convenient platform for transcript profiling and transcriptome sequencing in non-model amphibian species like R. arenarum 16,17. Here, we report for the first time the de novo assembly of R. arenarum transcriptome using massive RNA-Seq, followed by gen...

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Section: Resultscontrasting

confidence: 56%

The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction

Ceschin

Pires

Mardirosian

et al. 2020

Sci Rep

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“…Here, this result revealed a potential role of m 6 A modi cation sites of lncRNAs in testes of X. laevis induced by environmental agents such as AZ. Interestingly, we found lncRNA "XR_001933134" which was up-regulated in the testis of X. laevis exposed to AZ in our previous study was down-regulated in m 6 A modi cation [39], which may that m 6 A modi cation may negatively regulate the expression of lncRNA "XR_001933134". Wu et al demonstrated that m 6 A modi cation of lncRNAs may increase lncRNA RP11 expression [29].…”

Section: Discussionmentioning

confidence: 62%

Comprehensive Analysis of Differences of N6-Methyladenosine of Lncrnas Between Atrazine-Inducedand Normal Xenopus Laevis Testis

Qi¹,

Geng²,

Zhang³

et al. 2021

Preprint

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Background: Increasing evidence suggested N6-methyladenosine (m6A) plays an important role in RNA stability, degradation, splicing and translation. M6A is found in different RNA including long non-coding RNA (lncRNA) which has been found possess significant biological functions. Our previous study examined the m6A profile of mRNAs in testis tissues of Xenopus laevis (X. laevis) with and without treatment with 100 µg/L atrazine (AZ). The result revealed that m6A is a highly conserved modification across the species. Methods: In this study, we apply previous approach to further investigate m6A modification profile of lncRNAs and predict the potential mechanism. In brief, m6A was sequenced by MeRIP sequencing using the latest Illumina HiSeq sequencer. Pathway enrichment analysis was used to maps genes to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Results: The results showed that m6A of lncRNAs enriched around intergenic region in testes of X. laevis. We further investigated the differential expression of lncRNAs m6A in testes of AZ-exposed compared with that in animals from control group. The results indicated that up to 198 differentially methylated m6A sites were detected within 188 lncRNAs, in which 89 sites were significantly up-regulated and 109 sites were significantly down-regulated. Data from Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that AZ-affected lncRNAs m6A sites were mainly involved in 10 pathways in which 3 mutual pathways were found in the result of differentially m6A-methylated mRNAs. Conclusions: These findings suggest that differentially m6A-methylated lncRNAs and these 3 pathways may act on regulatory roles in abnormal testis development of AZ-exposed X. laevis. This study for the first time provide insights into the profile of lncRNAs m6A modifications in amphibian species.

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“…Here, this result revealed a potential role of m 6 A modification sites of lncRNAs in testes of X. laevis induced by environmental agents such as AZ. Interestingly, we found lncRNA “XR_001933134” was up-regulated in the testis of AZ-treated X. laevis in our previous study, but the m 6 A modification of which was down-regulated [ 50 ]. The result showed that m 6 A modification may negatively regulate the expression of lncRNA “XR_001933134”.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive analysis of differences of N6-methyladenosine of lncRNAs between atrazine-induced and normal Xenopus laevis testis

Geng

Zhang

et al. 2021

Genes and Environ

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Background Increasing evidence suggested N6-methyladenosine (m6A) modification is crucial for male germline development. However, m6A modification of lncRNAs gains a little attention in amphibians in recent years. Xenopus laevis (X. laevis) was chosen to be an ideal model organism for testing environmental endocrine disrupting chemicals (EDCs) exposure and resultant effects. Atrazine (AZ) as an endocrine disrupt can effect development of testis in amphibians. Our previous study revealed that m6A is a highly conserved modification across the species. Results The results of m6A sequences showed that m6A-methylated lncRNAs enriched in intergenic region in testes of X. laevis. We further examined the differential expression of lncRNAs m6A sites in testes of AZ-exposed and compared with that in animals from control group. The results indicated that up to 198 differentially methylated m6A sites were detected within 188 lncRNAs, in which 89 significantly up-methylated sites and 109 significantly down-methylated sites. Data from KEGG pathway analysis indicated that AZ-affected lncRNAs m6A sites were mainly involved in 10 pathways in which 3 mutual pathways were found in the result of differentially m6A-methylated mRNAs. Conclusions These findings suggested that differentially m6A-methylated lncRNAs and these 3 pathways may act on regulatory roles in abnormal testis development of AZ-exposed X. laevis. This study for the first time provides insights into the profile of lncRNAs m6A modifications in amphibian species.

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Analysis of long non‐coding RNA involved in atrazine‐induced testicular degeneration of Xenopus laevis

Cited by 20 publications

References 28 publications

The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction

The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction

Comprehensive Analysis of Differences of N6-Methyladenosine of Lncrnas Between Atrazine-Inducedand Normal Xenopus Laevis Testis

Comprehensive analysis of differences of N6-methyladenosine of lncRNAs between atrazine-induced and normal Xenopus laevis testis

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