Alternative splicing in the fiddler crab cognate ecdysteroid receptor: Variation in receptor isoform expression and DNA binding properties in response to hormone

Durica, David S.; Das, Sunetra; Najar, Fares Z.; Roe, Bruce A.; Phillips, Barret C.; Kappalli, Sudha; Anilkumar, Gopinathan

doi:10.1016/j.ygcen.2014.05.034

Cited by 11 publications

(8 citation statements)

References 87 publications

(133 reference statements)

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“…The SpEcR isoforms of S. paramamosain were differentiated by one deletion site in the D domain and one substitution site in the LBD, which is similar to what has been reported for other crustaceans (Asazuma et al 2007, Techa & Chung 2013. In fact, the results of recent research on the genomic organization of the EcR gene in the fiddler crab U. pugilator (Up gDNA) further verified the existence of the D domain and LBD isoforms (Durica et al 2014). Interestingly, the LBD substitutive sequences of SpEcR from S. paramamosain were almost the same as the two alternative LBD exons of Up gDNA, and the D domain deletion sequence of SpEcR was also similar to its D domain alternative exon.…”

Section: Discussionsupporting

confidence: 82%

“…The concurrent upregulation of SpEcR transcripts in the ovary with ovarian development implied that they probably participated in the regulation of the process of yolk protein accumulation. However, there are also reports indicating that the expression level of EcR does not differ significantly during ovarian development in other crabs (Durica et al 2014, Techa et al 2014. These results may be caused by the possible species-specific mechanisms of regulation of EcR during ovarian development.…”

Section: Discussionmentioning

confidence: 88%

“…Interestingly, the LBD substitutive sequences of SpEcR from S. paramamosain were almost the same as the two alternative LBD exons of Up gDNA, and the D domain deletion sequence of SpEcR was also similar to its D domain alternative exon. These results indicated that the three isoforms of SpEcR might result from alternative splicing of a single-gene locus and multiple variant sites might be a characteristic of EcR isoforms in crustaceans (Durica et al 2014). However, it was not clear whether these isoforms had different functions and this warranted further investigation.…”

Section: Discussionmentioning

confidence: 93%

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Ecdysone receptor in the mud crab Scylla paramamosain: a possible role in promoting ovarian development

Gong¹,

Ye²,

Xie³

et al. 2015

Journal of Endocrinology

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In arthropods, it is known that ecdysteroids regulate molting, limb regeneration, and reproduction through activation of the ecdysone receptor (EcR). However, the ecdysteroid signaling pathway for promotion of ovarian development in crustaceans is still unclear. In this study, three cDNA isoforms of EcR were cloned from the mud crab Scylla paramamosain. qRT-PCR revealed that the SpEcR mRNA was abundant in the eyestalk, ovary and epidermis. During ovarian development, the SpEcR transcripts increased from stage I (undeveloped stage) and reached a peak at stage IV (late vitellogenic stage) before dropping to a lower level at stage V (mature stage). Meanwhile, levels of 20-hydroxyecdysone (20E) in the hemolymph, detected by HPLC-MS, displayed a similar pattern of increase with ovarian development. Results from in situ hybridization indicated that SpEcR mRNA was present in the follicular cells during vitellogenesis. Results from in vivo experiments revealed that 20E at 0.2 mg/g body weight significantly stimulated the expression of SpEcR and vitellogenin (SpVg) in female crabs during the early vitellogenic stage but not during the previtellogenic stage. This was confirmed by results from in vitro experiments which indicated that SpEcR and SpVg expression levels were significantly upregulated in early vitellogenic ovarian explants incubated with 5.0 mM 20E at 3 and 6 h but not in previtellogenic ovarian explants. Finally, results from in vitro gene silencing experiments indicated that the expression of SpEcR and SpVg in the ovary was significantly inhibited by SpEcR dsRNA. All these results together indicated that in S. paramamosain, 20E, and SpEcR, located in the follicular cells, play important roles in the promotion of ovarian development via regulating the expression of SpVg.

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Section: Discussionsupporting

confidence: 82%

Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 93%

See 1 more Smart Citation

Ecdysone receptor in the mud crab Scylla paramamosain: a possible role in promoting ovarian development

Gong¹,

Ye²,

Xie³

et al. 2015

Journal of Endocrinology

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“…Over half of the 13 sequences had greater than 99% identity in protein alignment. The small discrepancy of 1% to 3% between the nucleotide and protein sequences was attributed to differences between the two technologies, the tissue sources used, novel isoforms, and sequencing errors (Durica et al, 2014). These comparisons confirmed the accuracy of the sequence generation and assembly protocols, validating the use of this data for further analysis.…”

Section: Assembly and Analysis Of The Baseline Transcriptomementioning

confidence: 59%

Transcriptome analysis of the molting gland (Y-organ) from the blackback land crab, Gecarcinus lateralis

Das

Pitts

Mudron

et al. 2016

Comparative Biochemistry and Physiology Part D: Genomics and Pr

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In decapod crustaceans, arthropod steroid hormones or ecdysteroids regulate molting. These hormones are synthesized and released from a pair of molting glands called the Y-organs (YO). Cyclic nucleotide, mTOR, and TGFβ/Smad signaling pathways mediate molt cycle-dependent phase transitions in the YO. To further identify the genes involved in the regulation of molting, a YO transcriptome was generated from three biological replicates of intermolt blackback land crab, Gecarcinus lateralis. Illumina sequencing of cDNA libraries generated 227,811,829 100-base pair (bp) paired-end reads; following trimming, 90% of the reads were used for further analyses. The trimmed reads were assembled de novo using Trinity software to generate 288,673 contigs with a mean length of 872 bp and a median length of 1842 bp. Redundancy among contig sequences was reduced by CD-HIT-EST, and the output constituted the baseline transcriptome database. Using Bowtie2, 92% to 93% of the reads were mapped back to the transcriptome. Individual contigs were annotated using BLAST, HMMER, TMHMM, SignalP, and Trinotate, resulting in assignments of 20% of the contigs. Functional and pathway annotations were carried out via gene ontology (GO) and KEGG orthology (KO) analyses; 58% and 44% of the contigs with BLASTx hits were assigned to GO and KO terms, respectively. The gene expression profile was similar to a crayfish YO transcriptome database, and the relative abundance of each contig was highly correlated among the three G. lateralis replicates. Signal transduction pathway orthologs were well represented, including those in the mTOR, TGFβ, cyclic nucleotide, MAP kinase, calcium, VEGF, phosphatidylinositol, ErbB, Wnt, Hedgehog, Jak-STAT, and Notch pathways.

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“…Transcriptomics using NGS technology has revealed genes involved in stress response, reproduction, development, molting and growth, limb regeneration, immune response, endocrinology, and nutrition and digestion in decapod crustaceans (Sagi et al 2013; Tom et al 2013; Durica et al 2014; Ghaffari et al 2014; Hao et al 2014; Lv et al, 2014, 2015; Shen et al 2014; Song et al 2014; Tom et al 2014; Wei et al 2014a, 2014b; Abehsera et al 2015; Chandler et al 2015; Christiaens et al 2015; Huang et al 2015; Johnson et al 2015; Li et al 2015a, 2015b; Ventura et al 2014, 2015; Verbruggen et al 2015; Wang et al 2015; Das et al 2016a). It is clear from the input received at the SICB meeting and the ten symposium papers in this issue (Armstrong and Stillman 2016; Chandler et al 2016; Clark and Greenwood 2016; Das and Mykles 2016; Das et al 2016b; Havird and Santos 2016a, 2016b; Johnson et al 2016; Powell et al 2016; Tarrant et al 2016) that a greater understanding of the relationship between transcriptomic and phenotypic change in decapod crustaceans will not be achieved until more powerful and applicable “-omic” tools and resources are developed.…”

Section: Future Directions and Recommendationsmentioning

confidence: 99%

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

Mykles

Burnett

Durica

et al. 2016

Integr. Comp. Biol.

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High-throughput RNA sequencing (RNA-seq) technology has become an important tool for studying physiological responses of organisms to changes in their environment. De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence. The contributions from the “Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology” symposium in this issue show the successes and limitations of using RNA-seq in the study of crustaceans. In conjunction with the symposium, the Animal Genome to Phenome Research Coordination Network collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Many were unaware of the bioinformatics analysis resources currently available on the CyVerse platform. Our analysis of community responses led to three recommendations for advancing the field: (1) integration of genomic and RNA-seq sequence assemblies for crustacean gene annotation and comparative expression; (2) development of methodologies for the functional analysis of genes; and (3) information and training exchange among laboratories for transmission of best practices. The field lacks the methods for manipulating tissue-specific gene expression. The decapod crustacean research community should consider the cherry shrimp, Neocaridina denticulata, as a decapod model for the application of transgenic tools for functional genomics. This would require a multi-investigator effort.

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Alternative splicing in the fiddler crab cognate ecdysteroid receptor: Variation in receptor isoform expression and DNA binding properties in response to hormone

Cited by 11 publications

References 87 publications

Ecdysone receptor in the mud crab Scylla paramamosain: a possible role in promoting ovarian development

Ecdysone receptor in the mud crab Scylla paramamosain: a possible role in promoting ovarian development

Transcriptome analysis of the molting gland (Y-organ) from the blackback land crab, Gecarcinus lateralis

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

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