Genome-wide identification and characterization of a panel of house-keeping genes in Schistosoma japonicum

Liu, Shuai; Cai, Pengfei; Hou, Nan; Piao, Xiangshu; Wang, Heng; Hung, Tao; Chen, Qijun

doi:10.1016/j.molbiopara.2011.12.007

Cited by 69 publications

(74 citation statements)

References 58 publications

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“…Identification of housekeeping genes has been greatly facilitated by the progress of transcriptome profiling technologies. Hybridization-based approaches were among the earliest to be used for housekeeping gene analysis (Warrington et al 2000;Eisenberg and Levanon 2003;Czechowski et al 2005;Liu et al 2012). Using high-density oligonucleotide arrays, Warrington et al (2000) identified a set of 535 maintenance genes through 11 tissues in humans.…”

Section: Discussionmentioning

confidence: 99%

“…Hybridization-based approaches such as microarray, which contain thousands of specific DNA sequences for probe-target hybridization to create a profile of all transcripts being expressed, were used for housekeeping genes studies (Warrington et al 2000;Czechowski et al 2005;Liu et al 2012). Eisenberg and Levanon (2003) identified a set of 575 human genes that are expressed in all tested conditions in a publicly available microarray database.…”

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confidence: 99%

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Genome-wide identification of housekeeping genes in maize

et al. 2014

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In the wake of recent progress of high throughput transcriptome profiling technologies, extensive housekeeping gene mining has been conducted in humans. However, very few studies have been reported in maize (Zea mays L.), an important crop plant, and none were conducted on a genome -wide level. In this study, we surveyed housekeeping genes throughout the maize transcriptome using RNA-seq and microarray techniques, and validated the housekeeping profile with quantitative polymerase chain reaction (qPCR) under a series of conditions including different genotypes and nitrogen supplies. Seven microarray datasets and two RNA-seq libraries representing 40 genotypes at more than 20 developmental stages were selected to screen for commonly expressed genes. A total of 1,661 genes showed constitutive expression in both microarray and RNA-seq datasets, serving as our starting housekeeping gene candidates. To determine for stably expressed housekeeping genes, NormFinder was used to select the top 20 % invariable genes to be the more likely candidates, which resulted in 48 and 489 entries from microarray and RNA-seq data, respectively. Among them, nine genes (2OG-Fe, CDK, DPP9, DUF, NAC, RPN, SGT1, UPF1 and a hypothetical protein coding gene) were expressed in all 40 maize diverse genotypes tested covering 16 tissues at more than 20 developmental stages under normal and stress conditions, implying these as being the most reliable reference genes. qPCR analysis confirmed the stable expression of selected reference gene candidates compared to two widely used housekeeping genes. All the reference gene candidates showed higher invariability than ACT and GAPDH. The hypothetical protein coding gene exhibited the most stable expression across 26 maize lines with different nitrogen treatments with qPCR, followed by CDK encoding the cyclin-dependent kinase. As the first study to systematically screen for housekeeping genes in maize, we identified candidates by examining the transcriptome atlas generated from RNA-seq and microarray technologies. The nine top-ranked qPCR-validated novel housekeeping genes provide a valuable resource of reference genes for maize gene expression analysis.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Genome-wide identification of housekeeping genes in maize

et al. 2014

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“…The cDNA was subsequently used as template in real time PCR analysis to determine the transcriptional levels of several key genes including SjAChE , AchR1α (nicotinic acetylcholine receptor 1α), AchR1β , AchR2β , SGT1 (Glucose transporter protein 1), SGT4 (Glucose transporter protein 4), and GYS (Glycogen synthase). PSMD4 (26S proteasome non-ATPase regulatory subunit 4) was used as reference gene [46]. Primers were designed using Primer 3 software () and a primer melting temperature of 55–62 °C.…”

Section: Methodsmentioning

confidence: 99%

Suppression of Schistosoma japonicum Acetylcholinesterase Affects Parasite Growth and Development

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Liu

et al. 2018

IJMS

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To further investigate the importance of Schistosoma japonicum acetylcholinesterase (SjAChE) in cholinergic signaling for parasite growth and development, we used RNA interference (RNAi) to knock-down its expression in adults and eggs in vitro. This resulted in its reduced transcription but also expression of other important genes involved both in cholinergic signaling and glucose uptake were impacted substantially. Significant decreases in AChE protein expression, AChE enzymatic activity, and glucose uptake were observed in the SjAChE-knockdown parasites compared with luciferase controls. In vaccine/challenge experiments, we found that immunization of mice with recombinant SjAChE (rSjAChE) expressed in Escherichia coli elicited reductions in male worm numbers (33%), liver granuloma density (41%), and reduced numbers of mature intestinal eggs (73%) in the vaccinated group compared with the control group. These results indicate AChE plays an important role in the metabolism of male worms, and impacts indirectly on female fecundity leading to increased numbers of immature eggs being released and reduced sizes of liver granulomas. Furthermore, cytokine analysis showed that immunization of mice with rSjAChE elicited a predominantly Th1-type immune response characterized by increased production of IFNγ in splenic CD4+ T cells of vaccinated mice. The study confirms the potential of SjAChE as a vaccine/drug candidate against zoonotic schistosomiasis japonica.

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“…PSMD4 was selected as the reference because it maintains steady expression levels during the developmental stages (Liu S et al 2012), and the egg stage was used as a calibrator. The experiment was repeated three times.…”

Section: Real-time Quantitative Rt-pcr and Western Blot Of Sj-vasamentioning

confidence: 99%

Preliminary characterization and expression of Vasa-like gene in Schistosoma japonicum

et al. 2015

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The Vasa gene is a vital germline marker to study the origin and development of germ cells and gonads in many organisms. Until now, little information was available about the characteristics of the Vasa gene in Schistosoma japonicum (S. japonicum). In this study, we cloned the open reading frame (ORF) of the S. japonicum Vasa-like gene (Sj-Vasa). The expression pattern and tissue localization of Sj-Vasa were also analyzed. Our results showed that Sj-Vasa shared the general feature of DEAD-box family member proteins. Sj-Vasa was transcribed and expressed throughout the S. japonicum life cycle with transcription exhibiting high levels at day 24 in both male and female worms, and the expression level in the female was always higher than that in the male. Sj-Vasa protein was localized in a variety of tissues of adult schistosomes, including the gonads (ovary, vitellarium, and testes), the subtegument, and some cells of the parenchyma. To our knowledge, this is the first report of preliminary characterization and expression of the Vasa-like gene that may play an important role in the development of the worm, especially in reproductive organs of S. japonicum.

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Genome-wide identification and characterization of a panel of house-keeping genes in Schistosoma japonicum

Cited by 69 publications

References 58 publications

Genome-wide identification of housekeeping genes in maize

Genome-wide identification of housekeeping genes in maize

Suppression of Schistosoma japonicum Acetylcholinesterase Affects Parasite Growth and Development

Preliminary characterization and expression of Vasa-like gene in Schistosoma japonicum

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