Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing

Xiong, Jie; Lu, Xianbo; Zhou, Zhemin; Chang, Yue; Yuan, Dan; Tian, Miao; Zhou, Zhigang; Wang, Lei; Fu, Chengjie; Orias, Eduardo; Miao, Wei

doi:10.1371/journal.pone.0030630

Cited by 118 publications

(138 citation statements)

References 66 publications

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“…Due to the advantages of high-throughput technologies, the reliability, accuracy, and comprehensive data from RNA-Seq can not only help us understand gene structure, but also provide a better understanding of the biological function of genes (Wang et al, 2009). In addition, efficient Illumina high-throughput sequencing can help us discover new transcripts (Hansey et al, 2012), single nucleotide polymorphisms (Esteve-Codina et al, 2011), AS sites (Xiong et al, 2012), and other information. In this study, the transcriptomes of Mongolian and Lanzhou fat-tailed sheep were compared.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, data from RNA-Seq can help identify new transcripts (Hansey et al, 2012), single nucleotide polymorphisms (Esteve-Codina et al, 2011), alternative splicing events (Xiong et al, 2012), and other information. Several recent studies have used this type of next-generation sequencing platform in the liver tissue of pigs (Gunawan et al, 2013a,b;Sodhi et al, 2014), cows (Graugnard et al, 2013), rats (Tran and Huang, 2014;Wang et al, 2014), and fish (Yang et al, 2012;Lau et al, 2014;Magnanou et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

Xu¹,

Zhao²,

Yuan³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Research on gene regulation has been made possible with the help of RNA sequencing applications such as RNA-Seq technology for high-throughput sequencing platforms. Recent studies have explored the transcriptomes from different tissues of domestic animals using RNA-Seq technology, but little research has been done to study the transcriptomes of breeds of sheep having different adipose tissue deposition mechanisms, such as Mongolian and Lanzhou fattailed sheep. In this study, Mongolian and Lanzhou fat-tailed sheep were selected as experimental breeds, and six libraries (three libraries per breed) were constructed. A total of 286 Mb of high-quality reads was obtained, and three-quarters of the reads were mapped to the reference genome per library. In addition, there were 16,257, 16,186, 16,254, 16,827, 16,437, and 15,761 known reference genes in the six constructed libraries (LCL1, LCL2, LCL3, MCL1, MCL2, and MCL3, respectively). Seven genes were differentially expressed: four were upregulated and three were downregulated in liver tissue between the MCL and LCL groups; 65,303, 65,442, 63,426, 76,267, 69,853, and 57,439 potential cSNPs were detected in the six libraries, respectively, with the G/R substitution occurring most commonly. There were 24,239, 22,283, 22,457, 26,635, 27,093, and 18,700 alternate splicing (AS) events in the six libraries. Intron retention was the most common AS event, followed by alternative 3' splice sites. These results indicate that there are many differences in the liver transcriptomes of Mongolian and Lanzhou fat-tailed sheep breeds. Such results may provide fundamental information for further research on defining the sheep genome.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

Xu¹,

Zhao²,

Yuan³

et al. 2016

Genet. Mol. Res.

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“…The cell density matched that used by a recently published Tetrahymena RNA-seq study (Xiong et al 2012). To obtain starved samples, the cells were centrifuged at 1100g for 2 min, resuspended in 1.75 volumes of 10 mM Tris pH 7.5, and incubated at 25°C without shaking for 15 h.…”

Section: Cell Culturementioning

confidence: 99%

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

et al. 2015

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A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream from transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes and affects codon usage and amino acid composition in genes. Given that the AT-rich Tetrahymena genome is intrinsically unfavorable for nucleosome formation, we propose that these “seed” nucleosomes—together with trans-acting factors—may facilitate the establishment of nucleosome arrays within genes in vivo, while minimizing changes to the underlying coding sequences.

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“…30 RNA-seq analysis At 1, 2, and 3 h post mixing, total RNA was extracted from WT and cdk3D pairs using the RNeasy Protect Cell Mini Kit (Qiagen), as described (TetraFGD: http://tfgd.ihb.ac.cn/index/ smphelp). 44 mRNA with Poly-A tail were then enriched by the Sera-Mag magnetic oligo (dT) beads (GE). Illumina sequencing libraries were then constructed based on manufacturer's recommendations.…”

Section: Detection Of Dsbs By Pulsed-field Gel Electrophoresismentioning

confidence: 99%

Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in Tetrahymena thermophila

et al. 2016

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Meiosis is an important process in sexual reproduction. Meiosis initiation has been found to be highly diverse among species. In yeast, it has been established that cyclin-dependent kinases (Cdks) and cyclins are essential components in the meiosis initiation pathway. In this study, we identified 4 Cdks in the model ciliate, Tetrahymena thermophila, and we found one of them, Cdk3, which is specifically expressed during early conjugation, to be essential for meiosis initiation. Cdk3 deletion led to arrest at the pair formation stage of conjugation. We then confirmed that Cdk3 acts upstream of double-strand break (DSB) formation. Moreover, we detected that Cdk3 is necessary for the expression of many genes involved in early meiotic events. Through proteomic quantification of phosphorylation, co-expression analysis and RNA-Seq analyses, we identified a conjugation-specific cyclin, Cyc2, which most likely partners with Cdk3 to initiate meiosis.

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Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing

Cited by 118 publications

References 66 publications

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in Tetrahymena thermophila

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