A transcriptome for the study of early processes of retinal regeneration in the adult newt, Cynops pyrrhogaster.
A transcriptome for the study of early processes of retinal regeneration in the adult newt, Cynops pyrrhogaster.
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DOI：
10.1371/journal.pone.0109831
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Chiba C
中科院分区：
文献类型：
--
作者：
Nakamura K;Islam MR;Takayanagi M;Yasumuro H;Inami W;Kunahong A;Casco-Robles RM;Toyama F;Chiba C
成年蝾螈的视网膜再生是一个有用的系统，可以揭示该动物身体部位再生的基本机制，并找到治疗增殖性玻璃体视网膜病变等视网膜疾病的线索。在这里，为了促进视网膜再生早期过程的研究，我们提供了日本火腹蝾螈（Cynopspyrrogaster）的从头组装转录组和推断的蛋白质组，这是从手术切除晶状体和神经视网膜后第0-14天的眼球样本中获得的。该转录组（237,120 个计算机转录本）包含迄今为止在蝾螈（C.pyrrogaster、Pleurodeles waltl 和 Notophasemus viridescent）中报道的大部分 cDNA/EST 信息。另一方面，最近报道的 N. viridescent 的从头组装转录组仅覆盖了该转录组的 16-31%，这表明该转录组的大多数成分是 C.pyrrogaster 再生眼组织所特有的。该转录组共有 87,102 个计算机转录本进行了功能注释。编码序列预测与功能注释相结合表明，迄今为止，公共数据库中记录的 76,968 个计算机转录本编码蛋白质/肽，而 17,316 个可能是独特的。 qPCR 和桑格测序表明，该转录组包含许多与视网膜再生早期阶段的细胞重编程、细胞周期重新进入/增殖和组织模式相关调节的基因相关的信息。这些数据还为进一步研究解决视网膜再生的细胞机制和分子网络以及视网膜再生和疾病之间的差异提供了重要的见解。该转录组可用于随后的全面基因筛选步骤，提供候选基因（无论是注释的还是独特的），以揭示视网膜再生早期过程的基本机制。
Retinal regeneration in the adult newt is a useful system to uncover essential mechanisms underlying the regeneration of body parts of this animal as well as to find clues to treat retinal disorders such as proliferative vitreoretinopathy. Here, to facilitate the study of early processes of retinal regeneration, we provide a de novo assembly transcriptome and inferred proteome of the Japanese fire bellied newt (Cynops pyrrhogaster), which was obtained from eyeball samples of day 0–14 after surgical removal of the lens and neural retina. This transcriptome (237,120 in silico transcripts) contains most information of cDNAs/ESTs which has been reported in newts (C. pyrrhogaster, Pleurodeles waltl and Notophthalmus viridescence) thus far. On the other hand, de novo assembly transcriptomes reported lately for N. viridescence only covered 16–31% of this transcriptome, suggesting that most constituents of this transcriptome are specific to the regenerating eye tissues of C. pyrrhogaster. A total of 87,102 in silico transcripts of this transcriptome were functionally annotated. Coding sequence prediction in combination with functional annotation revealed that 76,968 in silico transcripts encode protein/peptides recorded in public databases so far, whereas 17,316 might be unique. qPCR and Sanger sequencing demonstrated that this transcriptome contains much information pertaining to genes that are regulated in association with cell reprogramming, cell-cycle re-entry/proliferation, and tissue patterning in an early phase of retinal regeneration. This data also provides important insight for further investigations addressing cellular mechanisms and molecular networks underlying retinal regeneration as well as differences between retinal regeneration and disorders. This transcriptome can be applied to ensuing comprehensive gene screening steps, providing candidate genes, regardless of whether annotated or unique, to uncover essential mechanisms underlying early processes of retinal regeneration.
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DOI：
10.1093/bioinformatics/bts094
发表时间：
2012-04-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Schulz MH;Zerbino DR;Vingron M;Birney E
通讯作者：
Birney E
影响因子：
14.8
作者：
Casco-Robles, Martin Miguel;Yamada, Shouta;Chiba, Chikafumi
通讯作者：
Chiba, Chikafumi
影响因子：
4.5
作者：
Bharti K;Gasper M;Ou J;Brucato M;Clore-Gronenborn K;Pickel J;Arnheiter H
通讯作者：
Arnheiter H
影响因子：
7
作者：
Simpson, Jared T.;Wong, Kim;Birol, Inanc
通讯作者：
Birol, Inanc
DOI：
10.1111/j.1600-0749.2007.00407.x
发表时间：
2007-10-01
期刊：
PIGMENT CELL RESEARCH
影响因子：
--
作者：
Susaki, Kanako;Chiba, Chikafumi
通讯作者：
Chiba, Chikafumi