Identification and comparative analysis of piRNAs in ovary and testis of Nile tilapia (Oreochromis niloticus)
Identification and comparative analysis of piRNAs in ovary and testis of Nile tilapia (Oreochromis niloticus)
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尼罗罗非鱼(Oreochromis niloticus)卵巢和睾丸piRNA的鉴定及比较分析
DOI：
10.1007/s13258-016-0400-z
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发表时间：
2016-03
期刊：
影响因子：
2.1
通讯作者：
Yu Fan
中科院分区：
文献类型：
--
作者：
Zhou Yi;Zhong Huan;Xiao Jun;Yan Jinpeng;Luo Yongju;Gan Xi;Yu Fan
研究表明，皮尔纳是动物生殖细胞中最大的一类非编码小RNA，在转座子调控和转录活性中起着关键作用。本研究从尼罗罗非鱼卵巢和精巢两个小RNA文库中提取piRNA，并对其进行鉴定和分析。通过基于长度和k-mer的小RNA预测算法，分别确认279，059和583，230个小RNA读数为来自卵巢和睾丸的皮尔纳。鉴定的piRNA显示进化上保守的特征，例如5′端的尿苷偏好。分别将来自卵巢和睾丸的142，961和296，775个piRNA定位到罗非鱼基因组的草图组装中。卵巢和睾丸piRNA均富集自连锁（LG）6和LG 7。同时，正链和负链的均匀分布提示了乒乓途径（正链和负链的双置换反应）假说。这些piRNA来自上游-2 kb和下游+2 kb以及对转录活性具有调节功能的基因区域。在基因区域中，大量的piRNA来源于5′UTR、3′UTR和CDS。此外，我们表征了卵巢和睾丸之间差异表达的piRNA。总共有1979和2453个piRNA在卵巢中的表达分别显著高于和低于睾丸中的表达。其中，上调和下调最集中的piRNA均来自不同转录本的丝/苏蛋白激酶PIM基因。这些发现将有助于研究piRNA在硬骨鱼性腺发育过程中对基因的调控。
It has been shown that piRNA is the largest class of small non-coding RNA in germline cells of animals which plays key roles in transposons regulation and transcriptional activities. In the present study, piRNAs from two small RNA libraries including ovary and testis of Nile tilapia were identified and characterized. By length and k-mer based small RNA prediction algorithm, 279,059 and 583,230 small RNA reads were confirmed as piRNA from ovary and testis, respectively. The identified piRNAs showed evolutionarily conserved characterization, such as uridine bias in the 5′ ends. The 142,961 and 296,775 piRNAs from ovary and testis were mapped to the draft assembly of the tilapia genome, respectively. Both ovary and testis piRNAs were enriched from linkage (LG)6 and LG7. Meanwhile, the even distribution of +strand and −strand suggested the Ping–pong pathway (a double-displacement reaction of +strand and −strand) hypothesis. These piRNAs were derived from the upstream −2 kb and downstream +2 kb as well as gene regions which suggested a regulatory function on transcription activities. In gene regions, abundant piRNAs were derived from 5′UTR, 3′UTR and CDS. Furthermore, we characterized the differentially expressed piRNAs between ovary and testis. In total, 1979 and 2453 piRNAs were significantly higher and lower expressed in ovary compared to that in testis, respectively. Thereinto, the most concentrated up-regulate and down-regulate piRNAs were both from serine/threonine–protein kinase PIM genes of different transcripts. These findings will be helpful to facilitate studies on the piRNAs regulation on genes during gonad development of teleosts.
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影响因子：
2.7
作者：
Yi Zhou;Fenghua Wang;Shaojun Liu;H. Zhong;Zhen Liu;M. Tao;Chun Zhang;Yun Liu
通讯作者：
Yi Zhou;Fenghua Wang;Shaojun Liu;H. Zhong;Zhen Liu;M. Tao;Chun Zhang;Yun Liu
预测 piRNA 和表征蝗虫 piRNA 的 k-mer 方案
DOI：
10.1093/bioinformatics/btr016
发表时间：
2011-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Zhang Y;Wang X;Kang L
通讯作者：
Kang L
影响因子：
10.5
作者：
Watanabe, Toshiaki;Takeda, Atsushi;Imai, Hiroshi
通讯作者：
Imai, Hiroshi
DOI：
10.1016/s1095-6433(00)80018-5
发表时间：
2000-07
影响因子：
2.3
作者：
J. Baroiller;H. D'cotta
通讯作者：
J. Baroiller;H. D'cotta
DOI：
10.1016/s1532-0456(01)00267-8
发表时间：
2001-12-01
影响因子：
3.9
作者：
Baroiller, JF;D'Cotta, H
通讯作者：
D'Cotta, H