RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation.
RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation.
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DOI：
10.1186/s12864-016-2396-9
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发表时间：
2016-01-25
期刊：
影响因子：
4.4
通讯作者：
Iguchi T
中科院分区：
文献类型：
--
作者：
Yatsu R;Miyagawa S;Kohno S;Parrott BB;Yamaguchi K;Ogino Y;Miyakawa H;Lowers RH;Shigenobu S;Guillette LJ Jr;Iguchi T
美洲短吻鳄（Alligator mississippiensis）显示温度依赖性性别决定（TSD），其中胚胎发育期间的孵化温度决定个体的性命运。然而，这一过程的分子机制仍然是一个谜，包括初始环境温度对TSD期间发生的综合性腺基因表达模式的影响。我们在鳄鱼TSD转录组的表征，使我们能够确定新的候选基因参与TSD启动。高通量RNA测序（RNA-seq）是在从A.在性发育过程中，在雄性和雌性生产温度（分别为33.5 °C和30 °C）下以时间序列孵育的密西西比河胚胎。RNA-seq产生了3.752亿个双端读段，这些读段被映射和组装，并用于表征差异基因表达。转录组的变化发生作为一个功能的发展和性别分化进行了广泛的分析。结果表明，在雄性生殖温度下，Wnt信号转导因子WNT 11、组蛋白去甲基化酶KDM 6 B、转录因子C/EBPA等基因在雄性生殖温度下的表达差异显著。此外，发育和性别依赖的差异基因表达的比较分析显示，230个候选基因参与鳄鱼的性别决定和分化，和早期的细节，可疑的男性命运的承诺进行了分析。我们还发现了未表征的ncRNA和其他新元件的性二态表达，例如HEMGN和ARX的独特表达模式。在我们的分析中鉴定的25个差异表达基因是推定的转录调节因子，其中包括MYBL 2、MYCL和HOXC 10，此外还有传统的性别分化基因如SOX 9和FOXL 2。构建了推测的基因调控网络，并预测了基因与基因、温度与基因的相互作用。在性别决定过程中的性腺全球基因表达动力学已被广泛剖析的第一次在TSD物种。这些发现提供了深入了解TSD背后的遗传框架，并扩大了我们目前对脊椎动物性别决定过程中发育命运途径的理解。本文的在线版本（doi：10.1186/s12864-016-2396-9）包含补充材料，可供授权用户使用。
The American alligator (Alligator mississippiensis) displays temperature-dependent sex determination (TSD), in which incubation temperature during embryonic development determines the sexual fate of the individual. However, the molecular mechanisms governing this process remain a mystery, including the influence of initial environmental temperature on the comprehensive gonadal gene expression patterns occurring during TSD. Our characterization of transcriptomes during alligator TSD allowed us to identify novel candidate genes involved in TSD initiation. High-throughput RNA sequencing (RNA-seq) was performed on gonads collected from A. mississippiensis embryos incubated at both a male and a female producing temperature (33.5 °C and 30 °C, respectively) in a time series during sexual development. RNA-seq yielded 375.2 million paired-end reads, which were mapped and assembled, and used to characterize differential gene expression. Changes in the transcriptome occurring as a function of both development and sexual differentiation were extensively profiled. Forty-one differentially expressed genes were detected in response to incubation at male producing temperature, and included genes such as Wnt signaling factor WNT11, histone demethylase KDM6B, and transcription factor C/EBPA. Furthermore, comparative analysis of development- and sex-dependent differential gene expression revealed 230 candidate genes involved in alligator sex determination and differentiation, and early details of the suspected male-fate commitment were profiled. We also discovered sexually dimorphic expression of uncharacterized ncRNAs and other novel elements, such as unique expression patterns of HEMGN and ARX. Twenty-five of the differentially expressed genes identified in our analysis were putative transcriptional regulators, among which were MYBL2, MYCL, and HOXC10, in addition to conventional sex differentiation genes such as SOX9, and FOXL2. Inferred gene regulatory network was constructed, and the gene-gene and temperature-gene interactions were predicted. Gonadal global gene expression kinetics during sex determination has been extensively profiled for the first time in a TSD species. These findings provide insights into the genetic framework underlying TSD, and expand our current understanding of the developmental fate pathways during vertebrate sex determination. The online version of this article (doi:10.1186/s12864-016-2396-9) contains supplementary material, which is available to authorized users.