Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing.
Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing.
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通过小RNA和降解组测序相结合鉴定玉米穗发育过程中的miRNA及其靶基因
DOI：
10.1186/1471-2164-15-25
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发表时间：
2014-01-14
期刊：
影响因子：
4.4
通讯作者：
Pan G
中科院分区：
文献类型：
--
作者：
Liu H;Qin C;Chen Z;Zuo T;Yang X;Zhou H;Xu M;Cao S;Shen Y;Lin H;He X;Zhang Y;Li L;Ding H;Lübberstedt T;Zhang Z;Pan G
在植物中，microRNAs（miRNAs）是一种内源性的~22 nt的RNA，在植物生物学的许多方面发挥着重要的调节作用，包括代谢、激素反应、转座因子的表观遗传控制和胁迫反应。已经在模式植物如水稻和拟南芥中进行了广泛的miRNA研究。在玉米中，大多数miRNAs及其靶基因通过明显不同的处理进行分析和鉴定，例如对低硝酸盐、盐和干旱胁迫的响应。然而，对参与玉米穗发育的miRNAs知之甚少。本研究的目的是通过结合小RNA和degradome测序技术，在4个花序发育阶段鉴定保守和新的miRNAs及其靶基因。我们使用深度测序，miRNA微阵列分析和计算方法来识别，描述和描述四个穗发育阶段的保守和非保守miRNA，从而鉴定出22个保守和21个玉米特异性miRNA家族及其相应的miRNA *。比较这些发育阶段的miRNA表达，发现18个差异表达的miRNA家族。最后，通过对miRNA切割的mRNA进行基因组规模的高通量测序，鉴定了由102种小RNA（包括98种miRNA和4种ta-siRNA）靶向的总共141个基因（251个转录本）。此外，差异表达的miRNA介导的途径，调节耳朵的发育进行了讨论。本研究在玉米中确认了22个保守的miRNA家族，并发现了26个新的miRNA。此外，我们确定了141个已知和新的miRNAs和ta-siRNAs的靶基因。其中，72个基因（117个转录本）的62个差异表达的miRNA的目标可能归因于玉米穗的发育。鉴定和鉴定这些重要的玉米调控基因可以提高我们对控制穗发育的分子机制的理解。
In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages. We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed. This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.
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影响因子：
14.9
作者：
Chen C;Ridzon DA;Broomer AJ;Zhou Z;Lee DH;Nguyen JT;Barbisin M;Xu NL;Mahuvakar VR;Andersen MR;Lao KQ;Livak KJ;Guegler KJ
通讯作者：
Guegler KJ
影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
玉米种子萌发过程杂种优势的 MicroRNA 转录组分析
影响因子：
3.7
作者：
Ding D;Wang Y;Han M;Fu Z;Li W;Liu Z;Hu Y;Tang J
通讯作者：
Tang J
影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
9.2
作者：
Addo-Quaye, Charles;Eshoo, Tifani W.;Axtell, Michael J.
通讯作者：
Axtell, Michael J.