Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.).
Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.).
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DOI：
10.1186/gb-2009-10-11-r122
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发表时间：
2009
期刊：
影响因子：
12.3
通讯作者：
Chen ZJ
中科院分区：
文献类型：
--
作者：
Pang M;Woodward AW;Agarwal V;Guan X;Ha M;Ramachandran V;Chen X;Triplett BA;Stelly DM;Chen ZJ
在异源四倍体棉花胚珠和纤维发育过程中，小rna的表达发生了快速而动态的变化。棉纤维的发育在单一细胞类型中经历了从纤维起始、伸长、初级和次级壁生物合成到纤维成熟的快速动态变化。先前的研究表明，棉花基因编码MYB转录因子和植物激素应答因子在胚珠和纤维发育早期被诱导。这些因子中的许多都是通过mRNA降解或翻译抑制介导靶基因调控的microRNAs （miRNAs）的靶标。在这里，我们测序和分析了来自棉花纤维和非纤维组织的400多万个小rna。相对于叶片，24核苷酸小干扰rna （sirna）在胚珠和结纤维胚珠中含量更丰富，富集程度更高。在至少一种棉花组织中共鉴定出31个miRNA家族，其中包括27个保守miRNA家族，4个新miRNA家族和一个候选新miRNA。在鉴定的代表19个独特miRNA家族的32个miRNA前体中，有7个是之前报道的，本研究中发现了25个新的miRNA前体。测序、miRNA微阵列和小RNA印迹分析显示，在胚珠和纤维发育过程中，miRNA（包括新型miRNA）有抑制的趋势，这与几种靶基因的上调有关。此外，从棉花组织（包括胚珠和纤维）中表达的序列标签中预测了223个棉花mirna靶标。检测的棉花mirna在胚珠和纤维中推测的棉花靶点的预测位点上触发了裂解。在胚珠和纤维中sirna的富集表明在纤维发育过程中活跃的小RNA代谢和染色质修饰，而在纤维中miRNA的普遍抑制与编码转录和植物激素应答因子的十几个经过验证的miRNA靶标上调相关，包括在棉纤维中发现的高表达基因。sirna和mirna的快速动态变化可能与异源四倍体棉花胚珠和纤维的发育有关。
Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton. Cotton fiber development undergoes rapid and dynamic changes in a single cell type, from fiber initiation, elongation, primary and secondary wall biosynthesis, to fiber maturation. Previous studies showed that cotton genes encoding putative MYB transcription factors and phytohormone responsive factors were induced during early stages of ovule and fiber development. Many of these factors are targets of microRNAs (miRNAs) that mediate target gene regulation by mRNA degradation or translational repression. Here we sequenced and analyzed over 4 million small RNAs derived from fiber and non-fiber tissues in cotton. The 24-nucleotide small interfering RNAs (siRNAs) were more abundant and highly enriched in ovules and fiber-bearing ovules relative to leaves. A total of 31 miRNA families, including 27 conserved, 4 novel miRNA families and a candidate-novel miRNA, were identified in at least one of the cotton tissues examined. Among 32 miRNA precursors representing 19 unique miRNA families identified, 7 were previously reported, and 25 new miRNA precursors were found in this study. Sequencing, miRNA microarray, and small RNA blot analyses showed a trend of repression of miRNAs, including novel miRNAs, during ovule and fiber development, which correlated with upregulation of several target genes tested. Moreover, 223 targets of cotton miRNAs were predicted from the expressed sequence tags derived from cotton tissues, including ovules and fibers. The cotton miRNAs examined triggered cleavage in the predicted sites of the putative cotton targets in ovules and fibers. Enrichment of siRNAs in ovules and fibers suggests active small RNA metabolism and chromatin modifications during fiber development, whereas general repression of miRNAs in fibers correlates with upregulation of a dozen validated miRNA targets encoding transcription and phytohormone response factors, including the genes found to be highly expressed in cotton fibers. Rapid and dynamic changes in siRNAs and miRNAs may contribute to ovule and fiber development in allotetraploid cotton.
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影响因子：
6.5
作者：
Barozai, Muhammad Younas Khan;Irfan, Muhammad;Riazuddin, Sheikh
通讯作者：
Riazuddin, Sheikh
Mirbase：MicroRNA基因组学的工具。
影响因子：
14.9
作者：
Griffiths-Jones, Sam;Saini, Harpreet Kaur;van Dongen, Stijn;Enright, Anton J.
通讯作者：
Enright, Anton J.
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
9.2
作者：
Fahlgren, Noah;Montgomery, Talowa A.;Carrington, James C.
通讯作者：
Carrington, James C.
影响因子：
3.3
作者：
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通讯作者：
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