The Rise and Fall of Billionaire siRNAs during Reproductive Development in Rice

RNA polymerase IV-dependent siRNAs, usually 24 nt in length, function in the RNAdirected DNA methylation that is responsible for de novo methylation in plants. We analyzed 24 nt siRNAs in inflorescences and found that among the 20,200 24 nt siRNA clusters, the top 0.81% highly expressed clusters accounted for more than 68% of the 24 nt siRNA reads in inflorescences. We named the highly expressed siRNAs as billionaire siRNAs (bill-siRNAs) and the less-expressed siRNAs as pauper siRNAs (pau-siRNAs). The bill-siRNAs in inflorescences are mainly derived from the ovary. Female gametes produced more bill-siRNAs than male gametes. In embryos and seedlings developed from fertilized egg cells, the bill-siRNAs from gametes disappeared. The endosperm, which develops from the fertilized central cell, also contained no bill-siRNAs from gametes but did contain newly and highly expressed siRNAs produced in different regions. In contrast, bill-siRNAs from the ovaries were maintained in the seed coat. The biosynthesis of bill-siRNAs in various tissues and cells is dependent on OsRDR2 (RNA-dependent RNA polymerase 2) and Pol IV (DNA-dependent RNA polymerase IV). Similar to the pau-siRNAs, the first base of bill-siRNAs is enriched at adenine, and bill-siRNAs can direct DNA methylation in various tissues. Overall design: Transcriptome sequencing

RNA聚合酶IV依赖的小干扰RNA（small interfering RNA，siRNA）通常长度为24 nt，在植物中参与介导从头甲基化的RNA指导的DNA甲基化（RNA-directed DNA methylation，RdDM）过程。本研究针对花序中的24 nt siRNA展开分析，发现20200个24 nt siRNA簇中，占比仅0.81%的高表达簇，其所对应的测序读段（reads）占花序中总24 nt siRNA测序读段的68%以上。我们将此类高表达的siRNA命名为亿万富翁siRNA（billionaire siRNAs，简称bill-siRNAs），低表达的siRNA则称为贫民siRNA（pauper siRNAs，简称pau-siRNAs）。花序中的bill-siRNAs主要源自子房；雌配子产生的bill-siRNAs数量多于雄配子。在由受精卵发育而来的胚胎与幼苗中，源自配子的bill-siRNAs完全消失。由受精中央细胞发育形成的胚乳，同样不含源自配子的bill-siRNAs，但存在不同区域中新产生的高表达siRNA。与之相反，子房来源的bill-siRNAs在种皮中得以保留。各类组织与细胞中bill-siRNAs的生物合成依赖于OsRDR2（RNA依赖的RNA聚合酶2，RNA-dependent RNA polymerase 2）与Pol IV（DNA依赖的RNA聚合酶IV，DNA-dependent RNA polymerase IV）。与pau-siRNAs类似，bill-siRNAs的首个碱基富含腺嘌呤，且可在多种组织中指导DNA甲基化。整体实验设计：转录组测序（Transcriptome sequencing）