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. 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，在介导植物从头DNA甲基化的RNA指导的DNA甲基化（RNA-directed DNA methylation, RdDM）途径中发挥功能。我们对花序中的24 nt siRNA进行了分析，发现20200个24 nt siRNA簇中，占比0.81%的高表达簇贡献了花序中超过68%的24 nt siRNA测序读段。我们将这类高表达的siRNA命名为亿万富翁siRNA（bill-siRNAs），低表达的siRNA则命名为贫民siRNA（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，来自配子的bill-siRNAs完全消失。而由受精中央细胞发育形成的胚乳，同样未携带来自配子的bill-siRNAs，但存在不同区域新合成的高表达siRNA。与之相对，种皮中保留了来自子房的bill-siRNAs。各类组织和细胞中bill-siRNAs的生物合成依赖于OsRDR2（RNA依赖的RNA聚合酶2）与Pol IV（DNA依赖的RNA聚合酶IV）。与pau-siRNAs类似，bill-siRNAs的首个碱基偏好腺嘌呤，且能够在多种组织中指导DNA甲基化。转录组测序（Transcriptome sequencing）