Unique and common OsCLSY3 and OsCLSY4 loci.

In plants, RNA-directed DNA methylation (RdDM) sequence-specifically targets transposable elements (TEs) and repeats, often in a tissue-specific manner. In triploid endosperm tissue, RdDM also acts as a parental dosage regulator, mediating spatio-temporal expression of genes required for its development. It is unclear how RdDM is initiated and established in endosperm. Rice endosperm-specific imprinted chromatin remodeler OsCLSY3 recruits RNA polymerase IV to specific genomic sites for silencing and optimal gene expression. Here we show that, in addition to OsCLSY3, ubiquitously expressed OsCLSY4 is also crucial for proper reproductive growth and endosperm development. Loss of function of OsCLSY4 led to reproductive and nutrient-filling defects in endosperm. Using genetic and molecular analysis, we show that both OsCLSY3 and OsCLSY4 play overlapping and unique silencing roles in rice endosperm, by targeting specific and shared genomic regions such as TEs, repeats and genic regions. These results indicate the importance of optimal expression of two OsCLSYs in regulating endosperm-specific gene expression, genomic imprinting and suppression of specific TEs. Results presented here provide new insights into the functions of rice CLSYs as upstream RdDM regulators in rice endosperm development, and we propose that functions of their homologs might be conserved across monocots.

在植物中，RNA指导的DNA甲基化（RNA-directed DNA methylation，RdDM）能够以序列特异性靶向转座因子（transposable element，TE）和重复序列，且通常具有组织特异性。在三倍体胚乳组织中，RdDM还可作为亲本剂量调控因子，介导其发育所需基因的时空表达。目前尚不清楚RdDM在胚乳中是如何起始并建立的。
水稻胚乳特异性印记染色质重塑因子OsCLSY3可将RNA聚合酶IV招募至特定基因组位点，以实现基因沉默并维持适宜基因表达。本研究表明，除OsCLSY3外，广泛表达的OsCLSY4对水稻正常生殖生长与胚乳发育同样至关重要。OsCLSY4功能缺失会导致生殖缺陷及胚乳养分填充异常。
通过遗传与分子分析，我们发现OsCLSY3与OsCLSY4在水稻胚乳中既存在功能重叠，又具备独特的沉默调控作用，二者分别靶向特定及共享的基因组区域，例如转座因子、重复序列及基因区域。
上述结果表明，两个OsCLSY基因的适宜表达对于调控胚乳特异性基因表达、基因组印记以及特定转座因子的抑制具有重要意义。本研究结果为水稻CLSY家族作为RdDM上游调控因子在水稻胚乳发育中的功能提供了新见解，并提出其同源基因的功能可能在单子叶植物中具有保守性。