Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

Liya Wei; Lianfeng Gu; Xianwei SongXiekui CuiZhike LuMing ZhouLulu WangFengyi HuJixian ZhaiBlake C. MeyersXiaofeng Cao

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Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

机译：Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

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Transposable elements (TEs) and repetitive sequences make up over 35 of the rice (Oryza sativa) genome. The host regulates the activity of different TEs by different epigenetic mechanisms, including DNA methylation, histone H3K9 methylation, and histone H3K4 demethylation. TEs can also affect the expression of host genes. For example, miniature inverted repeat TEs (MITEs), dispersed high copy-number DNA TEs, can influence the expression of nearby genes. In plants, 24-nt small interfering RNAs (siRNAs) are mainly derived from repeats and TEs. However, the extent to which TEs, particularly MITEs associated with 24-nt siRNAs, affect gene expression remains elusive. Here, we show that the rice Dicer-like 3 homolog OsDCL3a is primarily responsible for 24-nt siRNA processing. Impairing OsDCL3a expression by RNA interference caused phenotypes affecting important agricultural traits; these phenotypes include dwarfism, larger flag leaf angle, and fewer secondary branches. We used small RNA deep sequencing to identify 535,054 24-nt siRNA clusters. Of these clusters, ～82 were OsDCL3a-dependent and showed significant enrichment of MITEs. Reduction of OsDCL3a function reduced the 24-nt siRNAs predominantly from MITEs and elevated expression of nearby genes. OsDCL3a directly targets genes involved in gibberellin and brassinosteroid homeostasis; OsDCL3a deficiency may affect these genes, thus causing the phenotypes of dwarfism and enlarged flag leaf angle. Our work identifies OsDCL3a-dependent 24-nt siRNAs derived from MITEs as broadly functioning regulators for fine-tuning gene expression, which may reflect a conserved epigenetic mechanism in higher plants with genomes rich in dispersed repeats or TEs.

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《Proceedings of the National Academy of Sciences of the United States of America》 |2014年第10期|3877-3882|共6页
作者
Liya Wei; Lianfeng Gu; Xianwei SongXiekui CuiZhike LuMing ZhouLulu WangFengyi HuJixian ZhaiBlake C. MeyersXiaofeng Cao;
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作者单位

Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711;

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;

Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;

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收录信息美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
原文格式 PDF
正文语种英语
中图分类自然科学总论;
关键词
transposon; plant architecture; plant hormone;

Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

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