Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1.
MicroRNAs (miRNAs) originate from primary transcripts (pri-miRNAs) with characteristic stem-loop structures, and their accurate processing is required for the production of functional miRNAs. Here, using the pri-miR-166 family in Arabidopsis thaliana as a paradigm, we report the crucial role of pri-miRNA terminal loops in miRNA biogenesis. We found that multibranched terminal loops in pri-miR-166s substantially suppress miR-166 expression in vivo. Unlike canonical processing of pri-miRNAs, terminal loop-branched pri-miRNAs can be processed by Dicer-like 1 (DCL1) complexes bidirectionally from base to loop and from loop to base, resulting in productive and abortive processing of miRNAs, respectively. In both cases, DCL1 complexes canonically cut pri-miRNAs at a distance of 16-17 bp from a reference single-stranded loop region. DCL1 also adjusts processing sites toward an internal loop through its helicase domain. These results provide new insight into the poorly understood processing mechanism of pri-miRNAs with complex secondary structures.
1] Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA. [2] Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, USA. [3] College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
Hongliang
H
Zhu
Yuyi
Y
Zhou
Claudia
C
Castillo-González
Amber
A
Lu
Chunxiao
C
Ge
Ying-Tao
YT
Zhao
Liusheng
L
Duan
Zhaohu
Z
Li
Michael J
MJ
Axtell
Xiu-Jie
XJ
Wang
Xiuren
X
Zhang
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D018797:Cell Cycle Proteins / Q000737:chemistry / Q000378:metabolism*; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D030821:Plants, Genetically Modified; D017434:Protein Structure, Tertiary; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D043244:Ribonuclease III / Q000737:chemistry / Q000378:metabolism*
D029681:Arabidopsis Proteins; D018797:Cell Cycle Proteins; C583141:MIRN165 microRNA, Arabidopsis; C580969:MIRN166 microRNA, Arabidopsis; D035683:MicroRNAs; D018749:RNA, Plant; C402383:DCL1 protein, Arabidopsis; D043244:Ribonuclease III