Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize
Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize
ABSTRACT MicroRNAs (miRNAs) are endogenous 20-to 24-nucleotide (nt) noncoding RNAs that play important regulatory roles in many biological processes in eukaryotes. miRNAs modulate the expression of target genes at the post-transcriptional level by transcript cleavage or translational inhibition. Identification of miRNA target genes have been extensively investigated in Arabidopsis and rice, but an in-depth global analysis of miRNA-mediated target regulation is still lacking in maize. Here, we report a transcriptome-wide identification of miRNA targets by analyzing Parallel Analysis of RNA Ends (PARE) datasets derived from nine different tissues at five developmental stages of the maize (Zea mays L.) B73 cultivar. 246 targets corresponding to 60 miRNAs from 25 families were identified, including transcription factors and other genes. In addition, PARE analysis revealed that miRNAs guide specific target transcript cleavage in a tissue-preferential manner. Interestingly, primary transcripts of MIR159c and MIR169e were found to be cleaved by mature miR159 and miR169, respectively, indicating a positive-feedback regulatory mechanism in miRNA biogenesis. Moreover, several new miRNA-target gene pairs involved in seed germination were identified and experimentally validated. Our PARE analyses generated a wide and detailed miRNA-target interaction atlas, which provides a valuable resource for investigating the roles of miRNAs and their targets in maize.
Gao Lei、Mo Beixin、He Juan、Xu Chi、Liu Lin、Chen Xuemei、You Chenjiang
Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen UniversityGuangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen UniversityGuangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University||Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of ChinaGuangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen UniversityGuangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen UniversityDepartment of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of CaliforniaDepartment of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California||State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University
分子生物学植物学遗传学
Gao Lei,Mo Beixin,He Juan,Xu Chi,Liu Lin,Chen Xuemei,You Chenjiang.Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize[EB/OL].(2025-03-28)[2025-05-17].https://www.biorxiv.org/content/10.1101/2022.06.02.494554.点此复制
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