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Series GSE149800 Query DataSets for GSE149800
Status Public on Sep 24, 2020
Title 21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells
Organism Oryza sativa
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary In grasses, phased small interfering RNAs (phasiRNAs), 21- or 24-nucleotide (nt) in length, are predominantly expressed in anthers and regulate male fertility. However, their targets and mode of action on the targets remain unknown. Here we profile phasiRNA expression in premeiotic and meiotic spikelets as well as in purified male meiocytes at early prophase I, tetrads and microspores in rice. We show that 21-nt phasiRNAs are most abundant in meiocytes at early prophase I while 24-nt phasiRNAs are more abundant in tetrads and microspores. By performing highly sensitive degradome sequencing, we find that 21-nt phasiRNAs direct target mRNA cleavage in male germ cells, especially in meiocytes at early prophase I. The target genes in early prophase I meiocytes show an enrichment for carbohydrate biosynthetic and metabolic pathways. Our study provides strong evidence that 21-nt phasiRNAs act in a target-cleavage mode and may facilitate the progression of meiosis by fine-tuning carbohydrate biosynthesis and metabolism in male germ cells.
 
Overall design To profile phasiRNAs and explore the potential targets of phasiRNAs in male germ cells at different stages, we collected highly pure meiocytes at early prophase I tetrads, and microspores, respectively, by micromanipulation. Pre-meiotic spikelets, in which anthers are at stage 2 to stage 3 , meiotic spikelets in which germ cells are mostly at the early prophase of meiosis I, and embryos from seeds germinated 24h at 28℃, were also collected as controls. We then using these samples performed low-input sRNA-seq, sRNA-seq and high sensitive degradome-seq in three biological replicates.
 
Contributor(s) Jiang P, Lian B, Liu C, Fu Z, Shen Y, Cheng Z, Qi Y
Citation(s) 33060587
Submission date May 04, 2020
Last update date Oct 27, 2020
Contact name Yijun Qi
E-mail(s) qiyijun@mail.tsinghua.edu.cn
Organization name Tsinghua University
Department School of Life Sciences
Street address NO.1 Qinghuayuan
City Beiing
ZIP/Postal code 100084
Country China
 
Platforms (1)
GPL24468 HiSeq X Ten (Oryza sativa)
Samples (65)
GSM4512858 embryo_sRNA_rep1
GSM4512859 embryo_sRNA_rep2
GSM4512860 embryo_sRNA_rep3
Relations
BioProject PRJNA630172
SRA SRP259996

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE149800_RAW.tar 419.1 Mb (http)(custom) TAR (of TXT)
GSE149800_genes.fpkm_table.xlsx.gz 4.4 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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