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Series GSE254583 Query DataSets for GSE254583
Status Public on May 15, 2024
Title Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [TraPR small RNA-seq]
Organism Zea mays subsp. mays
Experiment type Other
Non-coding RNA profiling by high throughput sequencing
Summary Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs–named premeiotic 24-nt phasiRNAs–have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 for biogenesis, but premeiotic 24-nt phasiRNAs are unique in that they are likely (i) not triggered by microRNAs, (ii) not loaded by AGO18 proteins, and (iii) not capable of mediating cis-cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass lineage than previously known.
Overall design Small RNA and degradome profiling of anther materials from five maize inbred lines, a maize mutant, and three teosinte species or subspecies
Please note that the *mm in sample titles represents the length of the anther used for the corresponding sample (e.g. 0.4-mm anther for 'B73-0.4mm-rep1' sample), and that the 'ago18HM' and 'ago18HT' represents 'ago18 triple homozygous mutant' and 'ago18 triple heterozygote', respectively.
Contributor(s) Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon M, Nodine M, Meyers BC
Citation(s) 38739785
Submission date Jan 30, 2024
Last update date Jun 12, 2024
Contact name Junpeng Zhan
Organization name Huazhong Agricultural University
Street address 1 Shizishan Street, Hongshan District
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
Platforms (1)
GPL34147 NextSeq 550 (Zea mays subsp. mays)
Samples (11)
GSM8046619 TraPR small RNA-seq: ago18HM-2mm-rep1
GSM8046620 TraPR small RNA-seq: ago18HM-2mm-rep2
GSM8046621 TraPR small RNA-seq: ago18HM-5mm-rep1
This SubSeries is part of SuperSeries:
GSE254584 Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function.
BioProject PRJNA1071086

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Supplementary file Size Download File type/resource
GSE254583_TraPR_sRNAseq_ago18_PHAS_CPM.txt.gz 43.8 Kb (ftp)(http) TXT
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Raw data are available in SRA

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