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Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [TraPR small RNA-seq]

ABSTRACT: Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [TraPR small RNA-seq]

PROVIDER: PRJNA1071086 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27787437.fastq.gz	Fastqsanger.gz
	SRR27787438.fastq.gz	Fastqsanger.gz
	SRR27787439.fastq.gz	Fastqsanger.gz
	SRR27787440.fastq.gz	Fastqsanger.gz
	SRR27787441.fastq.gz	Fastqsanger.gz

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Similar Datasets

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [small_RNA]

Project description: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.

2024-05-15 | GSE254581 | GEO

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [Smart-seq2+nanoPARE]

2024-05-15 | GSE254582 | GEO

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [TraPR small RNA-seq]

2024-05-15 | GSE254583 | GEO

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function.

Project description:Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function.

| PRJNA1071082 | ENA

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [small_RNA]

Project description:Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [small_RNA]

| PRJNA1071084 | ENA

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [Smart-seq2+nanoPARE]

Project description:Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [Smart-seq2+nanoPARE]

| PRJNA1071085 | ENA

24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers

Project description:In maize, 24-nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known. Using laser capture microdissection we analyzed tapetal cells, meiocytes, and other somatic cells at several stages of anther development to establish the timing of 24-PHAS precursor transcripts and the 24-nt phasiRNA products. By integrating RNA and small RNA (sRNA) profiling plus single-molecule and sRNA FISH (smFISH or sRNA-FISH) spatial detection, we demonstrate that the tapetum is the primary site of 24-PHAS precursor and Dcl5 transcripts and the resulting 24-nt phasiRNAs. Interestingly, 24-nt phasiRNAs accumulate in all cell types, with the highest levels in meiocytes, followed by tapetum. Our data support the conclusion that 24-nt phasiRNAs are mobile from tapetum to meiocytes and to other somatic cells. We discuss possible roles for 24-nt phasiRNAs in anther cell types.

2022-03-23 | GSE182588 | GEO

bHLH cascade regulate 24-nt phasiRNA biogenesis in maize anther

Project description:Anthers are the male reproductive floral organs, but loss of the 24-nt class of phased small-interfering RNAs (phasiRNAs) may confer temperature-sensitive male sterility in maize. 24-nt phasiRNAs from 176 loci are abundant coordinately in fertile maize anthers after the last periclinal divisions are complete, all four wall layers are formed, and meiosis has initiated in the pollen mother cells. In this study, we found male sterile maize ms23, ms32, and bhlh122 mutants with various degrees of tapetal defects lack 24-PHAS mRNA precursors and 24-nt phasiRNAs, which were not affected in another male sterile mutant, bhlh51. Transcription from most of 24-PHAS loci depends on bHLH122 while bHLH122 and Dcl5 transcription depends on both Ms23 and Ms32. Multiple lines of evidence suggest that 24-nt phasiRNAs biogenesis is primarily controlled at multiple layers by MS23 and MS32, with distinctive action on 24-PHAS transcription by bHLH122, creating a transcription factor cascade in maize tapetal cells.

2022-01-10 | GSE175915 | GEO

21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells

Project description: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.

2020-09-24 | GSE149800 | GEO

mRNA cleavage by 21-nt phasiRNAs dependent on AGO1d is important for temperature-sensitive male sterility in rice

Project description:Temperature-sensitive male sterility is one of the core components for hybrid rice breeding based on two-line system. We previously found that knockout of ARGONAUTE 1d (AGO1d) caused temperature-sensitive male sterility in rice by influencing phased small interfering RNA (phasiRNA) biogenesis and function. However, the specific phasiRNAs and their targets underlying the temperature-sensitive male sterility in ago1d mutant remain to be determined. Here, we demonstrate that the ago1d mutant displays normal female fertility but complete male sterility at low temperature. Through a multi-omics analysis of small RNA, degradome, and transcriptome, we found that 21-nt phasiRNAs account for the greatest proportion of the 21-nt small RNA (sRNA) species in rice anthers and are sensitive to low temperature and markedly down-regulated in ago1d mutant. Moreover, we found that 21-nt phasiRNAs are essential for the mRNA cleavage of a set of fertility- and cold tolerance-associated genes, such as EDT1, TDR, OsPCF5 and OsTCP21, directly or indirectly determined by AGO1d-mediated gene silencing. The loss-of-function of 21-nt phasiRNAs can result in up-regulation of their targets and causes varying degrees of defects in male fertility and grain setting. Our results highlight the essential functions of 21-nt phasiRNAs in temperature-sensitive male sterility in rice and suggest their promising application in two-line hybrid rice breeding in the future.

2024-01-01 | GSE232779 | GEO

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