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Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [degradome-seq]

ABSTRACT: Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [degradome-seq]

PROVIDER: PRJNA1174801 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31043755_1.fastq.gz	Fastqsanger.gz
	SRR31043755_2.fastq.gz	Fastqsanger.gz
	SRR31043756_1.fastq.gz	Fastqsanger.gz
	SRR31043756_2.fastq.gz	Fastqsanger.gz
	SRR31043757_1.fastq.gz	Fastqsanger.gz

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Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [degradome-seq]

Project description:In grasses, 21- and 24-nt phasiRNAs are abundantly expressed in anthers and play crucial roles in anther development and male reproduction. 21-nt phasiRNAs can act in cis to direct the cleavage of their own precursor transcripts and is thought to lack trans cleavage targets in maize. Here we show that 21-nt phasiRNAs direct the cleavage of hundreds of target mRNAs in maize, with the cleavage activity being enriched in male germ cells. Interestingly, whereas 21-nt phasiRNAs in anthers (somatic anther wall cells) do not have obvious preference for a particular nucleotide at the 5’ end and target genes implicated in stress response and cellular homeostasis, 21-nt phasiRNAs in male germ cells preferentially initiate with 5’ C and associate with ZmAGO5c/MAGO2/MS28 to target genes related to meiotic processes. Our results indicate that mRNA cleavage is a conserved mechanism used by 21-nt phasiRNAs for gene regulation. However, the sequences of 21-nt phasiRNAs and their targets show low conservation in maize and rice, suggesting that 21PHAS loci and 21-nt phasiRNA targets have undergone fast divergence in monocots.

2025-05-26 | GSE279865 | GEO

Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [sRNA-seq]

2025-05-26 | GSE279862 | GEO

Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [RNA-seq]

2025-05-26 | GSE279861 | 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

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

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

2022-03-23 | GSE182476 | 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

HD-ZIP IV transcription factor OCL4 and 21-nt phasiRNAs are dispensable for male fertility in maize anthers

Project description:The maize ocl4 mutants showed differing levels of male sterility, which seems correlating with the quantity of 21-nt phasiRNA remaining during pre-meiotic stage. In this case, sRNA and transcriptome was profiled and compared in this study, showed that OCL4 and 21-nt phasiRNAs are dispensable for male fertility in maize anthers.

2021-09-09 | GSE150446 | GEO

Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [RNA-seq]

Project description:Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [RNA-seq]

| PRJNA1174797 | ENA

Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [sRNA-seq]

Project description:Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [sRNA-seq]

| PRJNA1174799 | ENA