Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide identification of AGO18b-bound miRNAs and phasiRNAs in maize by cRIP-seq

ABSTRACT: As a key member of the grass-specific subclade of argonaute proteins, AGO18b protein has been proposed to bind 24-nt meiotic phasiRNAs based on their co-expression in tapetal and meiotic cells. Here we show that expression of in maize tassels is strictly induced by developmental stages. Interestingly, reduced expression of AGO18b in both Mutator-mediated (ago18b::mum) and RNAi mutants leads to an increase in plant height and tassel length, suggesting its non-meiotic function as a negative regulator of SAM/IM maintenance. During the premiotic stage, AGO18b primarily binds to 21-nt phasiRNAs with 5’-uridine and less binds to 24-nt phasiRNAs with 5’-adenosine, coincident with its enrichment of miR2275 required for the 24-nt phasiRNA production. MiR166a, the negative regulator of SAM, is mostly enriched among AGO18b-bound miRNAs, implicating a novel negative regulator of IM. We suggest that AGO18b regulates maize tassel development via both phasiRNAs and miRNA pathways.

ORGANISM(S): Zea mays

PROVIDER: GSE93983 | GEO | 2019/08/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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

2022-03-23 | GSE182476 | 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

Transcriptome and sRNA profiling of Maize dcl5 CRISPR null alleles

Project description:Small RNAs play important roles during plant development by regulating transcript levels of target mRNAs, maintaining genome integrity, and reinforcing DNA methylation. Dicer-like 5 (Dcl5) is proposed to be responsible for precise slicing to generate diverse 24-nt phased, secondary small interfering RNAs (phasiRNAs), which are exceptionally abundant in meiotic anthers of maize, rice, and other grasses 1. Importance and functions of these phasiRNAs remain unclear. Here we used the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas9 system to mutate Dcl5. We report that dcl5 mutants have few or no 24-nt phasiRNAs, develop short anthers and defective tapetal cells, and exhibit temperature-sensitive male fertility. We propose that DCL5 and 24-nt phasiRNAs are critical for fertility under growth regimes for optimal yield.

2018-12-17 | GSE122449 | 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

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (RNA-seq2)

Project description:Maize anthers, the male reproductive floral organs, express two classes of phased, small interfering RNAs (phasiRNAs). RNA profiling from ten sequential cohorts of staged maize anthers plus mature pollen revealed that 21-nt phased siRNAs (21-phasiRNAs) from 463 loci appear abruptly after germinal and initial somatic cell fate specification and then diminish, while 24-nt phased siRNAs (24-phasiRNAs) from 176 loci coordinately accumulate during meiosis and persist as haploid gametophytes differentiate into pollen. RNA sequencing of anther developmental mutants, together with in situ RNA hybridization detection of phasiRNA biogenesis factors, demonstrated that 21-phasiRNAs and 24-phasiRNAs are independently regulated. Furthermore, 21-phasiRNAs require epidermal cells while 24-phasiRNAs require functional tapetal cells. Maize phasiRNAs and mammalian PIWI-interacting RNAs (piRNAs) illustrate convergent evolution of small RNAs to support male reproduction.

2020-05-15 | GSE150597 | GEO

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (small RNA-seq)

2015-02-11 | GSE52293 | GEO

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (RNA-seq)

2015-02-11 | GSE52290 | GEO

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (PARE)

2015-02-11 | GSE52297 | GEO

24-nt phasiRNAs move from tapetal to meiotic cellsin maize anthers

Project description:24-nt phasiRNAs move from tapetal to meiotic cellsin maize anthers

| PRJNA756318 | ENA

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (PARE)

2015-02-11 | E-GEOD-52297 | biostudies-arrayexpress