Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA865280 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20750600.fastq.gz | Fastqsanger.gz | |||
| SRR20750900.fastq.gz | Fastqsanger.gz | |||
| SRR20751000.fastq.gz | Fastqsanger.gz | |||
| SRR20750601.fastq.gz | Fastqsanger.gz | |||
| SRR20750901.fastq.gz | Fastqsanger.gz |
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Project description:The anther-enriched phased, small interfering RNAs (phasiRNAs) play vital roles in regulating male fertility in grass species. The long non-coding precursors of phasiRNAs are products of RNA polymerase II and are likely regulated by transcription factors (TFs). A few putative transcriptional regulators of the 21- or 24-nucleotide phasiRNA loci (i.e., 21- or 24-PHAS loci) have been identified in maize (Zea mays), but whether any of the individual TFs or TF combinations are sufficient to activate the PHAS loci is unclear. Here, we identified the temporal gene coexpression networks (modules) associated with maize anther development, including two modules highly enriched for the 21- or 24-PHAS loci. Comparisons of these coexpression modules and gene sets dysregulated in several reported male sterile TF mutants revealed new insights into the timing of activities of the TFs, including antagonistic roles for OUTER CELL LAYER 4 and Male sterile 32. Trans-activation assays of individual TFs using bulk-protoplast RNA sequencing (RNA-seq) showed that two of the TFs coexpressed with 21-PHAS loci could activate several 21-nt phasiRNA pathway genes, but none was sufficient to activate 21-PHAS loci. Screens for combinatorial activities of these TFs and, separately, the recently reported putative transcriptional regulators of 24-PHAS loci using single-cell (protoplast) RNA-seq, did not detect reproducible activation of 21-PHAS or 24-PHAS loci. Collectively, our results suggest that the endogenous transcriptional machineries and/or chromatin states in the anthers are necessary to activate reproductive PHAS loci. Nonetheless, the single-cell RNA-seq approach shows potential for future studies of combinatorial activities of TFs.
2022-11-21 | GSE210327 | GEO
Project description:Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci [scRNA-seq]
| PRJNA865274 | ENA
Project description:The anther-enriched phased, small interfering RNAs (phasiRNAs) play vital roles in regulating male fertility in grass species. The long non-coding precursors of phasiRNAs are products of RNA polymerase II and are likely regulated by transcription factors (TFs). A few putative transcriptional regulators of the 21- or 24-nucleotide phasiRNA loci (i.e., 21- or 24-PHAS loci) have been identified in maize (Zea mays), but whether any of the individual TFs or TF combinations are sufficient to activate the PHAS loci is unclear. Here, we identified the temporal gene coexpression networks (modules) associated with maize anther development, including two modules highly enriched for the 21- or 24-PHAS loci. Comparisons of these coexpression modules and gene sets dysregulated in several reported male sterile TF mutants revealed new insights into the timing of activities of the TFs, including antagonistic roles for OUTER CELL LAYER 4 and Male sterile 32. Trans-activation assays of individual TFs using bulk-protoplast RNA sequencing (RNA-seq) showed that two of the TFs coexpressed with 21-PHAS loci could activate several 21-nt phasiRNA pathway genes, but none was sufficient to activate 21-PHAS loci. Screens for combinatorial activities of these TFs and, separately, the recently reported putative transcriptional regulators of 24-PHAS loci using single-cell (protoplast) RNA-seq, did not detect reproducible activation of 21-PHAS or 24-PHAS loci. Collectively, our results suggest that the endogenous transcriptional machineries and/or chromatin states in the anthers are necessary to activate reproductive PHAS loci. Nonetheless, the single-cell RNA-seq approach shows potential for future studies of combinatorial activities of TFs.
2022-11-21 | GSE210322 | GEO
Project description:Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci [bulk RNA-seq]
| PRJNA865273 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-11-21 | GSE210330 | GEO
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. Examination of maize phasiRNAs by high throughput sequencing for RNA-seq, small RNA, and PARE profiling
2015-02-11 | E-GEOD-52297 | biostudies-arrayexpress
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. Examination of maize phasiRNAs by high throughput sequencing for RNA-seq, small RNA and PARE profiling.
2015-02-11 | E-GEOD-52290 | biostudies-arrayexpress
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.
2015-02-11 | GSE52297 | GEO
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. Examination of maize phasiRNAs by high throughput sequencing for small RNA profiling
2015-02-11 | E-GEOD-52293 | biostudies-arrayexpress
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