Investigation on different small RNA expression of TT19 suppressors under anthocyanin induction condition (AIC) using Small RNA-seq
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE136901 | GEO | 2020/04/20
REPOSITORIES: GEO
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Project description:Dicer enzymes function at the core of RNA silencing to defend against exogenous RNA, or as an endogenous mechanism of gene regulation. Plant DICER-LIKE4 (DCL4) performs dual functions, acting in antiviral defense, as well as in development via the biogenesis of tasiR-ARFs. These small RNAs play an essential role in the grasses and act to spatially define the expression domain of AUXIN RESPONSE FACTOR3 (ARF3) transcription factors. However, contrary to tasiR-ARFs’ essential function in development, DCL4 proteins exhibit strong evidence of recurrent adaptation typical of host factors involved in antiviral immunity. Here, we address how DCL4 balances its role in development with pressures to diversify in response to viral attack. We show that, in contrast to other tasiR-ARF biogenesis mutants, dcl4 null alleles condition an uncharacteristically mild phenotype, correlated with normal expression of select arf3 targets. Loss of DCL4 activity yields a class of 22-nt tasiR-ARF variants associated with the processing of arf3 transcripts into 22-nt secondary siRNAs by DCL1. Our findings uncover the presence of a novel DCL1-dependent siRNA pathway that bypasses the otherwise adverse developmental effects of DCL4 mutations. This novel pathway is predicted to have important implications for DCL4’s role in antiviral defense by reducing the selective constraints on DCL4 and allowing it to diversify in response to viral suppressors. Examination of small RNAs isolated from dcl4, dcl1 and double mutants in imbibed kernels of maize
2015-09-01 | E-GEOD-66986 | biostudies-arrayexpress
Project description:Dicer enzymes function at the core of RNA silencing to defend against exogenous RNA, or as an endogenous mechanism of gene regulation. Plant DICER-LIKE4 (DCL4) performs dual functions, acting in antiviral defense, as well as in development via the biogenesis of tasiR-ARFs. These small RNAs play an essential role in the grasses and act to spatially define the expression domain of AUXIN RESPONSE FACTOR3 (ARF3) transcription factors. However, contrary to tasiR-ARFs’ essential function in development, DCL4 proteins exhibit strong evidence of recurrent adaptation typical of host factors involved in antiviral immunity. Here, we address how DCL4 balances its role in development with pressures to diversify in response to viral attack. We show that, in contrast to other tasiR-ARF biogenesis mutants, dcl4 null alleles condition an uncharacteristically mild phenotype, correlated with normal expression of select arf3 targets. Loss of DCL4 activity yields a class of 22-nt tasiR-ARF variants associated with the processing of arf3 transcripts into 22-nt secondary siRNAs by DCL1. Our findings uncover the presence of a novel DCL1-dependent siRNA pathway that bypasses the otherwise adverse developmental effects of DCL4 mutations. This novel pathway is predicted to have important implications for DCL4’s role in antiviral defense by reducing the selective constraints on DCL4 and allowing it to diversify in response to viral suppressors.
2015-09-01 | GSE66986 | GEO
Project description:Investigation on different small RNA expression of TT19 suppressors under anthocyanin induction condition (AIC) using Small RNA-seq
| PRJNA564017 | ENA
Project description:Investigation on different gene and small RNA expression of TT19 suppressors under anthocyanin inducing conditions (AIC)
| PRJNA564253 | ENA
Project description:Investigation on different gene expression of TT19 suppressors under anthocyanin inducing conditions (AIC) using RNA-seq
| PRJNA563055 | ENA
Project description:Maize LEAFBLADELESS1 (LBL1) and Arabidopsis SUPPRESSOR OF GENE SILENCING3 (SGS3) play orthologous roles in the biogenesis of 21 nucleotide trans-acting short-interfering RNAs (tasiRNAs). The phenotypes conditioned by mutation of lbl1 and SGS3 are, however, strikingly different, suggesting that the activities of these small RNA biogenesis components, or the tasiRNAs and their targets might not be entirely conserved. To investigate the basis for this phenotypic variation, we compared the small RNA content between wild-type and lbl1 seedling apices. We show that LBL1 affects all major classes of small RNAs, and reveal unexpected crosstalk between tasiRNA biogenesis and other small RNA pathways regulating miRNAs, retrotransposons, and DNA transposons. We further identified genomic regions generating phased siRNAs, including numerous loci generating 22-nt phased small RNAs from long hairpin RNAs or overlapping antisense transcripts not previously described in other plant species. By combining both analyses, we identified nine TAS loci, all belonging to the conserved TAS3 family. Contrary to other plant species, no TAS loci targeted by a single miRNA were identified. Information from target prediction, RNAseq, and PARE analyses identified the tasiARFs as the major functional tasiRNAs in the maize vegetative apex where they regulate expression of ARF3 homologs. As such, divergence in TAS pathways is unlikely to account for the distinct phenotypes of tasiRNA biogenesis mutants in Arabidopsis and maize. Instead, the data suggests variation in the spatiotemporal regulation of ARF3, or divergence in its function, as a plausible basis for the dramatic phenotypic differences observed upon mutation of SGS3/lbl1 in Arabidopsis and maize. An analysis of tasiRNA biogenesis, activity, and contribution to developmental phenotypes in the maize leaf. Data generated includes small RNA sequencing data and mRNA sequencing data. All data was generated in both wild type and lbl1 mutant maize leaf apices. Three replicates were generated for each genotype for the small RNA data. Two of these replicates were also used for the RNA-seq data.
2014-11-20 | E-GEOD-50557 | biostudies-arrayexpress
Project description:To assay siRNA movement in the pollen grain, we took advantage of the known behavior of 22nt siRNAs to target transcripts for cleavage and initiate secondary siRNA biogenesis. Previous research has demonstrated that when targeted by a 22nt microRNA, a transcript containing a truncated non-fluorescent ~400 bp version of GFP (trGFP) will produce GFP secondary siRNAs that can target a second copy of a functional full-length GFP mRNA in trans. Therefore, we created a ~400 bp non-fluorescent version of trGFP with a 5’ 22nt microRNA target site driven by the vegetative cell-specific KRP6 promoter and transformed this construct into a line homozygous for the sperm-specific functional full-length GFP driven by the MGH3 promoter. If cleaved by a 22nt microRNA, the vegetative cell-driven trGFP will be cleaved into secondary siRNAs, and if the RNA components of this system are mobile and transferred into the sperm cells, the sperm-specific fluorescence of GFP will be reduced. We used two versions of the microRNA target site, which included a mock target site that is not targeted by small RNAs, the target site of microRNA173 (which is a 22nt known to induce the production of secondary siRNAs). We demonstrate that when the 22nt microRNA173 target site is used in the vegetative cell transcript, a corresponding decrease in sperm cell fluorescence is observed. In the mock small RNA target site this reduction in fluorescence was not observed. To ensure the transitive silencing sperm cell transcripts is occurring via secondary small RNAs, we transferred this trGFP experiment into a dcl2/dcl4 mutant background that is defective in TE 21-22nt siRNA silencing. In dcl2/dcl4 double mutants with the trGFP system, we find that the GFP fluorescence of the mock target site transgene does not change, while the repression found in wild-type pollen with the 22nt microRNA173 target site is alleviated. The data for microRNA173 is particularly important, as DCL2 and DCL4 are not necessary for microRNA173 production, and therefore this demonstrates that specifically secondary siRNAs acting downstream of microRNA action are required to silence the sperm cell GFP. We further analyzed the production of sRNAs derived from GFP in pollen grains of transgenic lines expressing the 22nt miR173 or 22nt mock target sites inserted on the 5’ region of the trGFP transgene in both wt and dcl2/dcl4 backgrounds.
2016-03-24 | GSE68154 | GEO
Project description:The osdcl4-1 mutant exhibits much severer developmental defects than dcl4 in Arabidopsis, suggesting that Os DCL4 may process broader substrates in rice. By deep sequencing of small RNAs from different tissues of wild types and osdcl4-1, we revealed that 21-nucleotide siRNAs were largely dependent on Os DCL4. Besides several tasiRNA loci reported in Arabidopsis and rice, over one thousand 21-nucleotide and several dozen 24-nucleotide phased siRNA (phasiRNA) clusters were identified in panicles but not in seedlings and grains. Further analyses identified two conserved 22-nucleotide motifs among the cleavage sites of the 21- and 24- phasiRNA loci, and the cleavage sites of over 90% of 21- and 24-nucleotide phasing clusters were confirmed by PARE/degradome analysis from 93-11 panicles. MiR2118 and miR2275, expressed specifically in panicles, were predicted to trigger cleavages at 21- and 24-nucleotide phasiRNA clusters, respectively. The triggers of phasiRNAs are more dependent on Os DCL4 than Os DCL1. Furthermore, the processing of 21-nucleotide phasiRNAs was largely Os DCL4-dependent, whereas the processing of 24-nucleotide phasiRNAs was slightly affected by Os DCL4, but not by Os DCL3a and Os DCL1. Our results revealed distinct roles of Os DCL4 in a novel 21- and 24-nucleotide phasiRNA biogenesis pathway in rice.
2012-03-30 | GSE22763 | GEO
Project description:Maize LEAFBLADELESS1 (LBL1) and Arabidopsis SUPPRESSOR OF GENE SILENCING3 (SGS3) play orthologous roles in the biogenesis of 21 nucleotide trans-acting short-interfering RNAs (tasiRNAs). The phenotypes conditioned by mutation of lbl1 and SGS3 are, however, strikingly different, suggesting that the activities of these small RNA biogenesis components, or the tasiRNAs and their targets might not be entirely conserved. To investigate the basis for this phenotypic variation, we compared the small RNA content between wild-type and lbl1 seedling apices. We show that LBL1 affects all major classes of small RNAs, and reveal unexpected crosstalk between tasiRNA biogenesis and other small RNA pathways regulating miRNAs, retrotransposons, and DNA transposons. We further identified genomic regions generating phased siRNAs, including numerous loci generating 22-nt phased small RNAs from long hairpin RNAs or overlapping antisense transcripts not previously described in other plant species. By combining both analyses, we identified nine TAS loci, all belonging to the conserved TAS3 family. Contrary to other plant species, no TAS loci targeted by a single miRNA were identified. Information from target prediction, RNAseq, and PARE analyses identified the tasiARFs as the major functional tasiRNAs in the maize vegetative apex where they regulate expression of ARF3 homologs. As such, divergence in TAS pathways is unlikely to account for the distinct phenotypes of tasiRNA biogenesis mutants in Arabidopsis and maize. Instead, the data suggests variation in the spatiotemporal regulation of ARF3, or divergence in its function, as a plausible basis for the dramatic phenotypic differences observed upon mutation of SGS3/lbl1 in Arabidopsis and maize.
2014-11-20 | GSE50557 | GEO
Project description:The osdcl4-1 mutant exhibits much severer developmental defects than dcl4 in Arabidopsis, suggesting that Os DCL4 may process broader substrates in rice. By deep sequencing of small RNAs from different tissues of wild types and osdcl4-1, we revealed that 21-nucleotide siRNAs were largely dependent on Os DCL4. Besides several tasiRNA loci reported in Arabidopsis and rice, over one thousand 21-nucleotide and several dozen 24-nucleotide phased siRNA (phasiRNA) clusters were identified in panicles but not in seedlings and grains. Further analyses identified two conserved 22-nucleotide motifs among the cleavage sites of the 21- and 24- phasiRNA loci, and the cleavage sites of over 90% of 21- and 24-nucleotide phasing clusters were confirmed by PARE/degradome analysis from 93-11 panicles. MiR2118 and miR2275, expressed specifically in panicles, were predicted to trigger cleavages at 21- and 24-nucleotide phasiRNA clusters, respectively. The triggers of phasiRNAs are more dependent on Os DCL4 than Os DCL1. Furthermore, the processing of 21-nucleotide phasiRNAs was largely Os DCL4-dependent, whereas the processing of 24-nucleotide phasiRNAs was slightly affected by Os DCL4, but not by Os DCL3a and Os DCL1. Our results revealed distinct roles of Os DCL4 in a novel 21- and 24-nucleotide phasiRNA biogenesis pathway in rice. Six small RNA libraries were constructed from seedlings and panicles of 93-11 (a wild-type Indica rice variety) and osdcl4-1, as well as those from Nipponbare panicles and seedlings (a wild-type Japonica rice variety).
2012-03-29 | E-GEOD-22763 | biostudies-arrayexpress