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Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under abiotic stress

ABSTRACT: To identify RDR1/2/6-dependent antisense RNA loci under 2hr drought stress, expression profiles of Poly (A+) RNA and Poly (A-) RNA between rdr1/2/6 and wild-type using the custom microarray (GPL19830) were analyzed.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE72309 | GEO | 2016/07/31

SECONDARY ACCESSION(S): PRJNA293711

REPOSITORIES: GEO

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Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under abiotic stress

Project description:To identify RDR1/2/6-dependent antisense RNA loci under 2hr drought stress, expression profiles of Poly (A+) RNA and Poly (A-) RNA between rdr1/2/6 and wild-type using the custom microarray (GPL19830) were analyzed. rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2 hours. Then, the plants were transferred to plastic dish and kept for 1 week. Poly (A+) RNA and Poly (A-) fractions were separated from 100Î¼g total RNA by treating with Ambion Poly A purist twice. Poly (A-) RNA sample was prepared by depleting rRNA using Invitrogen RiboMinus Plant Kit. 5 ng of Poly (A+) RNA and 1.4 Î¼g of Poly (A-) RNA samples were used for the expression profiling using the custom array (GPL19830).

2016-07-31 | E-GEOD-72309 | biostudies-arrayexpress

Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under rehydration

Project description:To identify RDR1/2/6-dependent antisense RNA loci under 2hr drought stress and 2hr rehydration, expression profiles of Poly (A+) RNA between rdr1/2/6 and wild-type using the custom microarray (GPL19830) were analyzed. rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2 weeks. Then, the plants were transferred to plastic dish and kept for 2hr. Poly (A+) RNA from 100Î¼g total RNA by treating with Ambion Poly A purist twice.5 ng of Poly (A+) RNA were used for the expresion profiling using the custom array (GPL19830).

2016-07-31 | E-GEOD-83846 | biostudies-arrayexpress

Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under rehydration

2016-07-31 | GSE83846 | GEO

Identification of small RNA loci that are synthesized by RNA-dependent RNA polymerases1/2/6

2016-03-31 | GSE72982 | GEO

Indentification samll RNA loci that are synthesized by RNA-dependent RNA polymerases1/2/6

Project description:To identify RDR1/2/6 dependent small RNA loci of transcribed regions under 2hr drought stress- and untreated conditions, expression profiles of small RNA between rdr1/2/6 and wild-type using hi-seq 2000. rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2weeks. Then, their plants were transfered to dry plastic dish for 2 hours. small RNA fraction was s extracted from the sample using Ambion mirVana miRNA Isolation Kit. small RNA labrary was constructed using TruSeq Small RNA Library Preparation Kits and applied to hi-seq 2000.

2016-03-31 | E-GEOD-72982 | biostudies-arrayexpress

Deep sequencing of uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants

Project description:Our previous experiment on biogenesis mechanisim of stress-inducible antisense RNAs showed that accumulation of antisense RNA in a drought-inducible gene, RD29A locus was decreased in rdr1/2/6 triple mutant. The RD29A antisense RNA did not have CAP structure and poly(A) tail. We applied deep sequencing of uncapped RNA using SOLiD to identify RDR1/2/6-mediated antisense RNAs in genome-wide. We identified 1) 975 RDR1/2/6-mediated antisense RNA loci on which no. of sequence tags is decreased in rdr1/2/6 and makes peak and 2) 1,613 RDR1/2/6-mediated antisense RNA loci on which no. of the tags is decreased in rdr1/2/6 and enriched on antisense strand of exons. They were grouped into 1,959 non-redundant loci.

2017-07-13 | GSE39033 | GEO

RNA-dependent RNA polymerases-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway in C. elegans

Project description:The biogenesis of rRNA drives cell growth and proliferation, but mechanisms that modulate rRNA production remain poorly understood. We have conducted a genetic screen to look for factors that negatively regulate endo-siRNA generation in C. elegans, and identified the suppressor of siRNA (susi)-1and a new class of triphosphorylated antisense ribosomal siRNAs (risiRNAs). In susi-1 mutant, we observed an accumulation of siRNA sequences complementary to 18S and 26S rRNAs. risiRNAs are similar to 22G-RNA, as they are 22 nt in length and have a triphosphorylated guanidine at their 5'-end. The generation of risiRNAs depends on RNA-dependent RNA polymerases, but not the ERI/Dicer complex. risiRNAs act through the nuclear RNAi pathway and guide the Argonaute protein NRDE-3 to the nucleoli, which leads to a downregulation of pre-rRNA expression. Interestingly, low temperature and ultraviolet irradiation also induces the accumulation of risiRNA, suggesting potential regulatory functions. Cloned SUSI-1 shows homology to Dis3-like exonuclease 2 (Dis3L2) in other organisms, a gene identified as a key exonuclease involved in the 3' to 5' degradation of oligouridylated RNAs. We observed an accumulation of 3'-tail oligouridylated 26S rRNA in susi-1 mutant and in low temperature-treated animals. Consistently, the injection of 3'-tail oligouridylated 26S rRNA elicited a nuclear accumulation of NRDE-3. Our findings thus establish SUSI-1(ceDis3L2) as a suppressor of endo-siRNA generation, identify a novel class of risiRNAs that suppress pre-rRNA expression, and suggest a potential disease mechanism.

2016-12-07 | GSE90927 | GEO

TMV-derived Small RNAs Reveals Role for Arabidopsis thaliana RNA-dependent RNA Polymerases in Viral siRNA Biogenesis

Project description:Using a crucifer-infecting strain of Tobacco Mosaic Virus (TMV-Cg) and Arabidopsis thaliana as a model system, we analyzed the viral small RNA profile in wild-type plants as well as rdr mutants by applying small RNA deep sequencing technology. Over 100,000 TMV-Cg-specific small RNA reads, mostly of 21- (78.4%) and 22-nucleotide (12.9%) in size and originating predominately (79.9%) from the genomic sense RNA strand, were captured at an early infection stage, yielding the first high-resolution small RNA map for a plant virus. The TMV-Cg genome harbored multiple, highly reproducible small RNA-generating hot spots that corresponded to regions with no apparent local hairpin-forming capacity. Significantly, both the rdr1 and rdr6 mutants exhibited globally reduced levels of viral small RNA production as well as reduced strand bias in viral small RNA population, revealing an important role for these host RDRs in viral siRNA biogenesis. In addition, an informatics analysis showed that a large set of host genes could be potentially targeted by TMV-Cg-derived siRNAs for posttranscriptional silencing, raising the interesting possibility for a hidden layer of widespread virus-host interactions that may contribute to viral pathogenicity and host specificity. Profiling of TMV-Cg derived small RNAs in systemically infected tissues of wild type (Col-0) Arabidopsis as well as the rdr1and rdr6 mutants, at 3 days post-infection.

2009-03-24 | E-GEOD-12918 | biostudies-arrayexpress

TMV-derived Small RNAs Reveals Role for Arabidopsis thaliana RNA-dependent RNA Polymerases in Viral siRNA Biogenesis

2009-03-24 | GSE12918 | GEO

Polymerases IV and V affect Pol II transcription termination

Project description:Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes.

2017-12-10 | GSE101543 | GEO

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