Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements
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ABSTRACT:
PROVIDER: PRJNA303083 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2819870.fastq.gz | Fastqsanger.gz | |||
| SRR2819871.fastq.gz | Fastqsanger.gz | |||
| SRR2819862.fastq.gz | Fastqsanger.gz | |||
| SRR2819872.fastq.gz | Fastqsanger.gz | |||
| SRR2819863.fastq.gz | Fastqsanger.gz |
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Project description:The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). The frequencies and sizes of TE-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in control of different TE classes. We further provide evidence for involvement of PiAgo1 in the P. infestans miRNA pathway. Protein-coding genes are likely to be regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing CRN effectors was bound to PiAgo1, implicating this protein in regulation of the expanded CRN gene family. These findings highlight the different roles played by Ago proteins in an economically important plant pathogenic oomyce
2016-03-17 | GSE75281 | GEO
Project description:The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). The frequencies and sizes of TE-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in control of different TE classes. We further provide evidence for involvement of PiAgo1 in the P. infestans miRNA pathway. Protein-coding genes are likely to be regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing CRN effectors was bound to PiAgo1, implicating this protein in regulation of the expanded CRN gene family. These findings highlight the different roles played by Ago proteins in an economically important plant pathogenic oomyce
2016-03-17 | GSE74370 | GEO
Project description:Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements (RNA-Seq)
| PRJNA303084 | ENA
Project description:Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements (small RNA-Seq)
| PRJNA299833 | ENA
Project description:Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Reports suggest that pathogen-derived sRNAs can modulate the expression of plant defense genes. The experiments reported here were designed to shed light on impact of sRNAs in the potato-P. infestans interaction. We used the Argonaute or Ago1 from P. infestans tagged with GFP transformed into the 88069 strain to infect potato cv. Bintje plants. Collected leaf materials were used in co-immunoprecipitation experiments together with P. infestans harboring GFP (control GFP) and P. infestans mycelia grown on media (control mycelia). These three materials were sequenced at a Ion Proton platform. The reads length of 8-38 nt were adaptor-trimmed and mapped to the P. infestans genome and the Solanom tuberosum genome v4.04. Both P. infestans-associated and potato derived sRNAs were identified.
2021-06-30 | GSE119230 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2016-03-17 | GSE75282 | GEO
Project description:Background: Transposable element 24 nucleotide small RNAs are not efficiently incorporated into the AGO1 protein, which is involved in endogenous RNAi and gene regulation through the microRNA and tasiRNA pathways. Results: The AGO1 protein incorporates large quantities of transposable element siRNAs when transposable elements are epigenetically activated and transcribed. The incorporation of transposable element siRNAs is at the expense of the most abundant microRNAs. These transposable element siRNAs can act as tasiRNAs, regulating genes that they have partial complementarity to. Conclusion: Transposable element small RNAs are more dynamic than previously thought. They can be incorporated into AGO1 and regulate genes. Three biological replicates of small RNA sequencing from two genotypes
2014-04-07 | E-GEOD-45990 | biostudies-arrayexpress
Project description:Background: Transposable element 24 nucleotide small RNAs are not efficiently incorporated into the AGO1 protein, which is involved in endogenous RNAi and gene regulation through the microRNA and tasiRNA pathways. Results: The AGO1 protein incorporates large quantities of transposable element siRNAs when transposable elements are epigenetically activated and transcribed. The incorporation of transposable element siRNAs is at the expense of the most abundant microRNAs. These transposable element siRNAs can act as tasiRNAs, regulating genes that they have partial complementarity to. Conclusion: Transposable element small RNAs are more dynamic than previously thought. They can be incorporated into AGO1 and regulate genes.
2014-04-07 | GSE45990 | GEO
Project description:Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results: To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions: Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans. Small RNA sequence data from Phytophthora infestans-infected potato leaf tissue and P. infestans mycelium tissue. Three infection stage time-points. Two P. infestans lines: 88089 (wild-type) and PiDcl1 (transformant PiDcl1 knock-down). No replicates. Total number of samples: 8.
2014-12-12 | E-GEOD-63292 | biostudies-arrayexpress
Project description:Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results: In order to identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions: Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs whose levels are elevated during infection of P. infestans on potato. Small RNA sequence data from two Phytophthora infestans isolates. Four life-cycle stages from each isolate. No replicates. Total number of samples: 8.
2014-12-12 | E-GEOD-62674 | biostudies-arrayexpress