Abstract
BACKGROUND: Endogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA biogenesis. It has been established that RDR2 is involved in the 24 nt siRNA-dependent RNA-directed DNA methylation (RdDM) pathway. Recent studies have suggested that RDR1 is involved in a second RdDM pathway that relies mostly on 21 nt smRNAs and functions to silence a subset of genomic loci that are usually refractory to the normal RdDM pathway in Arabidopsis. Whether and to what extent the homologs of RDR1 may have similar functions in other plants remained unknown. RESULTS: We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.) derived from a retrotransposon Tos17 insertion. Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1. smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome. Some of the regions with altered smRNA clusters were associated with changes in DNA methylation. In addition, altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes. Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions. CONCLUSIONS: Our results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response.
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Claims 11
Claim · model-written summary
The Osrdr1 mutant showed 1,175 differentially expressed genes compared with WT in shoot tips.
- Taxon
- rice
Oryza sativat0 - Material
- Osrdr1e1
- Treatment
- loss-of-function mutante0
- Gene
- OsRDR1e0
- Outcome
- differentially expressed genese1
- Value
- 1,175e1
- Comparator
- WTe1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e0“We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.)”
e1“Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1”
Claim · model-written summary
In the Osrdr1 mutant, 896 genes were up-regulated relative to WT.
- Taxon
- riceOryza sativat0
- Material
- Osrdr1e1
- Treatment
- loss-of-function mutante0
- Gene
- OsRDR1e0
- Outcome
- genese1
- Direction
- increaseinferrede1
- Value
- 896e1
- Comparator
- WTe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e0“We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.)”
e1“Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1”
Claim · model-written summary
In the Osrdr1 mutant, 279 genes were down-regulated relative to WT.
- Taxon
- riceOryza sativat0
- Material
- Osrdr1e1
- Treatment
- loss-of-function mutante0
- Gene
- OsRDR1e0
- Outcome
- genese1
- Direction
- decreaseinferrede1
- Value
- 279e1
- Comparator
- WTe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e0“We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.)”
e1“Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1”
Claim · model-written summary
smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome.
- Taxon
- riceOryza sativat0
- Outcome
- regional alterations in smRNA clusterse2
- Qualifier
- across the rice genomee2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e2“smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome”
Claim · model-written summary
Some regions with altered smRNA clusters were associated with changes in DNA methylation.
- Taxon
- riceOryza sativat0
- Treatment
- altered smRNA clusterse3
- Outcome
- DNA methylatione3
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e3“Some of the regions with altered smRNA clusters were associated with changes in DNA methylation”
Claim · model-written summary
Several miRNAs showed altered expression in the Osrdr1 mutant.
- Taxon
- riceOryza sativat0
- Material
- Osrdr1e4
- Outcome
- expression of several miRNAse4
- Direction
- alterede4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e4“altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes”
Claim · model-written summary
Altered miRNA expression was associated with altered expression of predicted miRNA target genes.
- Taxon
- riceOryza sativat0
- Treatment
- altered expression of several miRNAse4
- Outcome
- expression of predicted miRNA target genese4
- Direction
- alterede4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e4“altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes”
Claim · model-written summary
The Osrdr1 mutant showed no phenotypic difference from WT under normal conditions.
- Taxon
- riceOryza sativat0
- Material
- Osrdr1e5
- Treatment
- normal conditione5
- Outcome
- phenotypic differencee5
- Comparator
- WTe5
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e5“Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions”
Claim · model-written summary
Ephemeral phenotypic fluctuations occurred in rice under some abiotic stress conditions.
- Taxon
- riceOryza sativat0
- Treatment
- some abiotic stress conditionse5
- Outcome
- phenotypic fluctuationse5
- Qualifier
- ephemerale5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e5“Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions”
Claim · model-written summary
OsRDR1 appears to regulate a substantial number of endogenous genes through smRNA-mediated pathways involving DNA methylation.
- Taxon
- riceOryza sativat0
- Gene
- OsRDR1e6
- Outcome
- regulating a substantial number of endogenous genese6
- Qualifier
- smRNA-mediated pathways involving DNA methylatione6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e6“Our results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response”
Claim · model-written summary
OsRDR1 appears to participate in the abiotic stress response of rice.
- Taxon
- riceOryza sativat0
- Gene
- OsRDR1e6
- Outcome
- abiotic stress responsee6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice”
e6“Our results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response”