Abstract
Plant specific SGS3-like proteins are composed of various combinations of an RNA-binding XS domain, a zinc-finger zf-XS domain, a coil-coil domain and a domain of unknown function called XH. In addition to being involved in de novo 2 (IDN2) and SGS3, the Arabidopsis genome encodes 12 uncharacterized SGS3-like proteins. Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis. Transcriptome co-expression analyses reveal significantly correlated expression of two SGS3-like proteins, factor of DNA methylation 1 (FDM1) and FDM2 with known genes required for RdDM. The fdm1 and fdm2 double mutations but not the fdm1 or fdm2 single mutations significantly impair DNA methylation at RdDM loci, release transcriptional gene silencing and dramatically reduce the abundance of siRNAs originated from high copy number repeats or transposons. Like IDN2 and SGS3, FDM1 binds dsRNAs with 5' overhangs. Double mutant analyses also reveal that IDN2 and three uncharacterized SGS3-like proteins FDM3, FDM4 and FDM5 have overlapping function with FDM1 in RdDM. Five FDM proteins and IDN2 define a group of SGS3-like proteins that possess all four-signature motifs in Arabidopsis. Thus, our results demonstrate that this group of SGS3-like proteins is an important component of RdDM. This study further enhances our understanding of the SGS3 gene family and the RdDM pathway.
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Claims 9
Claim · model-written summary
FDM1 and FDM2 expression is significantly correlated with known RdDM genes in Arabidopsis.
- Taxon
- Arabidopsis
Arabidopsise0 - Gene
- FDM1e1
- Outcome
- expressione1
- Comparator
- known genes required for RdDMe1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Transcriptome co-expression analyses reveal significantly correlated expression of two SGS3-like proteins, factor of DNA methylation 1 (FDM1) and FDM2 with known genes required for RdDM”
e0“Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis”
Claim · model-written summary
A group of SGS3-like proteins acts redundantly in RdDM in Arabidopsis.
- Taxon
- ArabidopsisArabidopsise0
- Gene
- a group of SGS3-like proteinse0
- Outcome
- act redundantly in RNA-directed DNA methylatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis”
Claim · model-written summary
The fdm1 and fdm2 double mutations significantly impaired DNA methylation at RdDM loci relative to the fdm1 or fdm2 single mutations.
- Taxon
- ArabidopsisArabidopsise0
- Treatment
- fdm1 and fdm2 double mutationse2
- Outcome
- DNA methylation at RdDM locie2
- Direction
- impaire2
- Comparator
- fdm1 or fdm2 single mutationse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The fdm1 and fdm2 double mutations but not the fdm1 or fdm2 single mutations significantly impair DNA methylation at RdDM loci”
e0“Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis”
Claim · model-written summary
The fdm1 or fdm2 single mutations did not significantly impair DNA methylation at RdDM loci.
- Taxon
- ArabidopsisArabidopsise0
- Treatment
- fdm1 or fdm2 single mutationse2
- Outcome
- DNA methylation at RdDM locie2
- Direction
- impaire2
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“The fdm1 and fdm2 double mutations but not the fdm1 or fdm2 single mutations significantly impair DNA methylation at RdDM loci”
e0“Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis”
Claim · model-written summary
The fdm1 and fdm2 double mutations released transcriptional gene silencing.
- Taxon
- ArabidopsisArabidopsise0
- Treatment
- fdm1 and fdm2 double mutationse2
- Outcome
- transcriptional gene silencinge3
- Direction
- releasee3
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e3“release transcriptional gene silencing and dramatically reduce the abundance of siRNAs originated from high copy number repeats or transposons”
e2“The fdm1 and fdm2 double mutations but not the fdm1 or fdm2 single mutations significantly impair DNA methylation at RdDM loci”
e0“Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis”
Claim · model-written summary
The fdm1 and fdm2 double mutations dramatically reduced the abundance of siRNAs originated from high copy number repeats or transposons.
- Taxon
- ArabidopsisArabidopsise0
- Treatment
- fdm1 and fdm2 double mutationse2
- Outcome
- abundance of siRNAse3
- Direction
- reducee3
- Qualifier
- originated from high copy number repeats or transposonse3
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e3“release transcriptional gene silencing and dramatically reduce the abundance of siRNAs originated from high copy number repeats or transposons”
e2“The fdm1 and fdm2 double mutations but not the fdm1 or fdm2 single mutations significantly impair DNA methylation at RdDM loci”
e0“Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis”
Claim · model-written summary
FDM1 binds dsRNAs with 5' overhangs.
- Taxon
- ArabidopsisArabidopsise0
- Gene
- FDM1e4
- Outcome
- binds dsRNAse4
- Qualifier
- with 5' overhangse4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“FDM1 binds dsRNAs with 5' overhangs”
e0“Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis”
Claim · model-written summary
IDN2 and FDM3, FDM4 and FDM5 have overlapping function with FDM1 in RdDM.
- Taxon
- ArabidopsisArabidopsise0
- Gene
- FDM3, FDM4 and FDM5e5
- Outcome
- overlapping functione5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“Double mutant analyses also reveal that IDN2 and three uncharacterized SGS3-like proteins FDM3, FDM4 and FDM5 have overlapping function with FDM1 in RdDM”
e0“Here, we show that a group of SGS3-like proteins act redundantly in RNA-directed DNA methylation (RdDM) pathway in Arabidopsis”
Claim · model-written summary
Five FDM proteins and IDN2 define a group of SGS3-like proteins that possess all four-signature motifs in Arabidopsis.
- Taxon
- ArabidopsisArabidopsise6
- Gene
- Five FDM proteins and IDN2e6
- Outcome
- possess all four-signature motifse6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e6“Five FDM proteins and IDN2 define a group of SGS3-like proteins that possess all four-signature motifs in Arabidopsis”
The same questions in other papers
loss of function · molecular: expression · ArabidopsisPositive and negative results
158 papers in the same direction as this paper · 38 in the opposite direction
- positive
- no effect
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