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Round 2 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

ABSTRACT: Round 2 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

PROVIDER: PRJNA637775 | ENA |

REPOSITORIES: ENA

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Round 1 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

Project description:Round 1 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

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RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice

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Round 2 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

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Project description:We report the comparison of transcript expression of Fe-sufficient roots and leaves of OsIMA overexpression lines IMA1OX-7, 9, IMA2OX-2, 5 and corresponding NTby RNA-Seq.

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Roles of RDR701 and DCLs in Rice PhasiRNA biogenesis

Project description:In this study, we analyzed function of the rice RDR701 and various DCLs proteins in small RNA processing. small RNA deep sequencing analyses revealed that RDR701 and OsDCL4 is involved in tasiRNAs and 21- and 24-nt phasiRNAs biogenesis. Further analyses indicate RDR701 coupling with OsDCL4 and OsDCL3b are required for the biogenesis of 21- and 24-nt phasiRNAs, respectively. The triggering miRNAs for intial both size phasiRNAs,are also shown RDR701- and OsDCL4-dependent, suggesting two sequential round activity of RDR701 in associated with different DCLs are essential for rice phasiRNAs biogenesis.

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mRNA cleavage by 21-nt phasiRNAs dependent on AGO1d is important for temperature-sensitive male sterility in rice

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The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

Project description:RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of Pol V, a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long non-coding RNAs. Pol V influences the accumulation of 24-nt siRNAs in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V-independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V-dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V-dependent loci but not on Pol V-independent loci. Our results reveal the function of rice Pol V for long non-coding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development. This SuperSeries is composed of the SubSeries listed below.

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