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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.

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

PROVIDER: PRJNA637772 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11940663_1.fastq.gz	Fastqsanger.gz
	SRR11940663_2.fastq.gz	Fastqsanger.gz
	SRR11940664_1.fastq.gz	Fastqsanger.gz
	SRR11940664_2.fastq.gz	Fastqsanger.gz
	SRR11940665_1.fastq.gz	Fastqsanger.gz

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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.

Project description: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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iTRAQ analyses of Fe-sufficient and Fe-deficient non-transformant and HRZ-knockdown rice roots

Project description:We conducted iTRAQ analyses using soluble proteins extracted from roots of non-transformant rice (NT) and previously generated HRZ-knockdown (HRZi) lines (Kobayashi et al., 2013 Nat Commun 4: 2792) cultivated under Fe-sufficient and Fe-deficient conditions. We identified and quantified 3,033 and 3,525 proteins in replicate 1 and 2, respectively, which totaled 4,884 proteins including 1,698 overlapping proteins between the two replicate experiments.

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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.

Project description:We report the comparison of transcript expression of Fe-sufficient roots of OsIMA overexpression lines IMA1OX-4, IMA2OX-1, OsIMA knockdown lines IMA1i-2, IMA2i-3, and corresponding NT, as well as Fe-deficient roots of NT, by RNA-Seq.

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

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

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.

2020-11-24 | GSE151938 | GEO

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-11-23 | GSE151941 | GEO

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

Project description:Temperature-sensitive male sterility is one of the core components for hybrid rice breeding based on two-line system. We previously found that knockout of ARGONAUTE 1d (AGO1d) caused temperature-sensitive male sterility in rice by influencing phased small interfering RNA (phasiRNA) biogenesis and function. However, the specific phasiRNAs and their targets underlying the temperature-sensitive male sterility in ago1d mutant remain to be determined. Here, we demonstrate that the ago1d mutant displays normal female fertility but complete male sterility at low temperature. Through a multi-omics analysis of small RNA, degradome, and transcriptome, we found that 21-nt phasiRNAs account for the greatest proportion of the 21-nt small RNA (sRNA) species in rice anthers and are sensitive to low temperature and markedly down-regulated in ago1d mutant. Moreover, we found that 21-nt phasiRNAs are essential for the mRNA cleavage of a set of fertility- and cold tolerance-associated genes, such as EDT1, TDR, OsPCF5 and OsTCP21, directly or indirectly determined by AGO1d-mediated gene silencing. The loss-of-function of 21-nt phasiRNAs can result in up-regulation of their targets and causes varying degrees of defects in male fertility and grain setting. Our results highlight the essential functions of 21-nt phasiRNAs in temperature-sensitive male sterility in rice and suggest their promising application in two-line hybrid rice breeding in the future.

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21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells

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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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