Evolution of lmiRNAs and their targets from MITEs for rice adaptation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA899815 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22244842_1.fastq.gz | Fastqsanger.gz | |||
| SRR22244842_2.fastq.gz | Fastqsanger.gz | |||
| SRR22244843_1.fastq.gz | Fastqsanger.gz | |||
| SRR22244843_2.fastq.gz | Fastqsanger.gz | |||
| SRR22244844_1.fastq.gz | Fastqsanger.gz |
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Project description:Twenty-four nucleotide long miRNAs (lmiRNAs) direct DNA methylation at target genes and regulate their transcription. The evolutionary origin of lmiRNAs and the range of lmiRNA-mediated regulation remain obscure. Here, we reannotated lmiRNAs and their targets in rice by applying stringent criteria. We found that the majority of lmiRNAs are derived from MITEs and most sites targeted by MITE-derived lmiRNAs reside within MITEs, suggesting co-evolution of lmiRNAs and their targets through MITE amplification. lmiRNAs undergo dynamically changes under stressed conditions and the genes targeted by lmiRNAs show an enrichment for stress responsive genes, suggesting that lmiRNAs are widely involved in plant response to stresses. We constructed the evolutionary histories of lmiRNAs and their targets. lmiRNAs emerged before or when the AA genome was diverged, while the emergence of lmiRNA targets coincided with or followed the emergence of lmiRNAs. Furthermore, we found that the sequences of a lmiRNA target site underwent variations, coincident with the divergence of rice accessions and the distribution of rice accessions in different geographical locations and climatic conditions. Our findings highlight MITEs as an important origin of lmiRNAs and suggest that the evolution of lmiRNA-target regulatory modules may contribute to rice adaptation to environmental changes.
2023-11-01 | GSE217602 | GEO
Project description:Transposable elements (TEs) and repetitive sequences comprise over 40% of rice genome. Different TEs are tightly regulated by distinct epigenetic mechanisms. For example, the activities of LTR retrotransposon Tos17 and non-LTR retrotransposon LINE element Karma are uniquely regulated by histone H3K9 methylation and histone H3K4 demethylation, respectively. Miniature inverted repeat transposable elements (MITEs) are one of the most high-copy-number DNA transposons, which are interspersed around rice genome and might influence nearby gene expression. In plants, 24-nucleotide (24-nt) heterochromatic small interfering RNAs (hc-siRNAs) derived from repeats and TEs. To what extent hc-siRNA associated TEs affect gene expression and therefore contribute to agricultural traits in rice remains elusive. Here, we show that OsDCL3a, one of Dicer-Like 3 (DCL3) homolog, is primarily responsible for 24-nt hc-siRNA processing in rice. Impaired OsDCL3a displayed altered important agricultural traits in rice. We found that genome-wide (281,563) 24-nt hc-siRNA clusters were OsDCL3a-dependent, among which MITEs were significantly enriched. Impaired OsDCL3a caused significant overlapping between reduced hc-siRNAs from MITEs and elevated nearby gene expression. Intriguingly, genes involved in Gibberellin and Brassinosteroid homeostasis were identified as direct targets of OsDCL3a, which may attribute to dwarfism and enlarged flag leaf angle upon OsDCL3a deficiency. Our work uncovers OsDCL3a-dependent hc-siRNAs derived from MITEs as broad spectrum of regulators for fine-tuning gene expression, and this observation may reflect a conserved mechanism in other higher plants with dispersed repeat- or TE-rich genomes. Examination of OsDCL3a-dependent hc-siRNAs derived from MITEs.
2014-02-04 | E-GEOD-50778 | biostudies-arrayexpress
Project description:Transposable elements (TEs) and repetitive sequences comprise over 40% of rice genome. Different TEs are tightly regulated by distinct epigenetic mechanisms. For example, the activities of LTR retrotransposon Tos17 and non-LTR retrotransposon LINE element Karma are uniquely regulated by histone H3K9 methylation and histone H3K4 demethylation, respectively. Miniature inverted repeat transposable elements (MITEs) are one of the most high-copy-number DNA transposons, which are interspersed around rice genome and might influence nearby gene expression. In plants, 24-nucleotide (24-nt) heterochromatic small interfering RNAs (hc-siRNAs) derived from repeats and TEs. To what extent hc-siRNA associated TEs affect gene expression and therefore contribute to agricultural traits in rice remains elusive. Here, we show that OsDCL3a, one of Dicer-Like 3 (DCL3) homolog, is primarily responsible for 24-nt hc-siRNA processing in rice. Impaired OsDCL3a displayed altered important agricultural traits in rice. We found that genome-wide (281,563) 24-nt hc-siRNA clusters were OsDCL3a-dependent, among which MITEs were significantly enriched. Impaired OsDCL3a caused significant overlapping between reduced hc-siRNAs from MITEs and elevated nearby gene expression. Intriguingly, genes involved in Gibberellin and Brassinosteroid homeostasis were identified as direct targets of OsDCL3a, which may attribute to dwarfism and enlarged flag leaf angle upon OsDCL3a deficiency. Our work uncovers OsDCL3a-dependent hc-siRNAs derived from MITEs as broad spectrum of regulators for fine-tuning gene expression, and this observation may reflect a conserved mechanism in other higher plants with dispersed repeat- or TE-rich genomes.
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2021-05-17 | GSE163417 | GEO
Project description:Intensive application of inorganic nitrogen underlies marked increase in crop production yet imposes detrimental impact on ecosystems, hence it is crucial for future sustainable agriculture to improve nitrogen-use efficiency (NUE). Here we report the genetic basis of NUE associated with the local soil adaptation in rice. With a diverse rice germplasm panel collected from different ecogeographic regions, we performed genome-wide association study on tillering response to nitrogen (TRN), the most correlated trait with NUE of rice, and identified OsTCP19 as a modulator of TRN via transcriptionally responding to nitrogen and targeting to Dwarf and Low-Tillering (DLT), a tiller-promoting gene. A 29-bp InDel in OsTCP19 promoter confers differential transcription response to nitrogen and TRN variation among rice varieties. The high-TRN allele of OsTCP19 (OsTCP19-H) is prevalent in wild rice population, but largely lost in modern cultivars correlating with increased local soil nitrogen content, suggesting that it might have contributed to geographic adaptation in rice. Introgression of OsTCP19-H into modern rice cultivars boosts grain yield and NUE under low or moderate nitrogen levels, demonstrating its enormous potential for rice breeding and environment amelioration through reducing nitrogen application.
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Project description:During transformation, tissue culture often carries epigenetic and genetic changes underlying somaclonal variations, leading to unpredictable phenotypes. Transformation treatments may individually and jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes have never been examined. Here, we examined the changes in methylomes and transcriptomes associated with each of the components with different combinations of treatments. We found that individual transformation components targeted specific gene sets. When T-DNA was integrated, the pathway of secondary metabolism was activated, whereas primary metabolism was repressed. The transformation treatments resulted in global hypomethylation at CHH sites enriched at promoters highly associated with downregulation. The promoters that colocalized with miniature inverted-repeat TEs (MITEs) were found to be associated with epigenetic responses to stress, and this was not observed at sites without MITEs. Our results demonstrated component-specific epigenetic regulation related to adaptation to the stress response during rice transformation.
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