Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA401794 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6001794.fastq.gz | Fastqsanger.gz | |||
| SRR6001795.fastq.gz | Fastqsanger.gz | |||
| SRR6001796.fastq.gz | Fastqsanger.gz | |||
| SRR6001797.fastq.gz | Fastqsanger.gz | |||
| SRR6001798.fastq.gz | Fastqsanger.gz |
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Project description:Arabidopsis MOS4-associated complex promotes microRNA biogenesis and pre-mRNA splicing
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Project description:Arabidopsis MOS4-associated complex promotes microRNA biogenesis and pre-mRNA splicing [RNA-seq]
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Project description:The evolutionarily conserved, putative RNA helicase MAC7 exists in both animals and plants. The human MAC7 homolog, Aquarius, is part of the spliceosome and plays a role in pre-mRNA splicing in vitro. In Arabidopsis, MAC7 was shown to be part of the MOS4-associated complex (MAC), which is required for plant defense and development. Here through RNA-seq analysis we discover that down-regulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus response, confirming a role of MAC in the regulation of biotic and abiotic stress responses. We also discover global intron retention defects in mutants in three members of MAC, thus linking the functions of MAC to splicing in Arabidopsis. In addition, we show that mac7-1, a partial loss-of-function mutant in MAC7, and two other MAC subunit mutants, mac3a mac3b and prl1 prl2, exhibit reduced microRNA levels in general, indicating that MAC promotes microRNA biogenesis. The mac7-1 mutant shows reduced primary miRNA (pri-miRNA) levels without affecting MIR promoter activity or the degradation of pri-miRNA transcripts, implicating functions of MAC7 during transcription elongation or maturation of pri-miRNAs. As a nuclear protein, MAC7 is not localized in dicing bodies, but it affects the localization of HYL1 to dicing bodies. We propose that MAC acts to link MIR transcription to pri-miRNA processing.
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Project description:The evolutionarily conserved, putative RNA helicase MAC7 exists in both animals and plants. The human MAC7 homolog, Aquarius, is part of the spliceosome and plays a role in pre-mRNA splicing in vitro. In Arabidopsis, MAC7 was shown to be part of the MOS4-associated complex (MAC), which is required for plant defense and development. Here through RNA-seq analysis we discover that down-regulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus response, confirming a role of MAC in the regulation of biotic and abiotic stress responses. We also discover global intron retention defects in mutants in three members of MAC, thus linking the functions of MAC to splicing in Arabidopsis. In addition, we show that mac7-1, a partial loss-of-function mutant in MAC7, and two other MAC subunit mutants, mac3a mac3b and prl1 prl2, exhibit reduced microRNA levels in general, indicating that MAC promotes microRNA biogenesis. The mac7-1 mutant shows reduced primary miRNA (pri-miRNA) levels without affecting MIR promoter activity or the degradation of pri-miRNA transcripts, implicating functions of MAC7 during transcription elongation or maturation of pri-miRNAs. As a nuclear protein, MAC7 is not localized in dicing bodies, but it affects the localization of HYL1 to dicing bodies. We propose that MAC acts to link MIR transcription to pri-miRNA processing.
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Project description:Cellular quiescence is coupled with cellular development, tissue homeostasis, and cancer progression. Both quiescence and cell cycle re-entry are controlled by active and precise regulation of gene expression. However, the roles of long noncoding RNAs (lncRNAs) during these processes remain to be elucidated. By performing a genome-wide transcriptome analyses, we identify thousands of differentially expressed lncRNAs, including ~30 of the less-characterized class of microRNA-host-gene lncRNAs (lnc-MIRHGs), during cellular quiescence and during serum-stimulation in human diploid cells. We observe that the mature MIR222HG display serum-stimulated induction due to enhanced pre-RNA splicing. Serum-stimulated binding of the pre-mRNA splicing factor SRSF1 to a micro-exon, which partially overlaps with the primary miR-222 precursor, facilitates enhanced MIR222HG splicing. In serum-stimulated cells, SRSF1 negatively regulates the Drosha/DGCR8-catalyzed cleavage of pri-miR-222, thereby increasing the cellular pool of the mature MIR222HG. Further, loss-of-function studies indicate that the mature MIR222HG facilitates the serum-stimulated cell cycle re-entry in a microRNA-independent manner. Mechanistically, MIR222HG, along with ILF3/2 complex, forms RNA:RNA duplex with DNM3OS lncRNA, thereby promoting DNM3OS stability. The current study identifies a mechanism in which the interplay between splicing versus microprocessor complex dictates the serum-induced expression of lnc-MIRHG MIR222HG for efficient cell cycle re-entry.
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