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Profiling of N6-methyladenosine (m6A) in salt-treated and control Arabidopsis

ABSTRACT: Profiling of N6-methyladenosine (m6A) in salt-treated and control Arabidopsis

PROVIDER: PRJNA478203 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7442202.fastq.gz	Fastqsanger.gz
	SRR7442203.fastq.gz	Fastqsanger.gz
	SRR7442204.fastq.gz	Fastqsanger.gz
	SRR7442205.fastq.gz	Fastqsanger.gz
	SRR7442206.fastq.gz	Fastqsanger.gz

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Identification of N6-methyladenosine (m6A) modification in sweet sorghum under salt stress

Project description:The N6-methyladenosine (m6A) modification is the most common internal post-transcriptional modification, with important regulatory effects on RNA export, splicing, stability，and translation. However, the effects of m6A modifications on the resistance of sweet sorghum to salt stress remain unclear. In this study, we mapped the m6A modifications in two sorghum inbred lines (salt-tolerant M-81E and salt-sensitive Roma) that differ regarding salt tolerance. Dynamic changes to m6A modifications in sweet sorghum were identified in response to salt stress. Our data suggest that the differences in the m6A modifications between salt-tolerant and salt-sensitive sweet sorghum might contribute to the diversity in salt tolerance.

2022-05-02 | GSE146936 | GEO

Profiling of N6-methyladenosine (m6A) in salt-treated and control Arabidopsis

Project description:In order to gain insight into m6A in control and salt stress, we performed an miCLIP-sequencing experiment in control and salt treated plants

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N6-methyladenosine Modulates Messenger RNA Translation Efficiency

Project description:N6-methyladenosine (m6A) is the most abundant internal messenger (mRNA) modification in mammalian mRNA. This modification is reversible and non-stoichiometric, which potentially adds an additional layer of variety and dynamic control of mRNA metabolism. The m6A-modified mRNA can be selectively recognized by the YTH family “reader” proteins. The preferential binding of m6A-containing mRNA by YTHDF2 is known to reduce the stability of the target transcripts; however, the exact effects of m6A on translation has yet to be elucidated. Here we show that another m6A reader protein, YTHDF1, promotes ribosome loading of its target transcripts. YTHDF1 forms a complex with translation initiation factors to elevate the translation efficiency of its bound mRNA. In a unified mechanism of translation control through m6A, the YTHDF2-mediated decay controls the lifetime of target transcripts; whereas, the YTHDF1-based translation promotion increases the translation efficiency to ensure effective protein production from relatively short-lived transcripts that are marked by m6A. PAR-CLIP and RIP was used to identify YTHDF1 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF1 siRNA knock-down

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YTHDF3 improves translation initiation of mRNAs with N6-methyladenosine methylation at 5’ untranslated region by facilitating eIF2AK2 recruitment in oxaliplatin-resistant colorectal cancer - RIP-seq dataset

Project description:Oxaliplatin as a first-line drug frequently causes the chemo-resistance on colorectal cancer (CRC). N6-methyladenosine (m6A) methylation has been largely acknowledged in multiple biological functions. However, the molecular mechanisms underlying the m6A methylation in modulating anticancer drug resistance in CRC are still obscure. In present study, RIP-seq was conducted to investigate the occupancy of N6-methyladenosine RNA binding protein 3 (YTHDF3) served as “readers” that can recognize m6A modification site in HCT116 cells with oxaliplatin resistance (HCT116R). Then, YTHDF3 was knockdown by siRNA in HCT116 cells with oxaliplatin resistance, and RIP-seq was further conducted to investigate m6A methylation of HCT116, HCT116R and HCT116R cells with YTHDF3 knockdown.

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Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

Project description:We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling. Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

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Project description:N6-methyladenosine (m6A), the most abundant messenger RNA (mRNA) modification, has emerged as a critical post-transcriptional mechanism that regulates various aspect of mRNA metabolism including pre-mRNA processing, mRNA export, mRNA stability and translation efficiency. However the genetics basis of m6A is largely unexplored. In this work, we mapped m6A-QTLs in 60 LCLs and used the resulting tens of thousands of QTLs to provide insights to m6A biology and its contribution to human complex trait.

2020-05-04 | GSE125377 | GEO

N6-methyladenosine and RNA secondary structure affect transcript stability and translation during systemic salt stress in Arabidopsis

Project description:After transcription, a messenger RNA (mRNA) is further post-transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N6-methyladenosine, m6A). Both RNA secondary structure and m6A have been demonstrated to regulate mRNA stability and translation as well as have been independently linked to plant response to excess salt concentrations in the soil. However, the effect of m6A on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA-protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure is highly dynamic during salt stress, which is independent of changes in RNA-protein interactions. Conversely, we find that m6A is anti-correlated with RNA secondary structure in a condition-specific manner, with salt-specific m6A resulting in a decrease in mRNA secondary structure during salt stress. Remarkably, we show that the combination of salt-specific m6A deposition and the associated loss of RNA secondary structure results in increases in mRNA stability and translation of transcripts encoding proteins involved in responses to abiotic stresses. In total, our comprehensive analyses reveal an important epitranscriptome, secondary structure-mediated post-transcriptional regulatory mechanism involved in plant long-term salt stress response and adaptation.

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