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A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS (RNA-Seq I)

ABSTRACT: A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS (RNA-Seq I)

PROVIDER: PRJNA843033 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19430015_1.fastq.gz	Fastqsanger.gz
	SRR19430015_2.fastq.gz	Fastqsanger.gz
	SRR19430016_1.fastq.gz	Fastqsanger.gz
	SRR19430016_2.fastq.gz	Fastqsanger.gz
	SRR19430017_1.fastq.gz	Fastqsanger.gz

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A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS

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UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency 1

Project description:The RNA helicase UPF1 interacts with mRNAs, mRNA decay machinery, and the terminating ribosome to promote nonsense-mediated mRNA decay (NMD). Structural and biochemical data have revealed that UPF1 exists in an enzymatically autoinhibited “closed” state. Upon binding the NMD protein UPF2, UPF1 undergoes an extensive conformational change into a more enzymatically active “open” state, which exhibits enhanced ATPase and helicase activity. However, mechanically deficient UPF1 mutants can support efficient NMD, bringing into question the roles of UPF1 enzymatic autoinhibition and activation in NMD. Here, we identify two additional important features of the activated open state: slower nucleic acid binding kinetics and enhanced ATP-stimulated nucleic acid dissociation kinetics. Computational modeling based on empirical measurements of UPF1, UPF2, and RNA interaction kinetics predicts that the majority of UPF1-RNA binding and dissociation events in cells occur independently of UPF2 binding. We find that UPF1 mutants with either reduced or accelerated dissociation from RNA have NMD defects, whereas UPF1 mutants that are more dependent on UPF2 for catalytic activity remain active on well-established NMD targets. These findings support a model in which the kinetics of UPF1-mRNA interactions are important determinants of cellular NMD efficiency.

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UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency 2

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A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS (CLIP-Seq)

Project description:To investigate binding of DHX34 protein to RNA, RNA IP was performed in HEK293T cells using the seCLIP protocol.

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