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Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (iCLIP-seq)

ABSTRACT: Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (iCLIP-seq)

PROVIDER: PRJNA416997 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6251540_1.fastq.gz	Fastqsanger.gz
	SRR6251540_2.fastq.gz	Fastqsanger.gz
	SRR6251541_1.fastq.gz	Fastqsanger.gz
	SRR6251541_2.fastq.gz	Fastqsanger.gz
	SRR6251542_1.fastq.gz	Fastqsanger.gz

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Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (iCLIP-seq)

Project description:Accurate gene expression requires the coordination of RNA processing with assembly of messenger RNA-protein (mRNP) complex. RNA helicases are a class of enzymes that unwind RNA duplexes in vitro and have been are proposed to remodel RNA structure in vivo. Herein, we provide evidence that the DEAD-box protein Dbp2 remodels RNA structure to facilitate efficient pre-mRNA processing in S. cerevisiae. First, we find that Dbp2 associates with the 3’ ends and 3’ splice-sites of mRNAs genome-wide. Using structure-seq to map RNA secondary structure, we find altered secondary structures in dbp2∆ cells that overlap polyadenylation elements and correlate with inefficient termination. We also identify a role for Dbp2 in pre-mRNA splicing and show that both splicing and termination require Dbp2 helicase activity. This reveals that DEAD-box RNA helicases unwind structure in vivo and that structural alteration of pre-mRNA is essential for proper gene expression.

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Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (Structure-seq)

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The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [iCLIP]

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DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using ChIP-seq, we determined the sites where HTP-tagged Dbp2 associates with chromatin. ChIP-seq of Srp2-HTP is included as a reference protein that is known to associate with transcribing RNA polymerase II (RNAPII).

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Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (RNA Pol II ChIP-seq)

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Project description:eIF4A is a RNA helicase considered the prototype for the DEAD-box family and it is required in different events associated with the metabolism of RNAs, with the DEAD motif important to its ATPase and helicase activities. Previous studies have indicated that EIF4AI is the functional homolog working on protein synthesis in trypanosomatids. In order to investigate in more detail the interactome of the T. brucei EIF4AI in the translation context, as well as the importance of the DEAD motif for the main protein-protein interactions, we performed co-immunoprecipitation assays of HA-tagged EIF4AI and a version with a mutation on the DEAD motif (DQAD), combined to mass spectrometry analysis. The analysis confirmed a specific association of EIF4AI with an eIF4F complex based on EIF4E4/EIF4G3 subunits, and other translation factors. A differential pattern of association was seen for the mutant protein, indicating that the DEAD motif might be important to the specific eIF4F assembly in T. brucei. This study helped to clarify functional aspects of the EIF4AI helicase during Trypanosoma mRNA translation/metabolism.

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