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A network of DZF proteins controls alternative splicing regulation and fidelity [RNA Bind-n-Seq]

ABSTRACT: A network of DZF proteins controls alternative splicing regulation and fidelity [RNA Bind-n-Seq]

PROVIDER: PRJNA848989 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19646444.fastq.gz	Fastqsanger.gz
	SRR19646445.fastq.gz	Fastqsanger.gz
	SRR19646446.fastq.gz	Fastqsanger.gz
	SRR19646447.fastq.gz	Fastqsanger.gz
	SRR19646448.fastq.gz	Fastqsanger.gz

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A network of DZF proteins controls alternative splicing regulation and fidelity [RNA Bind-n-Seq]

Project description:Proteins containing DZF (domain associated with zinc fingers) modules play important roles throughout gene expression, from transcription to translation. Derived from nucleotidyltransferases but lacking catalytic residues, DZF domains serve as heterodimerization surfaces between DZF protein pairs. Three DZF proteins are widely expressed in mammalian tissues, ILF2, ILF3, and ZFR, which form mutually exclusive ILF2-ILF3 and ILF2-ZFR heterodimers. Using eCLIP-Seq, we find that ZFR binds across broad intronic regions to regulate the alternative splicing of cassette and mutually exclusive exons. ZFR preferentially binds dsRNA in vitro and is enriched on introns containing conserved dsRNA elements in cells. Many splicing events are similarly altered upon depletion of any of the three DZF proteins; however, we also identify independent and opposing roles for ZFR and ILF3 in alternative splicing regulation. Along with widespread involvement in cassette exon splicing, the DZF proteins control the fidelity and regulation of over a dozen highly validated mutually exclusive splicing events. Our findings indicate that the DZF protein complexes form a complex regulatory network that leverages dsRNA binding by ILF3 and ZFR to modulate splicing regulation and fidelity.

2023-05-09 | GSE206060 | GEO

A network of DZF proteins controls alternative splicing regulation and fidelity [eCLIP-seq]

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A network of DZF proteins controls alternative splicing regulation and fidelity [RNA-seq]

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A network of DZF proteins controls alternative splicing regulation and fidelity.

Project description:A network of DZF proteins controls alternative splicing regulation and fidelity.

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A network of DZF proteins controls alternative splicing regulation and fidelity [RNA-seq]

Project description:A network of DZF proteins controls alternative splicing regulation and fidelity [RNA-seq]

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A network of DZF proteins controls alternative splicing regulation and fidelity [eCLIP-seq]

Project description:A network of DZF proteins controls alternative splicing regulation and fidelity [eCLIP-seq]

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A network of DZF proteins controls alternative splicing regulation and fidelity.

Project description:This SuperSeries is composed of the SubSeries listed below. GSE206058: Paired-end total RNA-seq of triplicate biological replicate treatments of HEK-293 cells with negative control siRNAs or siRNAs targeting ZFR, ILF2, or ILF3. GSE206059: eCLIP analysis of FLAG-ZFR binding in HEK-293 Flp-In TREx cell lines, with size-matched input control. GSE206060: RNA Bind-n-Seq of recombinantly expressed and purified ZFR-ILF2 complexes, with PTBP1 as a positive control for successful library generation.

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A network of DZF proteins controls alternative splicing regulation and fidelity.

Project description:Proteins containing DZF (domain associated with zinc fingers) modules play important roles throughout gene expression, from transcription to translation. Derived from nucleotidyltransferases but lacking catalytic residues, DZF domains serve as heterodimerization surfaces between DZF protein pairs. Three DZF proteins are widely expressed in mammalian tissues, ILF2, ILF3 and ZFR, which form mutually exclusive ILF2-ILF3 and ILF2-ZFR heterodimers. Using eCLIP-Seq, we find that ZFR binds across broad intronic regions to regulate the alternative splicing of cassette and mutually exclusive exons. ZFR preferentially binds dsRNA in vitro and is enriched on introns containing conserved dsRNA elements in cells. Many splicing events are similarly altered upon depletion of any of the three DZF proteins; however, we also identify independent and opposing roles for ZFR and ILF3 in alternative splicing regulation. Along with widespread involvement in cassette exon splicing, the DZF proteins control the fidelity and regulation of over a dozen highly validated mutually exclusive splicing events. Our findings indicate that the DZF proteins form a complex regulatory network that leverages dsRNA binding by ILF3 and ZFR to modulate splicing regulation and fidelity.

| S-EPMC10325889 | biostudies-literature

The impact of Prp18p on splicing fidelity and efficiency in budding yeast

Project description:Fidelity of 3´-splice site (3´SS) selection by the spliceosome is critical for proper gene expression but is a daunting task considering the low complexity of the 3´SS consensus YAG. Here we show that loss of the splicing factor Prp18p in budding yeast activates a diverse array of alternative 3´SS at more than half of all introns. Some alternative sites highly diverge from the YAG consensus, demonstrating a critical role for Prp18p in promoting spliceosome fidelity. Usage of alternative 3´SS is determined by distance from the branchpoint, local RNA secondary structures, upstream poly(U) content, and adenosine enrichment in exons. The 3´SS fidelity function of Prp18p can be genetically uncoupled from its role in splicing efficiency and is promoted by interactions with Slu7p and Prp8p. Taken together, these results provide a comprehensive mechanism into how the spliceosome achieves specificity of 3´SS selection and how it prevents aberrant activation of non-canonical splice sites.

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