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Series GSE206059 Query DataSets for GSE206059
Status Public on May 09, 2023
Title A network of DZF proteins controls alternative splicing regulation and fidelity [eCLIP-seq]
Organism Homo sapiens
Experiment type Other
Summary 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.
 
Overall design eCLIP analysis of FLAG-ZFR binding in HEK-293 Flp-In TREx cell lines, with size-matched input control.
 
Contributor(s) Haque N, Hogg JR
Citation(s) 37144502
Submission date Jun 14, 2022
Last update date May 11, 2023
Contact name J. Robert Hogg
E-mail(s) j.hogg@nih.gov
Organization name National Heart, Lung, and Blood Institute
Department Biochemistry and Biophysics Center
Street address 50 South Drive, Room 2341
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (4)
GSM6241092 ZFR-eCLIP-1
GSM6241093 ZFR-eCLIP-2
GSM6241094 ZFR-SMI-1
This SubSeries is part of SuperSeries:
GSE206061 A network of DZF proteins controls alternative splicing regulation and fidelity.
Relations
BioProject PRJNA848990

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Supplementary file Size Download File type/resource
GSE206059_RAW.tar 12.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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