Dataset Information

Profiling of protein interactions of the circRNA cZNF292 in endothelial cells

ABSTRACT: Circular RNAs are a class of non-coding RNAs mostly generated by back-splicing RNA transcripts of protein-coding gene loci. In difference to canoncial splicing, back-splicing ligates downstream splice donor site with an upstream splice acceptor generating a covalently closed circular RNA. CircRNAs have been reported to influence cellular functions by acting as miRNA sponges, regulation of host gene transcription or by protein interactions. The circRNA cZNF292 has been previously reported to be regulated under hypoxia and to influence endothelial cell angiogenesis and functions. The present data set aims to identfy protein interactions partners of cZNF292 in endothelial cells to further characterize the mechanism of action of cZNF292. Dataset comprises 8 replicates of proteins identified after biotin-based 2'O-Me RNA antisense affinity purification of the circRNA cZNF292 from HUVEC (human umbilical vein endothelial cell) lysates compared to a control probe dataset. Purification was performed without cross-linking under low salt and mild detergent conditions.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Ilka Wittig

LAB HEAD: Stefanie Dimmeler

PROVIDER: PXD029794 | Pride | 2022-11-29

REPOSITORIES: Pride

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Publications

Locus-Conserved Circular RNA cZNF292 Controls Endothelial Cell Flow Responses.

Heumüller Andreas W AW Jones Alisha N AN Mourão André A Klangwart Marius M Shi Chenyue C Wittig Ilka I Fischer Ariane A Muhly-Reinholz Marion M Buchmann Giulia K GK Dieterich Christoph C Potente Michael M Braun Thomas T Grote Phillip P Jaé Nicolas N Sattler Michael M Dimmeler Stefanie S

Circulation research 20211118 1

<h4>Background</h4>Circular RNAs (circRNAs) are generated by back splicing of mostly mRNAs and are gaining increasing attention as a novel class of regulatory RNAs that control various cellular functions. However, their physiological roles and functional conservation in vivo are rarely addressed, given the inherent challenges of their genetic inactivation. Here, we aimed to identify locus conserved circRNAs in mice and humans, which can be genetically deleted due to retained intronic elements no ...[more]

PMID: 34789007

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Project description:In platelets, splicing and translation occur in the absence of a nucleus. However, the integrity and stability of mRNAs derived from megakaryocyte progenitor cells remain poorly quantified on a transcriptome-wide level. As circular RNAs (circRNAs) are resistant to degradation by exonucleases, their abundance relative to linear RNAs can be used as a surrogate marker for mRNA stability in the absence of transcription. Here we show that circRNAs are enriched in human platelets 17-188 fold relative to nucleated tissues, and 14-26 fold relative to samples digested with RNAseR to selectively remove linear RNA. We compare RNAseq read depths inside and outside circRNAs to provide in silico evidence of transcript circularity, show that exons within circRNAs are enriched ~13X in platelets relative to nucleated tissues, and identify 3162 genes significantly enriched for circRNAs including some where all RNAs appear to be derived from circular molecules. We also confirm that this is a feature of other anucleate cells through transcriptome sequencing of mature erythrocytes, demonstrate that circRNAs are not enriched in megakaryocytes, and that linear RNAs decay more rapidly than circRNAs in platelet preparations. Collectively, these results suggest that circulating platelets have lost on aveage over 90% of their progenitor mRNAs, and that translation in platelets occurrs against the backdrop of a highly degraded transcriptome. Finally, we find that transcripts classified as products of reverse transcriptase template switching are both enriched in platelets and resistant to decay, countering the recent suggestion that up to 50% of rearranged RNAs are artefacts. A single rRNA depleted total RNA sample was sequenced. This together with 25 publicly available rRNA depleted total RNA samples (including 3 from platelets) were analysed using PTESFinder v 1 (http://sourceforge.net/projects/ptesfinder-v1/) to identify back-splice junctions, characteristic of circRNA transcripts. The contribution of circRNA producing exons was analysed on a gene by gene basis as follows: All circRNA transcripts identified in any sample were first pooled to define exons which can contribute to circRNA generation using custom scripts (available on request). For each sample, expression estimates (RPKMI) across all circRNA producing exons were computed for each locus using the total size of exons (in bp) and the read counts mapping to them. Similarly, total size and exonic read counts for exons for which no circRNA were detected in any sample were used to compute expression estimates (RPKME) for non-circRNA producing exons for each locus. Abundance ratios (RPKMI/RPKME and RPKMI/RPKMI+RPKME) were calculated and compared between Platelets and human tissues using Wilcoxon signed-rank test. Please note that the '25sample_info_accn_no.txt' contains the accession numbers and tissue/cell type information for 25 samples analyzed together.

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