Regulation, biogenesis and function of circDOCK1(2,27), an abundant epithelial-specific circRNA
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA940502 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23691928.fastq.gz | Fastqsanger.gz | |||
| SRR23691929.fastq.gz | Fastqsanger.gz | |||
| SRR23691930.fastq.gz | Fastqsanger.gz | |||
| SRR23691931.fastq.gz | Fastqsanger.gz | |||
| SRR23691932.fastq.gz | Fastqsanger.gz |
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Project description:We describe the regulation, biogenesis and function of circDOCK1(2,27), a large, abundant EMT-regulated circular RNA whose formation is dependent on the epithelial-specific splicing regulator ESRP1. CircDOCK1(2,27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis along with CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2,27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. Proximity-dependent biotinylation (BioID) assay suggests ESRP1 modifies the RNP landscape of intron 1 in a way that disfavours communication of exon 1 with exon 2, rather than physically bridging exon 2 to exon 27. The X-ray crystal structure of RNA-bound ESRP1 qRRM2 domain reveals it binds to GGU motifs, with the guanines embedded in clamp-like aromatic pockets in the protein.
2023-11-22 | GSE226538 | GEO
Project description:Circular RNAs (circRNAs) are natural outputs of eukaryotic transcription and RNA processing and have emerged as critical regulators in physiology and human diseases. Although a series of cis-elements and trans-factors are reported to globally regulate circRNA biogenesis, most of these regulations are unconserved or at most mammalian conserved. Here, using a genome-wide CRISPR knockout screen, we have identified an evolutionarily conserved polyadenosine RNA-binding protein ZC3H14 to regulate circRNA biogenesis in eukaryotes. Mechanistically, ZC3H14 associates with spliceosome to bind to 3' and 5' exon-intron boundaries of circularized exons, and forms a dimer to promote circRNA biogenesis. ZC3H14 knockout mice exhibit disrupted spermatogenesis and reduced testicular circRNA levels. Additionally, human ZC3H14 is associated with male infertility. Our findings reveal a conserved requirement for ZC3H14/Nab2 in the modulation of eukaryotic backsplicing and link ZC3H14 along with circRNAs to mammalian testicular disorders.
2024-02-10 | GSE254916 | GEO
Project description:Conserved regulation of ZC3H14/Nab2 in circRNA biogenesis
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Project description:Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs, however the principles of biogenesis are currently not fully understood. To elucidate features important for circRNA production, we performed global analyses of RNA-binding proteins associating with the flanking introns of circRNAs, and we identified two factors, SFPQ and NONO, to be highly enriched with circRNAs. We observe a subclass of circRNAs, coined DALI circRNAs, with distal inverted Alu elements and long introns to be highly deregulated upon SFPQ knockdown. Moreover, SFPQ depletion leads to increased intron retention with concomitant induction of cryptic splicing prevalent for long introns causing in some cases premature transcription termination and polyadenylation. Aberrant splicing in the upstream and downstream regions of circRNA producing exons are critical for shaping the circRNAome, and specifically, we identify a conserved impact of missplicing in the immediate upstream region to drive circRNA biogenesis. Collectively, our data show that SFPQ plays an important role in maintaining intron integrity by ensuring accurate splicing of long introns, and disclose novel features governing Alu-independent circRNA production.
2020-09-09 | GSE157622 | GEO
Project description:While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2-27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal transition (EMT) and whose formation depends on the epithelial splicing regulator ESRP1. CircDOCK1(2-27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis and CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2-27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. Proximity-dependent biotinylation (BioID) assay suggests ESRP1 may modify the RNP landscape of intron 1 in a way that disfavours communication of exon 1 with exon 2, rather than physically bridging exon 2 to exon 27. The X-ray crystal structure of RNA-bound ESRP1 qRRM2 domain reveals it binds to GGU motifs, with the guanines embedded in clamp-like aromatic pockets in the protein.
| S-EPMC10853802 | biostudies-literature
Project description:Unlike linear RNAs terminated with 5' caps and 3' tails, circular RNAs are characterized by covalently closed loop structures with neither 5' to 3' polarity nor polyadenylated tail. This intrinsic characteristic has led to the general under-estimation of the existence of circular RNAs in previous polyadenylated transcriptome analyses. With the advent of specific biochemical and computational approaches, a large number of circular RNAs from back-spliced exons (circRNAs) have been identified in various cell lines and across different species. Recent studies have uncovered that back-splicing requires canonical spliceosomal machinery and can be facilitated by both complementary sequences and specific protein factors. In this review, we highlight our current understanding of the regulation of circRNA biogenesis, including both the competition between splicing and back-splicing and the previously under-appreciated alternative circularization.
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Project description:Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human Alu repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified new circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched compared to linear controls. By scoring the presence of reverse complementary sequences in human introns we predicted and experimentally validated novel circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyper-editing events. Knockdown of the double-strand RNA editing ADAR1 enzyme significantly and specifically up-regulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA:RNA interactions of introns form larger structures which promote circularization of embedded exons, while ADAR1 antagonizes circRNA expression by melting stems within these interactions. Thus, we assign a new function to ADAR1. Examination of 12 samples in different stages of C.elegans development.
2015-01-06 | E-GEOD-63823 | biostudies-arrayexpress
Project description:Erythrocytes and platelets have high production rates, with 1012 cells released daily into the blood stream. This output from bone-marrow residing hematopoietic stem cells is tightly regulated by transcription factors and epigenetic modifications. Whether and how non-coding RNAs such as circular RNAs (circRNAs) contribute to the differentiation and/or identity of hematopoietic cells is to date not well understood. We recently published a circRNA expression map of hematopoietic cells, which showed that erythrocytes and platelets contain the highest levels and numbers of circRNAs. Whether and how circRNA expression alters during differentiation of erythrocytes and platelet precursors is however not known. Therefore, we here provide the first detailed and comprehensive analysis of circRNA expression during red blood cell and megakaryocyte differentiation. CircRNA expression significantly increased during erythroid precursor differentiation into red blood cells, and in differentiating megakaryocytes, in particular upon enucleation. Many functions have been attributed to circRNAs. To dissect their possible function in hematopoietic differentiation, we first focused on translation regulation. We compared circRNA and mRNA expression to ribosomal foot printing data, and found that only 20 (2.6%) circRNAs associated with translation regulation of their mRNA counterparts. We also identified thousands of putative open reading frames in circRNAs, suggesting that circRNAs may also encode proteins. However, deep ribosome-footprinting sequencing data and in-depth mass spectrometry data analysis provided little evidence for translation of endogenously expressed circRNAs in erythroblasts, megakaryocytes and platelets. In conclusion, circRNAs in platelets and red blood cells are highly abundant and alter their expression profile during differentiation, yet their contribution to regulate cellular processes remains enigmatic.
2021-03-04 | GSE159578 | GEO
Project description:Erythrocytes and platelets have high production rates, with 1012 cells released daily into the blood stream. This output from bone-marrow residing hematopoietic stem cells is tightly regulated by transcription factors and epigenetic modifications. Whether and how non-coding RNAs such as circular RNAs (circRNAs) contribute to the differentiation and/or identity of hematopoietic cells is to date not well understood. We recently published a circRNA expression map of hematopoietic cells, which showed that erythrocytes and platelets contain the highest levels and numbers of circRNAs. Whether and how circRNA expression alters during differentiation of erythrocytes and platelet precursors is however not known. Therefore, we here provide the first detailed and comprehensive analysis of circRNA expression during red blood cell and megakaryocyte differentiation. CircRNA expression significantly increased during erythroid precursor differentiation into red blood cells, and in differentiating megakaryocytes, in particular upon enucleation. Many functions have been attributed to circRNAs. To dissect their possible function in hematopoietic differentiation, we first focused on translation regulation. We compared circRNA and mRNA expression to ribosomal foot printing data, and found that only 20 (2.6%) circRNAs associated with translation regulation of their mRNA counterparts. We also identified thousands of putative open reading frames in circRNAs, suggesting that circRNAs may also encode proteins. However, deep ribosome-footprinting sequencing data and in-depth mass spectrometry data analysis provided little evidence for translation of endogenously expressed circRNAs in erythroblasts, megakaryocytes and platelets. In conclusion, circRNAs in platelets and red blood cells are highly abundant and alter their expression profile during differentiation, yet their contribution to regulate cellular processes remains enigmatic.
2021-03-04 | GSE159577 | GEO
Project description:Circular RNAs (circRNAs), a noncoding RNA class originating from alternative splicing, are highly abundant in neural tissues and were shown to regulate gene expression e.g. by interacting with microRNAs and RNA-binding proteins. Neuroblastoma is an embryonal neoplasia, which arises from undifferentiated neural crest cells. Here, we aimed to explore, whether circRNAs influence the pathogenesis of high-risk neuroblastoma. We performed whole-transcriptome sequencing of 104 primary neuroblastoma samples of all risk-groups and identified 5,203 unique circRNAs involving 2,302 genes. Candidate circRNA expression did not correlate with host gene expression, indicating independent regulatory mechanisms. circRNAs were significantly downregulated in the MYCN-amplified high-risk tumors. These findings were independently reproduced in a tetracycline-inducible MYCN-overexpression system based on a non MYCN-amplified neuroblastoma cell line, suggesting that MYCN drives this global circRNA repression. We identified the RNA helicase DHX9 as a mediator of this global suppressive effect of MYCN on circRNAs. Comparing our RNA sequencing data with other cancers and controls revealed a circRNA subset specifically upregulated in neuroblastoma that included a circRNA derived from the ARID1A tumor suppressor gene. Specific circARID1A knockdown resulted in reduced proliferation, cell numbers and viability, prompted apoptosis and induced a differentiated phenotype. Neither knockdown, nor overexpression of circARID1A influenced ARID1A mRNA and protein levels significantly. To dissect the potential mode of function, we performed a pulldown assay with subsequent mass spectrometry. We identified the RNA-binding protein KHSRP as an interaction partner that participates in the mechanism of action of circARID1A. In summary, this study highlights an important role of circRNAs in neuroblastoma biology and may establish this RNA class as a future therapeutic target and biomarker.
2023-04-06 | PXD026053 | Pride