scholarly journals BIQ: A method for searching circular RNAs in transcriptome databases by indexing backsplice junctions

2019 ◽  
Author(s):  
Peter Menzel ◽  
Irmtraud M Meyer
Keyword(s):  
Splice Site ◽  
Transcriptome Sequencing ◽  
Functional Characterization ◽  
Circular Rna ◽  
Free Software ◽  
Circular Rnas ◽  
Rna Transcripts ◽  
Link Type

Circular RNAs (circRNAs) are a class of RNA transcripts that originate from non-canonical splicing events and are characterized by a backsplice junction connecting the 3’ splice site to an upstream 5’ splice site. Here, we present the program BIQ for indexing and querying transcriptome sequencing datasets for backsplice junctions. BIQ can be used for instantaneously querying all indexed transcriptomes for occurrence and abundance of reads overlapping the backsplice junction of a particular circular RNA, which can help in the functional characterization of known and novel circular RNAs. BIQ is free software and available at https://github.com/pmenzel/biq.

scholarly journals Functional Characterization of Spliceosomal Introns and Identification of U2, U4, and U5 snRNAs in the Deep-Branching Eukaryote Entamoeba histolytica

2007 ◽  
Vol 6 (6) ◽  
pp. 940-948 ◽  
Author(s):  
Carrie A. Davis ◽  
Michael P. S. Brown ◽  
Upinder Singh
Keyword(s):  
Entamoeba Histolytica ◽  
Splice Site ◽  
Expressed Sequence Tag ◽  
Functional Characterization ◽  
Molecular Evidence ◽  
Spliceosomal Introns ◽  
Accurate Expression ◽  
Eukaryotic Organisms

ABSTRACT Pre-mRNA splicing is essential to ensure accurate expression of many genes in eukaryotic organisms. In Entamoeba histolytica, a deep-branching eukaryote, approximately 30% of the annotated genes are predicted to contain introns; however, the accuracy of these predictions has not been tested. In this study, we mined an expressed sequence tag (EST) library representing 7% of amoebic genes and found evidence supporting splicing of 60% of the testable intron predictions, the majority of which contain a GUUUGU 5′ splice site and a UAG 3′ splice site. Additionally, we identified several splice site misannotations, evidence for the existence of 30 novel introns in previously annotated genes, and identified novel genes through uncovering their spliced ESTs. Finally, we provided molecular evidence for the E. histolytica U2, U4, and U5 snRNAs. These data lay the foundation for further dissection of the role of RNA processing in E. histolytica gene expression.

scholarly journals Plugging Small RNAs into the Network

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Lars Barquist
Keyword(s):  
Small Rnas ◽  
Posttranscriptional Regulation ◽  
Network Inference ◽  
Functional Characterization ◽  
The State ◽  
Diverse Range ◽  
Regulatory Interactions ◽  
Link Type ◽  
Wide Range

ABSTRACT Small RNAs (sRNAs) have been discovered in every bacterium examined and have been shown to play important roles in the regulation of a diverse range of behaviors, from metabolism to infection. However, despite a wide range of available techniques for discovering and validating sRNA regulatory interactions, only a minority of these molecules have been well characterized. In part, this is due to the nature of posttranscriptional regulation: the activity of an sRNA depends on the state of the transcriptome as a whole, so characterization is best carried out under the conditions in which it is naturally active. In this issue of mSystems, Arrieta-Ortiz and colleagues (M. L. Arrieta-Ortiz, C. Hafemeister, B. Shuster, N. S. Baliga, et al., mSystems 5:e00057-20, 2020, https://doi.org/10.1128/mSystems.00057-20) present a network inference approach based on estimating sRNA activity across transcriptomic compendia. This shows promise not only for identifying new sRNA regulatory interactions but also for pinpointing the conditions in which these interactions occur, providing a new avenue toward functional characterization of sRNAs.

scholarly journals Identification and functional characterization of circular RNAs in pericytes

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Glaser ◽  
A.W Heumueller ◽  
M Klangwart ◽  
A Wiederer ◽  
D John ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Factors ◽  
Cell Biology ◽  
Functional Characterization ◽  
Cell Types ◽  
Circular Rna ◽  
Circular Rnas ◽  
Funding Source ◽  
Factor Screening ◽  
And Function

Abstract Background Circular RNAs (circRNAs) are generated by back-splicing. They are known to be robustly expressed in a variety of mammalian cell types and organism and have been reported to influence cell biology by acting e.g. as microRNA sponges or regulating host gene expression. Recently, our group reported functionally relevant circRNA expression in endothelial cells. Despite their important role in the cardiovascular system, the expression and function of circRNAs in pericytes is not well studied. Pericytes are perivascular mural cells, important for vessel maturation and endothelial barrier function. Their recruitment towards endothelial cells is mainly meditated by platelet-derived growth factor (PDGF) signaling. However, a more precise understanding of the regulation of pericyte differentiation and survival is necessary. Objective Here, we analyse circRNA expression in pericytes and demonstrate biological relevance of the hypoxia regulated circular RNA PLOD2 (cPLOD2). Methods and results Using RNA Sequencing in ribosomal depleted RNA we characterized the expression of circRNAs in human pericytes under normoxic and hypoxic (1% O2, 48h) conditions. We identified several circular RNAs being regulated upon hypoxia. The identified circular RNAs demonstrated resistance towards RNase-R digestion and lacking of poly-adenylation. Some of them were found to be localized and in the cytosol, whereas others also occur in the nucleus of the cells. Especially cPLOD2 raised our attention since it is significantly upregulated and robustly expressed upon hypoxia. Silencing cPLOD2 by siRNA resulted in significant de-differentiation of pericytes that went along with a loss of cell viability. Mechanistically, transcription factor screening assays revealed that silencing of cPLOD2 enhances the activity of the transcription factors ELK1/SRF, which have been documented to result in de-differentiation of smooth muscle cells. Conclusion Here we characterize the expression pattern of circRNAs in human primary pericytes. Among others, cPLOD2 significantly regulates pericyte function. Our results indicate hypoxia as a major regulator of circRNA expression in pericytes and show that circRNAs are capable of regulating pericyte function by modulating activity of transcription factors. Funding Acknowledgement Type of funding source: Foundation. Main funding source(s): Deutsche Forschungsgesellschaft (DFG) - SFB834; Deutsche Gesellschaft für Herz-Kreislaufforschung (DZHK)

scholarly journals Editorial: Structural and Functional Characterization of Circular RNAs

2021 ◽  
Vol 8 ◽  
Author(s):  
Ioannis Grammatikakis ◽  
Florian A. Karreth ◽  
Amaresh C. Panda
Keyword(s):  
Functional Characterization ◽  
Circular Rnas

scholarly journals Genetic tools for the stable overexpression of circular RNAs

2021 ◽  
Author(s):  
Nicol Mecozzi ◽  
Arianna Nenci ◽  
Olga Vera ◽  
Aimee Falzone ◽  
Gina M DeNicola ◽  
...  
Keyword(s):  
Mouse Model ◽  
Cultured Cells ◽  
Functional Characterization ◽  
Ectopic Expression ◽  
Circular Rnas ◽  
Genetic Tools ◽  
Mammalian Expression ◽  
Biological Studies ◽  
Genetically Engineered Mice

Circular RNAs (circRNAs) are a class of non-coding RNAs that feature a covalently closed ring structure formed through backsplicing. circRNAs are broadly expressed and contribute to biological processes through a variety of functions. Standard gain-of-function and loss-of-function approaches to study gene functions have significant limitations when studying circRNAs. Overexpression studies in particular suffer from the lack of efficient genetic tools. While mammalian expression plasmids enable transient overexpression of circRNAs in cultured cells, most cell biological studies require long-term ectopic expression. Here we report the development and characterization of genetic tools enabling stable circRNA overexpression in vitro and in vivo. We demonstrated that circRNA expression constructs can be delivered to cultured cells via transposons, whereas lentiviral vectors have limited utility for the delivery of circRNA constructs. We further showed that circRNA transposons can be supplied to mouse livers via hydrodynamic tail vein injection, resulting in ectopic circRNA expression in a hepatocellular carcinoma mouse model. Furthermore, we generated genetically engineered mice harboring circRNA expression constructs. We demonstrate that this approach enables constitutive, global circRNA overexpression as well as inducible circRNA expression directed specifically to melanocytes in a melanoma mouse model. Overall, these tools expand the genetic toolkit available for the functional characterization of circRNAs of interest.

scholarly journals Functional characterization of the transcription regulator WhiB1 from Gordonia sp. IITR100

Microbiology ◽  
2020 ◽  
Vol 166 (12) ◽  
pp. 1181-1190
Author(s):  
Pooja Murarka ◽  
Aditi Keshav ◽  
Bintu Kumar Meena ◽  
Preeti Srivastava
Keyword(s):  
Type Species ◽  
Functional Characterization ◽  
Rhodococcus Erythropolis ◽  
Multiple Sequence ◽  
Content Type ◽  
Transcription Regulator ◽  
Link Type ◽  
Family Protein ◽  
The Family

WhiB is a transcription regulator which has been reported to be involved in the regulation of cell morphogenesis, cell division, antibiotic resistance, stress, etc., in several members of the family Actinomycetes . The present study describes functional characterization of a WhiB family protein, WhiB1 (protein ID: WP_065632651.1), from Gordonia sp. IITR100. We demonstrate that WhiB1 affects chromosome segregation and cell morphology in recombinant Escherichia coli , Gordonia sp. IITR100 as well as in Rhodococcus erythropolis . Multiple sequence alignment suggests that WhiB1 is a conserved protein among members of the family Actinomycetes . It has been reported that overexpression of WhiB1 leads to repression of the biodesulfurization operon in recombinant E. coli , Gordonia sp. IITR100 and R. erythropolis . A WhiB1-mut containing a point mutation Q116A in the DNA binding domain of WhiB1 led to partial alleviation of repression of the biodesulfurization operon. We show for the first time that the WhiB family protein WhiB1 is also involved in repression of the biodesulfurization operon by directly binding to the dsz promoter DNA.

scholarly journals FUCHS - Towards full circular RNA characterization using RNAseq

2016 ◽  
Author(s):  
Franziska Metge ◽  
Lisa F Czaja-Hasse ◽  
Richard Reinhardt ◽  
Chistoph Dieterich
Keyword(s):  
Splice Site ◽  
Developmental Stages ◽  
Computational Prediction ◽  
Break Point ◽  
Circular Rna ◽  
Circular Rnas ◽  
Functional Studies ◽  
Long Reads ◽  
Mirna Sponges ◽  
Rna Maturation

Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5’ splice site is linked to an upstream 3’ splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs could act as miRNA-sponges, the function of most circRNAs remains unknown. To expand our understanding of possible roles of circular RNAs, we propose a new pipeline that could fully characterizes candidate circRNA structure from RNAseq data – FUCHS: FUll CHaracterization of circular RNA using RNA- Sequencing. Currently, most computational prediction pipelines use back-spliced reads to identify circular RNAs. FUCHS extends this concept by considering all RNA-seq information from long reads (typically > 150 bp) to learn more about the exon coverage, the number of double break point fragments, the different circular isoforms arising from one host-gene, and the alternatively spliced exons within the same circRNA boundaries. This new knowledge will enable the user to carry out differential-motif enrichment and miRNA-seed analysis to determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-use Python based pipeline that contributes a new aspect to the circRNA research. The pipeline is available as git repository: https://github.com/dieterich-lab/FUCHS

Functional Characterization of Novel Circular RNA Molecule, circzip-2 and Its Synthesizing Gene zip-2 in C. elegans Model of Parkinson’s Disease

2018 ◽  
Vol 55 (8) ◽  
pp. 6914-6926 ◽  
Author(s):  
Lalit Kumar ◽  
Shamsuzzama ◽  
Pooja Jadiya ◽  
Rizwanul Haque ◽  
Shikha Shukla ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Functional Characterization ◽  
Circular Rna ◽  
C Elegans
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