Circular RNA: an important player with multiple facets to regulate its parental gene expression

Endometriosis is a pathology form of endometrium that behaves in a similar way to malignancies, such as invasion and resistance to apoptosis. Circular RNAs (CircRNAs) are a class of noncoding RNAs that have several biological functions including, miRNA sponging, sequestering of proteins, enhancing parental gene expression and translation resulting in polypeptides. In this review, we highlighted the roles of circRNAs as potential diagnostic and therapeutic biomarkers in endometriosis. Moreover, we summarized the roles of circRNAs in the pathogenesis of endometriosis via different signaling pathways, such as the miRNA network and apoptosis.

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The Toolbox for Untangling Chromosome Architecture in Immune Cells

Frontiers in Immunology ◽

10.3389/fimmu.2021.670884 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shuai Liu ◽

Keji Zhao

Keyword(s):

Gene Expression ◽

Immune Cells ◽

Spatial Organization ◽

Chromosome Structure ◽

Immune Cell ◽

Genome Structure ◽

Chromosome Architecture ◽

The Past ◽

Important Player ◽

The Way

The code of life is not only encrypted in the sequence of DNA but also in the way it is organized into chromosomes. Chromosome architecture is gradually being recognized as an important player in regulating cell activities (e.g., controlling spatiotemporal gene expression). In the past decade, the toolbox for elucidating genome structure has been expanding, providing an opportunity to explore this under charted territory. In this review, we will introduce the recent advancements in approaches for mapping spatial organization of the genome, emphasizing applications of these techniques to immune cells, and trying to bridge chromosome structure with immune cell activities.

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An antisense circular RNA circSCRIB enhances cancer progression by suppressing parental gene splicing and translation

Molecular Therapy ◽

10.1016/j.ymthe.2021.08.002 ◽

2021 ◽

Author(s):

Jian Ma ◽

William W. Du ◽

Kaixuan Zeng ◽

Nan Wu ◽

Ling Fang ◽

...

Keyword(s):

Cancer Progression ◽

Circular Rna ◽

Gene Splicing ◽

Parental Gene

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Circular RNA circFAT1(e2) Promotes Osteosarcoma Progression and Metastasis by Sponging miR-181b and Regulating HK2 Expression

BioMed Research International ◽

10.1155/2020/3589871 ◽

2020 ◽

Vol 2020 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Huijie Gu ◽

Xiangyang Cheng ◽

Jun Xu ◽

Kaifeng Zhou ◽

Chong Bian ◽

...

Keyword(s):

Gene Expression ◽

Cancer Progression ◽

Therapeutic Target ◽

Critical Role ◽

Noncoding Rnas ◽

Circular Rna ◽

Expression Level ◽

Circular Rnas ◽

Competing Endogenous Rna ◽

Potential Therapeutic Target

As a subclass of noncoding RNAs, circular RNAs (circRNAs) have been demonstrated to play a critical role in regulating gene expression in eukaryotes. Recent studies have revealed the pivotal functions of circRNAs in cancer progression. Nevertheless, how circRNAs participate in osteosarcoma (OS) development and progression are not well understood. In the present study, we identified a circRNA circFAT1(e2) with an upregulated expression level in OS tissues. By functional experiments, we found that circFAT1(e2) depletion significantly suppressed the proliferation and reduced migration in OS. In terms of mechanism, we found that circFAT1(e2) inhibited miR-181b, while miR-181b targeted HK2. By releasing the inhibition of miR-181b on HK2 expression, leading to attenuated OS progression. Mechanistic investigations suggested that circFAT1(e2) served as a competing endogenous RNA (ceRNA) of miR-181b to enhance HK2 expression. On the whole, our study indicated that circFAT1(e2) exerted oncogenic roles in OS and suggested the circFAT1(e2)/miR-181b/HK2 axis might be a potential therapeutic target.

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Circular RNAs in Cardiovascular Disease: An Overview

BioMed Research International ◽

10.1155/2017/5135781 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 66

Author(s):

Ximin Fan ◽

Xinyu Weng ◽

Yifan Zhao ◽

Wei Chen ◽

Tianyi Gan ◽

...

Keyword(s):

Gene Expression ◽

Cardiovascular Disease ◽

Cardiovascular Diseases ◽

Noncoding Rna ◽

Essential Role ◽

Closed Loop ◽

Regulation Of Gene Expression ◽

Circular Rna ◽

Circular Rnas ◽

Mirna Sponges

Circular RNA (circRNA), a novel type of endogenous noncoding RNA (ncRNA), has become a research hotspot in recent years. CircRNAs are abundant and stably exist in creatures, and they are found with covalently closed loop structures in which they are quite different from linear RNAs. Nowadays, an increasing number of scientists have demonstrated that circRNAs may have played an essential role in the regulation of gene expression, especially acting as miRNA sponges, and have described the potential mechanisms of several circRNAs in diseases, hinting at their clinical therapeutic values. In this review, the authors summarized the current understandings of the biogenesis and properties of circRNAs and their functions and role as biomarkers in cardiovascular diseases.

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The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules?

Life ◽

10.3390/life11121354 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1354

Author(s):

Maciej Stasiak ◽

Tomasz Kolenda ◽

Joanna Kozłowska-Masłoń ◽

Joanna Sobocińska ◽

Paulina Poter ◽

...

Keyword(s):

Gene Expression ◽

Molecular Diagnostics ◽

Antisense Rna ◽

Biological Fluids ◽

Detection Methods ◽

Bioinformatic Tools ◽

The World ◽

Parental Gene ◽

Different Types ◽

Large Groups

Pseudogenes were once considered as “junk DNA”, due to loss of their functions as a result of the accumulation of mutations, such as frameshift and presence of premature stop-codons and relocation of genes to inactive heterochromatin regions of the genome. Pseudogenes are divided into two large groups, processed and unprocessed, according to their primary structure and origin. Only 10% of all pseudogenes are transcribed into RNAs and participate in the regulation of parental gene expression at both transcriptional and translational levels through senseRNA (sRNA) and antisense RNA (asRNA). In this review, about 150 pseudogenes in the different types of cancers were analyzed. Part of these pseudogenes seem to be useful in molecular diagnostics and can be detected in various types of biological material including tissue as well as biological fluids (liquid biopsy) using different detection methods. The number of pseudogenes, as well as their function in the human genome, is still unknown. However, thanks to the development of various technologies and bioinformatic tools, it was revealed so far that pseudogenes are involved in the development and progression of certain diseases, especially in cancer.

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Current view on the helicase activity of RNA helicase A and its role in gene expression

Current Protein and Peptide Science ◽

10.2174/1389203721666201103084122 ◽

2020 ◽

Vol 21 ◽

Author(s):

Yuan-Qing Pan ◽

Li Xing

Keyword(s):

Gene Expression ◽

Rna Splicing ◽

Rna Helicase ◽

Circular Rna ◽

Nucleoside Triphosphate ◽

Current View ◽

Helicase Activity ◽

Rna Helicase A ◽

Cellular Processes

: RNA helicase A (RHA) is a DExH-box helicase that plays regulatory roles in a variety of cellular processes including transcription, translation, RNA splicing, editing, transport, and processing, microRNA genesis and maintenance of genomic stability. It is involved in virus replication, oncogenesis, and innate immune response. RHA can unwind nucleic acid duplex by nucleoside triphosphate hydrolysis. The insight into molecular mechanism of helicase activity is fundamental to understanding the role of RHA in the cell. Herein, we reviewed the current advances on the helicase activity of RHA and its relevance to gene expression, particularly, to genesis of circular RNA.

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Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the AllotetraploidArabidopsis kamchatica

Molecular Biology and Evolution ◽

10.1093/molbev/msw141 ◽

2016 ◽

Vol 33 (11) ◽

pp. 2781-2800 ◽

Cited By ~ 23

Author(s):

Timothy Paape ◽

Masaomi Hatakeyama ◽

Rie Shimizu-Inatsugi ◽

Teo Cereghetti ◽

Yoshihiko Onda ◽

...

Keyword(s):

Gene Expression ◽

Parental Gene

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Circular RNA biogenesis can proceed through an exon-containing lariat precursor

eLife ◽

10.7554/elife.07540 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 184

Author(s):

Steven P Barrett ◽

Peter L Wang ◽

Julia Salzman

Keyword(s):

Gene Expression ◽

Mammalian Cell Culture ◽

Circular Rna ◽

Inverted Repeats ◽

Systematic Effect ◽

Eukaryotic Gene Expression ◽

Sequence Elements ◽

Eukaryotic Gene ◽

Rna Biogenesis ◽

Site Mutagenesis

Pervasive expression of circular RNA is a recently discovered feature of eukaryotic gene expression programs, yet its function remains largely unknown. The presumed biogenesis of these RNAs involves a non-canonical ‘backsplicing’ event. Recent studies in mammalian cell culture posit that backsplicing is facilitated by inverted repeats flanking the circularized exon(s). Although such sequence elements are common in mammals, they are rare in lower eukaryotes, making current models insufficient to describe circularization. Through systematic splice site mutagenesis and the identification of splicing intermediates, we show that circular RNA in Schizosaccharomyces pombe is generated through an exon-containing lariat precursor. Furthermore, we have performed high-throughput and comprehensive mutagenesis of a circle-forming exon, which enabled us to discover a systematic effect of exon length on RNA circularization. Our results uncover a mechanism for circular RNA biogenesis that may account for circularization in genes that lack noticeable flanking intronic secondary structure.

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Global Analysis of Tomato Gene Expression During Potato spindle tuber viroid Infection Reveals a Complex Array of Changes Affecting Hormone Signaling

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-09-11-0258 ◽

2012 ◽

Vol 25 (4) ◽

pp. 582-598 ◽

Cited By ~ 65

Author(s):

Robert A. Owens ◽

Kimberly B. Tech ◽

Jonathan Y. Shao ◽

Teruo Sano ◽

C. Jacyn Baker

Keyword(s):

Gene Expression ◽

Messenger Rna ◽

Large Scale ◽

Global Analysis ◽

Potato Spindle Tuber Viroid ◽

Circular Rna ◽

Small Interfering Rnas ◽

Viroid Infection ◽

Disease Induction ◽

Tomato Gene

Viroids like Potato spindle tuber viroid (PSTVd) are the smallest known agents of infectious disease—small, highly structured, circular RNA molecules that lack detectable messenger RNA activity, yet are able to replicate autonomously in susceptible plant species. To better understand the possible role of RNA silencing in disease induction, a combination of microarray analysis and large-scale RNA sequence analysis was used to compare changes in tomato gene expression and microRNA levels associated with PSTVd infection in two tomato cultivars plus a third transformed line expressing small PSTVd small interfering RNAs in the absence of viroid replication. Changes in messenger (m)RNA levels for the sensitive cultivar ‘Rutgers’ were extensive, involving more than half of the approximately 10,000 genes present on the array. Chloroplast biogenesis was down-regulated in both sensitive and tolerant cultivars, and effects on mRNAs encoding enzymes involved in the biosynthesis of gibberellin and other hormones were accompanied by numerous changes affecting their respective signaling pathways. In the dwarf cultivar ‘MicroTom’, a marked upregulation of genes involved in response to stress and other stimuli was observed only when exogenous brassinosteroid was applied to infected plants, thereby providing the first evidence for the involvement of brassinosteroid-mediated signaling in viroid disease induction.

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