1601
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Jarroux J, Morillon A, Pinskaya M. History, Discovery, and Classification of lncRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:1-46. [PMID: 28815535 DOI: 10.1007/978-981-10-5203-3_1] [Citation(s) in RCA: 606] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s. Thirty years later, the first regulatory non-coding RNAs (ncRNAs) were initially identified in bacteria and then in most eukaryotic organisms. A few long ncRNAs (lncRNAs) such as H19 and Xist were characterized in the pre-genomic era but remained exceptions until the early 2000s. Indeed, when the sequence of the human genome was published in 2001, studies showed that only about 1.2% encodes proteins, the rest being deemed "non-coding." It was later shown that the genome is pervasively transcribed into many ncRNAs, but their functionality remained controversial. Since then, regulatory lncRNAs have been characterized in many species and were shown to be involved in processes such as development and pathologies, revealing a new layer of regulation in eukaryotic cells. This newly found focus on lncRNAs, together with the advent of high-throughput sequencing, was accompanied by the rapid discovery of many novel transcripts which were further characterized and classified according to specific transcript traits.In this review, we will discuss the many discoveries that led to the study of lncRNAs, from Friedrich Miescher's "nuclein" in 1869 to the elucidation of the human genome and transcriptome in the early 2000s. We will then focus on the biological relevance during lncRNA evolution and describe their basic features as genes and transcripts. Finally, we will present a non-exhaustive catalogue of lncRNA classes, thus illustrating the vast complexity of eukaryotic transcriptomes.
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Affiliation(s)
- Julien Jarroux
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France.
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France
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1602
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Devaux Y. Transcriptome of blood cells as a reservoir of cardiovascular biomarkers. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:209-216. [DOI: 10.1016/j.bbamcr.2016.11.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 02/07/2023]
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1603
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Wang Z, Liu Y, Li D, Li L, Zhang Q, Wang S, Huang H. Identification of Circular RNAs in Kiwifruit and Their Species-Specific Response to Bacterial Canker Pathogen Invasion. FRONTIERS IN PLANT SCIENCE 2017; 8:413. [PMID: 28396678 PMCID: PMC5366334 DOI: 10.3389/fpls.2017.00413] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/10/2017] [Indexed: 05/19/2023]
Abstract
Research studies have recently focused on circle RNAs (circRNAs) in relation to their regulatory functions in animals. However, the systematic identification of circRNAs in plants, especially non-model plants, is limited. In addition, raw report on the prediction of the potential role of circRNAs in plant response to pathogen invasion is currently available. We conducted the systematic identification of circRNAs from four materials originating from three species belonging to genus Actinidia under different situations using ribosomal RNA (rRNA) depleted RNA-Seq data. A total of 3,582 circRNAs were identified in Actinidia, of which 64.01, 21.44, and 14.55% were intergenic circRNAs, exonic circRNAs, and intronic circRNAs, respectively. Tissue-specific expression of circRNAs was observed in kiwifruit, and a species-specific response was detected when infected with Pseudomonas syringae pv. actinidiae (Psa), which is the causative agent of kiwifruit bacterial canker disease. Furthermore, we found that both exonic and intronic circRNAs were significantly positively correlated to parent protein-coding genes, and intronic circRNAs are a class of highly remarkable regulators the parent genes comparing to that of exonic circRNAs. Expression and weighted gene co-expression network analysis (WGCNA) identified a set of circRNAs that were closely associated with plant defense response. The findings of the presents study suggest that circRNAs exhibit tissue- and species-specific expression, as well as play an important role in plant immune response.
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Affiliation(s)
- Zupeng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied BotanyGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied BotanyGuangzhou, China
- *Correspondence: Yifei Liu
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, The Chinese Academy of SciencesWuhan, China
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, The Chinese Academy of SciencesWuhan, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, The Chinese Academy of SciencesWuhan, China
| | - Shuaibin Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied BotanyGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Hongwen Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied BotanyGuangzhou, China
- Hongwen Huang
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1604
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Shen Y, Guo X, Wang W. Identification and characterization of circular RNAs in zebrafish. FEBS Lett 2016; 591:213-220. [DOI: 10.1002/1873-3468.12500] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Yudong Shen
- College of Fisheries; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding; Ministry of Agriculture; Huazhong Agricultural University; Wuhan Hubei China
| | - Xianwu Guo
- Lab of Biotecnología Genómica; Centro de Biotecnología Genómica; Instituto de Politécnico Nacional; Reynosa Tamaulipas Mexico
| | - Weimin Wang
- College of Fisheries; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding; Ministry of Agriculture; Huazhong Agricultural University; Wuhan Hubei China
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1605
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Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNA characterized by a covalently closed-loop structure generated through a special type of alternative splicing termed backsplicing. CircRNAs are emerging as a heterogeneous class of molecules involved in modulating gene expression by regulation of transcription, protein and miRNA functions. CircRNA expression is cell type and tissue specific and can be largely independent of the expression level of the linear host gene, indicating that regulation of expression might be an important aspect with regard to control of circRNA function. In this review, a brief introduction to the characteristics that define a circRNA will be given followed by a discussion of putative biogenesis pathways and modulators of circRNA expression as well as of the stage at which circRNA formation takes place. A brief summary of circRNA functions will also be provided and lastly, an outlook with a focus on unanswered questions regarding circRNA biology will be included.
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Affiliation(s)
- Karoline K Ebbesen
- a Department of Molecular Biology and Genetics (MBG) and Aarhus University , Aarhus , Denmark.,b Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Aarhus , Denmark
| | - Thomas B Hansen
- a Department of Molecular Biology and Genetics (MBG) and Aarhus University , Aarhus , Denmark
| | - Jørgen Kjems
- a Department of Molecular Biology and Genetics (MBG) and Aarhus University , Aarhus , Denmark.,b Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Aarhus , Denmark
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1606
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Dong WW, Li HM, Qing XR, Huang DH, Li HG. Identification and characterization of human testis derived circular RNAs and their existence in seminal plasma. Sci Rep 2016; 6:39080. [PMID: 27958373 PMCID: PMC5153637 DOI: 10.1038/srep39080] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs. Though they have been explored in some species and tissues, the expression and functions of circRNAs in human reproductive systems remain unknown. Here we revealed the expression profiles of circRNAs in human testis tissue using high-throughput sequencing. The conformation of these testis-derived circRNAs in seminal plasma was also investigated, aiming to provide a non-invasive liquid biopsy surrogate for testicular biopsy. We predicted >15,000 circRNAs in human testis, with most of them (10,792; 67%) new. In all the 5,928 circRNA forming genes, 1,017 are first reported by us to generate circRNAs. Interestingly, these genes are mostly related to spermatogenesis, sperm motility, fertilization, etc. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs in human testis were also explored. Moreover, we found that these testis-derived circRNAs could be stably detected in seminal plasma. Most of them were probably bound with proteins in seminal plasma and were very stable at room temperature. Our work has laid the foundations to decipher regulation mechanisms of circRNAs in spermatogenesis and to develop circRNAs as novel noninvasive biomarkers for male infertile diseases.
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Affiliation(s)
- Wei-Wei Dong
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Hui-Min Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xing-Rong Qing
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Dong-Hui Huang
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, 430030, P. R. China
| | - Hong-Gang Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, 430030, P. R. China
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1607
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Abstract
Circular RNAs (circRNAs) are a newly appreciated class of RNAs expressed across diverse phyla. These enigmatic transcripts are most commonly generated by back-splicing events from exons of protein-coding genes. This results in highly stable RNAs due to the lack of free 5′ and 3′ ends. CircRNAs are enriched in neural tissues, suggesting that they might have neural functions. Here, we sought to determine whether circRNA accumulation occurs during aging in mice. Total RNA-seq profiling of young (1 month old) and aged (22 month old) cortex, hippocampus and heart samples was performed. This led to the confident detection of 6,791 distinct circRNAs across these samples, including 675 novel circRNAs. Analysis uncovered a strong bias for circRNA upregulation during aging in neural tissues. These age-accumulation trends were verified for individual circRNAs by RT-qPCR and Northern analysis. In contrast, comparison of aged versus young hearts failed to reveal a global trend for circRNA upregulation. Age-accumulation of circRNAs in brain tissues was found to be largely independent from linear RNA expression of host genes. These findings suggest that circRNAs might play biological roles relevant to the aging nervous system.
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1608
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Gokoolparsadh A, Sutton GJ, Charamko A, Green NFO, Pardy CJ, Voineagu I. Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies. Cell Mol Life Sci 2016; 73:4517-4530. [PMID: 27405608 PMCID: PMC11108267 DOI: 10.1007/s00018-016-2304-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/16/2016] [Accepted: 07/05/2016] [Indexed: 01/07/2023]
Abstract
Autism spectrum disorder (ASD) is one of the most heritable neuropsychiatric conditions. The complex genetic landscape of the disorder includes both common and rare variants at hundreds of genetic loci. This marked heterogeneity has thus far hampered efforts to develop genetic diagnostic panels and targeted pharmacological therapies. Here, we give an overview of the current literature on the genetic basis of ASD, and review recent human brain transcriptome studies and their role in identifying convergent pathways downstream of the heterogeneous genetic variants. We also discuss emerging evidence on the involvement of non-coding genomic regions and non-coding RNAs in ASD.
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Affiliation(s)
- Akira Gokoolparsadh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Gavin J Sutton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Alexiy Charamko
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Nicole F Oldham Green
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Christopher J Pardy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia.
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1609
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Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes. Sci Rep 2016; 6:37982. [PMID: 27892494 PMCID: PMC5125100 DOI: 10.1038/srep37982] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 11/01/2016] [Indexed: 01/14/2023] Open
Abstract
Recent studies have shown that circular RNAs (circRNAs) are abundant, widely expressed in mammals, and can display cell-type specific expression. However, how production of circRNAs is regulated and their precise biological function remains largely unknown. To study how circRNAs might be regulated during colorectal cancer progression, we used three isogenic colon cancer cell lines that differ only in KRAS mutation status. Cellular RNAs from the parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically-matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRAS allele only) were analyzed using RNA-Seq. We developed a bioinformatics pipeline to identify and evaluate circRNA candidates from RNA-Seq data. Hundreds of high-quality circRNA candidates were identified in each cell line. Remarkably, circRNAs were significantly down-regulated at a global level in DLD-1 and DKO-1 cells compared to DKs-8 cells, indicating a widespread effect of mutant KRAS on circRNA abundance. This finding was confirmed in two independent colon cancer cell lines HCT116 (KRAS mutant) and HKe3 (KRAS WT). In all three cell lines, circRNAs were also found in secreted extracellular-vesicles, and circRNAs were more abundant in exosomes than cells. Our results suggest that circRNAs may serve as promising cancer biomarkers.
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1610
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Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis. PLoS Genet 2016; 12:e1006422. [PMID: 27870853 PMCID: PMC5147768 DOI: 10.1371/journal.pgen.1006422] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 10/12/2016] [Indexed: 11/19/2022] Open
Abstract
Lariat RNAs formed as by-products of splicing are quickly degraded by the RNA debranching enzyme 1 (DBR1), leading to their turnover. Null dbr1 mutants in both animals and plants are embryo lethal, but the mechanism underlying the lethality remains unclear. Here we characterized a weak mutant allele of DBR1 in Arabidopsis, dbr1-2, and showed that a global increase in lariat RNAs was unexpectedly accompanied by a genome-wide reduction in miRNA accumulation. The dbr1-2 mutation had no effects on expression of miRNA biogenesis genes or primary miRNAs (pri-miRNAs), but the association of pri-miRNAs with the DCL1/HYL1 dicing complex was impaired. Lariat RNAs were associated with the DCL1/HYL1 dicing complex in vivo and competitively inhibited the binding of HYL1 with pri-miRNA. Consistent with the impacts of lariat RNAs on miRNA biogenesis, over-expression of lariat RNAs reduced miRNA accumulation. Lariat RNAs localized in nuclear bodies, and partially co-localize with HYL1, and both DCL1 and HYL1 were mis-localized in dbr1-2. Together with our findings that nearly four hundred lariat RNAs exist in wild type plants and that these lariat RNAs also associate with the DCL1/HYL1 dicing complex in vivo, we thus propose that lariat RNAs, as decoys, inhibit miRNA processing, suggesting a hitherto unknown layer of regulation in miRNA biogenesis. It is known that lariat RNAs formed during pre-mRNA splicing are debranched by DBR1 (RNA debranching enzyme 1). Loss of function of DBR1 causes embryo lethality in both animals and plants. In animals, some debranched lariat RNAs could be further processed into mirtron miRNAs, a class of nonconventional miRNAs that bypass the microprocessor for their biogenesis. However, no mirtron has been functionally validated in plants, and how the accumulation of lariat RNA in dbr1 results in embryo lethality remains unclear. Here, we show that DBR1 is necessary for the regulation of genome-wide miRNA biogenesis in plants. By investigating the correlation between lariat RNA accumulation and miRNA processing, we showed that the DBR1-mediated lariat RNA debranching process provides a safeguard role for the binding of the dicing complex with miRNA precursors. As both the DBR1-mediated lariat RNA debranching process and miRNA biogenesis are common features in higher eukaryotes, the finding that lariat RNAs sequester the dicing complex in plants may have a broad implications for the non-coding RNA field.
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1611
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Frank S, Aguirre A, Hescheler J, Kurian L. A lncRNA Perspective into (Re)Building the Heart. Front Cell Dev Biol 2016; 4:128. [PMID: 27882316 PMCID: PMC5101577 DOI: 10.3389/fcell.2016.00128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/26/2016] [Indexed: 11/30/2022] Open
Abstract
Our conception of the human genome, long focused on the 2% that codes for proteins, has profoundly changed since its first draft assembly in 2001. Since then, an unanticipatedly expansive functionality and convolution has been attributed to the majority of the genome that is transcribed in a cell-type/context-specific manner into transcripts with no apparent protein coding ability. While the majority of these transcripts, currently annotated as long non-coding RNAs (lncRNAs), are functionally uncharacterized, their prominent role in embryonic development and tissue homeostasis, especially in the context of the heart, is emerging. In this review, we summarize and discuss the latest advances in understanding the relevance of lncRNAs in (re)building the heart.
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Affiliation(s)
- Stefan Frank
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of CologneCologne, Germany; Institute for Neurophysiology, University of CologneCologne, Germany; Center for Molecular Medicine (CMMC), University of CologneCologne, Germany
| | - Aitor Aguirre
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego La Jolla, CA, USA
| | - Juergen Hescheler
- Institute for Neurophysiology, University of Cologne Cologne, Germany
| | - Leo Kurian
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of CologneCologne, Germany; Institute for Neurophysiology, University of CologneCologne, Germany; Center for Molecular Medicine (CMMC), University of CologneCologne, Germany
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1612
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Xing YH, Bai Z, Liu CX, Hu SB, Ruan M, Chen LL. Research progress of long noncoding RNA in China. IUBMB Life 2016; 68:887-893. [DOI: 10.1002/iub.1564] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- Yu-Hang Xing
- State Key Laboratory of Molecular Biology; Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; Shanghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Zhiqiang Bai
- State Key Laboratory of Molecular Biology; Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; Shanghai China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology; Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; Shanghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Shi-Bin Hu
- State Key Laboratory of Molecular Biology; Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; Shanghai China
- University of Chinese Academy of Sciences; Beijing China
| | - Meihua Ruan
- Shanghai Information Center for Life Sciences; Chinese Academy of Sciences; Shanghai China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology; Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; Shanghai China
- School of Life Science; ShanghaiTech University; Shanghai China
- University of Chinese Academy of Sciences; Beijing China
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1613
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Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins. Mol Cell 2016; 64:534-548. [DOI: 10.1016/j.molcel.2016.10.007] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/22/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022]
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1614
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Kumar L, Shamsuzzama, Haque R, Baghel T, Nazir A. Circular RNAs: the Emerging Class of Non-coding RNAs and Their Potential Role in Human Neurodegenerative Diseases. Mol Neurobiol 2016; 54:7224-7234. [PMID: 27796758 DOI: 10.1007/s12035-016-0213-8] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023]
Abstract
The exciting world of research with RNAs has to its credit some breakthrough findings that led to newer insights on multiple problems including that of human diseases. After the advent of siRNA, microRNA, and lncRNA, exciting novel molecules called circular RNAs (circRNAs) have been recently described. circRNAs are a class of non-coding RNAs, which are produced by scrambling of exons at the time of splicing. They are primarily produced in the brain region and are naturally present inside the cell. The best known ones so far include a particular type of circRNA namely "circular RNA sponge for miR-7" (ciRS-7 and CDR1as) which is the inhibitor of miR-7 microRNA-known to regulate various diseases like, cancer, neurodegenerative diseases, diabetes, and atherosclerosis. Similarly, another circRNA molecule called circmbl modulates the ratio of linear mRNA by competing with linear muscleblind gene through which it is synthesized. Considering the complex association of these molecules with critical microRNAs and gene families, circRNAs might have important roles in the cause and progression of human diseases. In particular, the multi-factorial nature of neurodegenerative diseases does warrant studies employing novel approaches towards identifying underlying root causes of these ailments. The non-coding RNAs, like circRNAs and microRNAs, could well present a common genetic trigger to multiple factors associated with neurodegenerative diseases. A specific fingerprint of a combination of various marker circRNAs could be explored for early diagnostic purpose as well. Herein, we review the possibility of exploring the role of circRNAs in the context of the central nervous system (CNS) and age-associated neurodegenerative diseases.
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Affiliation(s)
- Lalit Kumar
- Laboratory of Functional Genomics and Molecular Toxicology, Division of Toxicology, CSIR-Central Drug Research Institute, Lucknow, 226 031, India
| | - Shamsuzzama
- Laboratory of Functional Genomics and Molecular Toxicology, Division of Toxicology, CSIR-Central Drug Research Institute, Lucknow, 226 031, India
| | - Rizwanul Haque
- Laboratory of Functional Genomics and Molecular Toxicology, Division of Toxicology, CSIR-Central Drug Research Institute, Lucknow, 226 031, India
| | - Tanvi Baghel
- Laboratory of Functional Genomics and Molecular Toxicology, Division of Toxicology, CSIR-Central Drug Research Institute, Lucknow, 226 031, India
| | - Aamir Nazir
- Laboratory of Functional Genomics and Molecular Toxicology, Division of Toxicology, CSIR-Central Drug Research Institute, Lucknow, 226 031, India.
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1615
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Bobola N, Merabet S. Homeodomain proteins in action: similar DNA binding preferences, highly variable connectivity. Curr Opin Genet Dev 2016; 43:1-8. [PMID: 27768937 DOI: 10.1016/j.gde.2016.09.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 09/28/2016] [Indexed: 12/18/2022]
Abstract
Homeodomain proteins are evolutionary conserved proteins present in the entire eukaryote kingdom. They execute functions that are essential for life, both in developing and adult organisms. Most homeodomain proteins act as transcription factors and bind DNA to control the activity of other genes. In contrast to their similar DNA binding specificity, homeodomain proteins execute highly diverse and context-dependent functions. Several factors, including genome accessibility, DNA shape, combinatorial binding and the ability to interact with many transcriptional partners, diversify the activity of homeodomain proteins and culminate in the activation of highly dynamic, context-specific transcriptional programs. Clarifying how homeodomain transcription factors work is central to our understanding of development, disease and evolution.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de Recherche Scientifique, Ecole Normale Supérieure de Lyon, France.
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1616
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Ye CY, Zhang X, Chu Q, Liu C, Yu Y, Jiang W, Zhu QH, Fan L, Guo L. Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice. RNA Biol 2016; 14:1055-1063. [PMID: 27739910 DOI: 10.1080/15476286.2016.1245268] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice. We further showed that alternative circularization of circRNA is a common feature in rice and, surprisingly, found that the junction sites of a large number of rice circRNAs are flanked by diverse non-GT/AG splicing signals while most human exonic circRNAs are flanked by canonical GT/AG splicing signals. Our study provides a method for genome-wide identification of full-length circRNAs and expands our understanding of splicing signals of circRNAs.
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Affiliation(s)
- Chu-Yu Ye
- a Institute of Crop Sciences, Zhejiang University , Hangzhou , China
| | - Xingchen Zhang
- a Institute of Crop Sciences, Zhejiang University , Hangzhou , China
| | - Qinjie Chu
- a Institute of Crop Sciences, Zhejiang University , Hangzhou , China
| | - Chen Liu
- a Institute of Crop Sciences, Zhejiang University , Hangzhou , China
| | - Yongyi Yu
- a Institute of Crop Sciences, Zhejiang University , Hangzhou , China
| | - Weiqin Jiang
- c The First Affiliated Hospital, Zhejiang University , Hangzhou , China
| | - Qian-Hao Zhu
- d CSIRO Agriculture and Food, Black Mountain Laboratories , Canberra , Australia
| | - Longjiang Fan
- a Institute of Crop Sciences, Zhejiang University , Hangzhou , China.,b Institute of Bioinformatics, Zhejiang University , Hangzhou , China
| | - Longbiao Guo
- e China National Rice Research Institute, Chinese Academy of Agricultural Sciences , Hangzhou , China
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1617
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Affiliation(s)
- Nicolas Jaé
- From the Institute of Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Germany (N.J., S.D.); and German Center of Cardiovascular Research (DZHK), Germany (S.D.)
| | - Stefanie Dimmeler
- From the Institute of Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Germany (N.J., S.D.); and German Center of Cardiovascular Research (DZHK), Germany (S.D.).
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1618
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Bonizzato A, Gaffo E, te Kronnie G, Bortoluzzi S. CircRNAs in hematopoiesis and hematological malignancies. Blood Cancer J 2016; 6:e483. [PMID: 27740630 PMCID: PMC5098259 DOI: 10.1038/bcj.2016.81] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022] Open
Abstract
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.
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Affiliation(s)
- A Bonizzato
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - E Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy
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1619
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circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations. Sci Rep 2016; 6:34985. [PMID: 27725737 PMCID: PMC5057092 DOI: 10.1038/srep34985] [Citation(s) in RCA: 349] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/21/2016] [Indexed: 11/09/2022] Open
Abstract
It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.
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1620
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Abstract
Circular RNAs (circRNAs) are novel endogenous non-coding RNAs characterized by the presence of a covalent bond linking the 3' and 5' ends generated by backsplicing. In this review, we summarize a number of the latest theories regarding the biogenesis, properties and functions of circRNAs. Specifically, we focus on the advancing characteristics and functions of circRNAs in the brain and neurological diseases. CircRNAs exhibit the characteristics of species conservation, abundance and tissue/developmental-stage-specific expression in the brain. We also describe the relationship between circRNAs and several neurological diseases and highlight their functions in neurological diseases.
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Affiliation(s)
- Tao-Ran Li
- a Department of Neurology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou University , Zhengzhou , PR. China.,b Department of Neurology, Beijing Tiantan Hospital , Capital Medical University , Beijing , PR. China ; China National Clinical Research Center for Neurological Diseases , Beijing , PR. China
| | - Yan-Jie Jia
- a Department of Neurology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou University , Zhengzhou , PR. China
| | - Qun Wang
- b Department of Neurology, Beijing Tiantan Hospital , Capital Medical University , Beijing , PR. China ; China National Clinical Research Center for Neurological Diseases , Beijing , PR. China
| | - Xiao-Qiu Shao
- b Department of Neurology, Beijing Tiantan Hospital , Capital Medical University , Beijing , PR. China ; China National Clinical Research Center for Neurological Diseases , Beijing , PR. China
| | - Rui-Juan Lv
- b Department of Neurology, Beijing Tiantan Hospital , Capital Medical University , Beijing , PR. China ; China National Clinical Research Center for Neurological Diseases , Beijing , PR. China
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1621
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Deciphering the roles of circRNAs on chilling injury in tomato. Biochem Biophys Res Commun 2016; 479:132-138. [DOI: 10.1016/j.bbrc.2016.07.032] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 01/17/2023]
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1622
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Beermann J, Piccoli MT, Viereck J, Thum T. Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches. Physiol Rev 2016; 96:1297-1325. [PMID: 27535639 DOI: 10.1152/physrev.00041.2015] [Citation(s) in RCA: 1320] [Impact Index Per Article: 146.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Advances in RNA-sequencing techniques have led to the discovery of thousands of non-coding transcripts with unknown function. There are several types of non-coding linear RNAs such as microRNAs (miRNA) and long non-coding RNAs (lncRNA), as well as circular RNAs (circRNA) consisting of a closed continuous loop. This review guides the reader through important aspects of non-coding RNA biology. This includes their biogenesis, mode of actions, physiological function, as well as their role in the disease context (such as in cancer or the cardiovascular system). We specifically focus on non-coding RNAs as potential therapeutic targets and diagnostic biomarkers.
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Affiliation(s)
- Julia Beermann
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Maria-Teresa Piccoli
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Janika Viereck
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; and National Heart and Lung Institute, Imperial College London, London, United Kingdom
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1623
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Rebijith KB, Asokan R, Hande HR, Krishna Kumar NK. The First Report of miRNAs from a Thysanopteran Insect, Thrips palmi Karny Using High-Throughput Sequencing. PLoS One 2016; 11:e0163635. [PMID: 27685664 PMCID: PMC5042526 DOI: 10.1371/journal.pone.0163635] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/12/2016] [Indexed: 12/15/2022] Open
Abstract
Thrips palmi Karny (Thysanoptera: Thripidae) is the sole vector of Watermelon bud necrosis tospovirus, where the crop loss has been estimated to be around USD 50 million annually. Chemical insecticides are of limited use in the management of T. palmi due to the thigmokinetic behaviour and development of high levels of resistance to insecticides. There is an urgent need to find out an effective futuristic management strategy, where the small RNAs especially microRNAs hold great promise as a key player in the growth and development. miRNAs are a class of short non-coding RNAs involved in regulation of gene expression either by mRNA cleavage or by translational repression. We identified and characterized a total of 77 miRNAs from T. palmi using high-throughput deep sequencing. Functional classifications of the targets for these miRNAs revealed that majority of them are involved in the regulation of transcription and translation, nucleotide binding and signal transduction. We have also validated few of these miRNAs employing stem-loop RT-PCR, qRT-PCR and Northern blot. The present study not only provides an in-depth understanding of the biological and physiological roles of miRNAs in governing gene expression but may also lead as an invaluable tool for the management of thysanopteran insects in the future.
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Affiliation(s)
- K. B. Rebijith
- Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India
- * E-mail: ;
| | - R. Asokan
- Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India
- * E-mail: ;
| | - H. Ranjitha Hande
- Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India
| | - N. K. Krishna Kumar
- Division of Horticultural Science, Indian Council of Agricultural Research, New Delhi, India
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1624
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Abstract
Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.
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Affiliation(s)
- Sabine Müller
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
| | - Bettina Appel
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
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1625
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Kulcheski FR, Christoff AP, Margis R. Circular RNAs are miRNA sponges and can be used as a new class of biomarker. J Biotechnol 2016; 238:42-51. [PMID: 27671698 DOI: 10.1016/j.jbiotec.2016.09.011] [Citation(s) in RCA: 597] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/18/2016] [Accepted: 09/23/2016] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that are involved in transcriptional and posttranscriptional gene expression regulation. The development of deep sequencing of ribosomal RNA (rRNA)-depleted RNA libraries, associated with improved computational tools, has provided the identification of several new circRNAs in all sorts of organisms, from protists, plants and fungi to animals. Recently, it was discovered that endogenous circRNAs can work as microRNA (miRNA) sponges. This means that the circRNAs bind to miRNAs and consequently repress their function, providing a new model of action for this class of ncRNA, as well as indicating another mechanism that regulates miRNA activity. As miRNAs control a large set of biological processes, circRNA sponge activity will also affect these pathways. Several studies have associated miRNA sponges with human diseases, including osteoarthritis, diabetes, neurodegenerative pathologies and several types of cancer. Additionally, high stability, abundance and tissue-specific expression patterns make circRNA sponges very attractive for clinical research. Herein, we review the biogenesis, properties and function of endogenous circRNA sponges, with a special focus on those related to human cancer. A list of web tools available for the study of circRNAs is also given. Additionally, we discuss the possibility of using circRNAs as molecular markers for the diagnosis of diseases.
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Affiliation(s)
- Franceli Rodrigues Kulcheski
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil
| | | | - Rogerio Margis
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil.
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1626
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A novel regulatory network among LncRpa, CircRar1, MiR-671 and apoptotic genes promotes lead-induced neuronal cell apoptosis. Arch Toxicol 2016; 91:1671-1684. [PMID: 27604105 PMCID: PMC5364257 DOI: 10.1007/s00204-016-1837-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/24/2016] [Indexed: 12/17/2022]
Abstract
Lead is a metal that has toxic effects on the developing nervous system. However, the mechanisms underlying lead-induced neurotoxicity are not well understood. Non-coding RNAs (ncRNAs) play an important role in epigenetic regulation, but few studies have examined the function of ncRNAs in lead-induced neurotoxicity. We addressed this in the present study by evaluating the functions of a long non-coding RNA (named lncRpa) and a circular RNA (named circRar1) in a mouse model of lead-induced neurotoxicity. High-throughput RNA sequencing showed that both lncRpa and circRar1 promoted neuronal apoptosis. We also found that lncRpa and circRar1 induced the upregulation of apoptosis-associated factors caspase8 and p38 at the mRNA and protein levels via modulation of their common target microRNA miR-671. This is the first report of a regulatory interaction among a lncRNA, circRNA, and miRNA mediating neuronal apoptosis in response to lead toxicity.
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1627
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Osman I, Tay MLI, Pek JW. Stable intronic sequence RNAs (sisRNAs): a new layer of gene regulation. Cell Mol Life Sci 2016; 73:3507-19. [PMID: 27147469 PMCID: PMC11108444 DOI: 10.1007/s00018-016-2256-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 02/05/2023]
Abstract
Upon splicing, introns are rapidly degraded. Hence, RNAs derived from introns are commonly deemed as junk sequences. However, the discoveries of intronic-derived small nucleolar RNAs (snoRNAs), small Cajal body associated RNAs (scaRNAs) and microRNAs (miRNAs) suggested otherwise. These non-coding RNAs are shown to play various roles in gene regulation. In this review, we highlight another class of intron-derived RNAs known as stable intronic sequence RNAs (sisRNAs). sisRNAs have been observed since the 1980 s; however, we are only beginning to understand their biological significance. Recent studies have shown or suggested that sisRNAs regulate their own host's gene expression, function as molecular sinks or sponges, and regulate protein translation. We propose that sisRNAs function as an additional layer of gene regulation in the cells.
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Affiliation(s)
- Ismail Osman
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Mandy Li-Ian Tay
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
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1628
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Xie W, Yuan S, Sun Z, Li Y. Long noncoding and circular RNAs in lung cancer: advances and perspectives. Epigenomics 2016; 8:1275-87. [DOI: 10.2217/epi-2016-0036] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Better understanding and management of lung cancer are needed. Although much has been learned from known protein coding genes, long noncoding RNAs (lncRNAs), a relatively new and fast evolving large family of transcripts, have recently generated much attention for new discoveries. LncRNAs play critical regulatory functions and are emerging as new players in tumorigenesis and phenotypic determinators of lung cancer. In this review, we highlight the latest development of lncRNAs, including circular RNAs in lung cancer. We start with well-characterized lncRNAs and circular RNAs as an oncogene or tumor suppressor and then extend our discussion on the impact of SNPs in lncRNA on its functions and lung cancer risk and the clinical applications of lncRNAs as biomarkers and therapeutic targets.
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Affiliation(s)
- Weijia Xie
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Shuai Yuan
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Yafei Li
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
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1629
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The long noncoding RNA ASNR regulates degradation of Bcl-2 mRNA through its interaction with AUF1. Sci Rep 2016; 6:32189. [PMID: 27578251 PMCID: PMC5006016 DOI: 10.1038/srep32189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 08/04/2016] [Indexed: 02/07/2023] Open
Abstract
The identification and characterization of long non-coding RNAs (lncRNAs) in diverse biological processes has recently developed rapidly. The large amounts of non-coding RNAs scale consistent with developmental complexity in eukaryotes, indicating that most of these transcripts may have functions in the regulation of biological processes and disorder in the organisms. In particular, Understanding of the overall biological significance of lncRNAs in cancers still remains limited. Here, we found a nuclear-retained lncRNA, termed Lnc_ASNR (apoptosis suppressing-noncoding RNA), which serves as a repressor of apoptosis. Lnc_ASNR was discovered in a set of microarray data derived from four kinds of tumor and adjacent normal tissue samples, and displayed significant up-regulation in the tumor tissues. Using an RNA-pull down assay, we found that Lnc_ASNR interacted with the protein ARE/poly (U)-binding/degradation factor 1(AUF1), which is reported to promote rapid degradation of the Bcl-2 mRNA, an inhibitor of apoptosis. Lnc_ASNR binds to AUFI in nucleus, decreasing the cytoplasmic proportion of AUF1 which targets the B-cell lymphoma-2 (Bcl-2) mRNA. Taken together, the overall effect of Lnc_ASNR expression is thus a decrease in cell apoptosis indicating that Lnc_ASNR may play a vital role in tumorigenesis and carcinogenesis.
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1630
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DNA and RNA topoisomerase activities of Top3β are promoted by mediator protein Tudor domain-containing protein 3. Proc Natl Acad Sci U S A 2016; 113:E5544-51. [PMID: 27582462 DOI: 10.1073/pnas.1605517113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Topoisomerase 3β (Top3β) can associate with the mediator protein Tudor domain-containing protein 3 (TDRD3) to participate in two gene expression processes of transcription and translation. Despite the apparent importance of TDRD3 in binding with Top3β and directing it to cellular compartments critical for gene expression, the biochemical mechanism of how TDRD3 can affect the functions of Top3β is not known. We report here sensitive biochemical assays for the activities of Top3β on DNA and RNA substrates in resolving topological entanglements and for the analysis of TDRD3 functions. TDRD3 stimulates the relaxation activity of Top3β on hypernegatively supercoiled DNA and changes the reaction from a distributive to a processive mode. Both supercoil retention assays and binding measurement by fluorescence anisotropy reveal a heretofore unknown preference for binding single-stranded nucleic acids over duplex. Whereas TDRD3 has a structure-specific binding preference, it does not discriminate between DNA and RNA. This unique property for binding with nucleic acids can have an important function in serving as a hub to form nucleoprotein complexes on DNA and RNA. To gain insight into the roles of Top3β on RNA metabolism, we designed an assay by annealing two single-stranded RNA circles with complementary sequences. Top3β is capable of converting two such single-stranded RNA circles into a double-stranded RNA circle, and this strand-annealing activity is enhanced by TDRD3. These results demonstrate that TDRD3 can enhance the biochemical activities of Top3β on both DNA and RNA substrates, in addition to its function of targeting Top3β to critical sites in subcellular compartments.
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1631
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Abstract
Pre-mRNAs from thousands of eukaryotic genes can be non-canonically spliced to generate circular RNAs, some of which accumulate to higher levels than their associated linear mRNA. Recent work has revealed widespread mechanisms that dictate whether the spliceosome generates a linear or circular RNA. For most genes, circular RNA biogenesis via backsplicing is far less efficient than canonical splicing, but circular RNAs can accumulate due to their long half-lives. Backsplicing is often initiated when complementary sequences from different introns base pair and bring the intervening splice sites close together. This process is further regulated by the combinatorial action of RNA binding proteins, which allow circular RNAs to be expressed in unique patterns. Some genes do not require complementary sequences to generate RNA circles and instead take advantage of exon skipping events. It is still unclear what most mature circular RNAs do, but future investigations into their functions will be facilitated by recently described methods to modulate circular RNA levels.
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Affiliation(s)
- Jeremy E Wilusz
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , PA , USA
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1632
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van Rossum D, Verheijen BM, Pasterkamp RJ. Circular RNAs: Novel Regulators of Neuronal Development. Front Mol Neurosci 2016; 9:74. [PMID: 27616979 PMCID: PMC4999478 DOI: 10.3389/fnmol.2016.00074] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are highly stable, circularized long non-coding RNAs. circRNAs are conserved across species and appear to be specifically enriched in the nervous system. Recent studies show that many circRNAs are expressed in a tissue- and developmental-stage-specific manner, reveal a striking regulation of circRNAs during neuronal development, and detect their presence at synaptic sites. The exact functions of circRNAs remain poorly understood, but evidence from analysis of some circRNA molecules suggests that they could substantially contribute to the regulation of gene expression, particularly in architecturally complex and polarized cells such as neurons. Emerging evidence also indicates that circRNAs are involved in the development and progression of various neurological disorders. In this review, we summarize the molecular characteristics of circRNAs and discuss their proposed functions and mechanism-of-action in developing neurons.
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Affiliation(s)
- Daniëlle van Rossum
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht Utrecht, Netherlands
| | - Bert M Verheijen
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center UtrechtUtrecht, Netherlands; Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center UtrechtUtrecht, Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht Utrecht, Netherlands
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1633
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Lin X, Han M, Cheng L, Chen J, Zhang Z, Shen T, Wang M, Wen B, Ni T, Han C. Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells. RNA Biol 2016; 13:1011-1024. [PMID: 27560004 DOI: 10.1080/15476286.2016.1218588] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Among all tissues of the metazoa, the transcritpome of testis displays the highest diversity and specificity. However, its composition and dynamics during spermatogenesis have not been fully understood. Here, we have identified 20,639 message RNAs (mRNAs), 7,168 long non-coding RNAs (lncRNAs) and 15,101 circular RNAs (circRNAs) in mouse spermatogenic cells, and found many of them were specifically expressed in testes. lncRNAs are significantly more testis-specific than mRNAs. At all stages, mRNAs are generally more abundant than lncRNAs, and linear transcripts are more abundant than circRNAs. We showed that the productions of circRNAs and piRNAs were highly regulated instead of random processes. Based on the results of a small-scale functional screening experiment using cultured mouse spermatogonial stem cells, many evolutionarily conserved lncRNAs are likely to play roles in spermatogenesis. Typical classes of transcription factor binding sites are enriched in the promoters of testis-specific m/lncRNA genes. Target genes of CREM and RFX2, 2 key TFs for spermatogenesis, were further validated by using ChIP-chip assays and RNA-seq on RFX2-knockout spermatogenic cells. Our results contribute to the current understanding of the transcriptomic complexity of spermatogenic cells and provide a valuable resource from which many candidate genes may be selected for further functional studies.
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Affiliation(s)
- Xiwen Lin
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China
| | - Miao Han
- b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China
| | - Lu Cheng
- c Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai , China
| | - Jian Chen
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.,d Graduate University of Chinese Academy of Sciences , Beijing , China
| | - Zhuqiang Zhang
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.,d Graduate University of Chinese Academy of Sciences , Beijing , China
| | - Ting Shen
- b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China
| | - Min Wang
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China
| | - Bo Wen
- b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China.,c Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai , China
| | - Ting Ni
- b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China
| | - Chunsheng Han
- a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China
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1634
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Floris G, Zhang L, Follesa P, Sun T. Regulatory Role of Circular RNAs and Neurological Disorders. Mol Neurobiol 2016; 54:5156-5165. [PMID: 27558238 DOI: 10.1007/s12035-016-0055-4] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/11/2016] [Indexed: 01/22/2023]
Abstract
Circular RNAs (circRNAs) are a class of long noncoding RNAs that are characterized by the presence of covalently linked ends and have been found in all life kingdoms. Exciting studies in regulatory roles of circRNAs are emerging. Here, we summarize classification, characteristics, biogenesis, and regulatory functions of circRNAs. CircRNAs are found to be preferentially expressed along neural genes and in neural tissues. We thus highlight the association of circRNA dysregulation with neurodegenerative diseases such as Alzheimer's disease. Investigation of regulatory role of circRNAs will shed novel light in gene expression mechanisms during development and under disease conditions and may identify circRNAs as new biomarkers for aging and neurodegenerative disorders.
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Affiliation(s)
| | | | - Paolo Follesa
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Tao Sun
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, 1300 York Avenue, Box 60, New York, NY, 10065, USA.
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1635
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Qu S, Zhong Y, Shang R, Zhang X, Song W, Kjems J, Li H. The emerging landscape of circular RNA in life processes. RNA Biol 2016; 14:992-999. [PMID: 27617908 PMCID: PMC5680710 DOI: 10.1080/15476286.2016.1220473] [Citation(s) in RCA: 324] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNA that assumes a covalently closed continuous conformation. CircRNAs were previously thought to be the byproducts of splicing errors caused by low abundance and the technological limitations. With the recent development of high-throughput sequencing technology, numerous circRNAs have been discovered in many species. Recent studies have revealed that circRNAs are stable and widely expressed, and often exhibit cell type-specific or tissue-specific expression. Most circRNAs can be generated from exons, introns, or both. Remarkably, emerging evidence indicates that some circRNAs can serve as microRNA (miRNA) sponges, regulate transcription or splicing, and can interact with RNA binding proteins (RBPs). Moreover, circRNAs have been reported to play essential roles in myriad life processes, such as aging, insulin secretion, tissue development, atherosclerotic vascular disease risk, cardiac hypertrophy and cancer. Although circRNAs are ancient molecules, they represent a newly appreciated form of noncoding RNA and as such have great potential implications in clinical and research fields. Here, we review the current understanding of circRNA classification, function and significance in physiological and pathological processes. We believe that future research will increase our understanding of the regulation and function of these novel molecules.
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Affiliation(s)
- Shibin Qu
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Yue Zhong
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China.,b Department of General Surgery , The Second People's Hospital of Shaanxi Province , Xi'an , China
| | - Runze Shang
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Xuan Zhang
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Wenjie Song
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Jørgen Kjems
- c Department of Molecular Biology and Genetics (MBG) and Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Aarhus , Denmark
| | - Haimin Li
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
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1636
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CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs. Sci Rep 2016; 6:31313. [PMID: 27510448 PMCID: PMC4980667 DOI: 10.1038/srep31313] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) constitute a new class of noncoding RNAs in higher eukaryotes generated from pre-mRNAs by alternative splicing. Here we investigated in mammalian cells the association of circRNAs with proteins. Using glycerol gradient centrifugation, we characterized in cell lysates circRNA-protein complexes (circRNPs) of distinct sizes. By polysome-gradient fractionation we found no evidence for efficient translation of a set of abundant circRNAs in HeLa cells. To identify circRNPs with a specific protein component, we focused on IMP3 (IGF2BP3, insulin-like growth factor 2 binding protein 3), a known tumor marker and RNA-binding protein. Combining RNA-seq analysis of IMP3-co-immunoprecipitated RNA and filtering for circular-junction reads identified a set of IMP3-associated circRNAs, which were validated and characterized. In sum, our data suggest that specific circRNP families exist defined by a common protein component. In addition, this provides a general approach to identify circRNPs with a given protein component.
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1637
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Chen LL. Linking Long Noncoding RNA Localization and Function. Trends Biochem Sci 2016; 41:761-772. [PMID: 27499234 DOI: 10.1016/j.tibs.2016.07.003] [Citation(s) in RCA: 774] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/23/2016] [Accepted: 07/01/2016] [Indexed: 02/06/2023]
Abstract
Recent studies have revealed the regulatory potential of many long noncoding RNAs (lncRNAs). Most lncRNAs, like mRNAs, are transcribed by RNA polymerase II and are capped, polyadenylated, and spliced. However, the subcellular fates of lncRNAs are distinct and the mechanisms of action are diverse. Investigating the mechanisms that determine the subcellular fate of lncRNAs has the potential to provide new insights into their biogenesis and specialized functions.
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Affiliation(s)
- Ling-Ling Chen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai, China.
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1638
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Chen L, Yu Y, Zhang X, Liu C, Ye C, Fan L. PcircRNA_finder: a software for circRNA prediction in plants. Bioinformatics 2016; 32:3528-3529. [PMID: 27493192 PMCID: PMC5181569 DOI: 10.1093/bioinformatics/btw496] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/03/2016] [Accepted: 07/21/2016] [Indexed: 12/18/2022] Open
Abstract
Motivation: Recent studies reveal an important role of non-coding circular RNA (circRNA) in the control of cellular processes. Because of differences in the organization of plant and mammal genomes, the sensitivity and accuracy of circRNA prediction programs using algorithms developed for animals and humans perform poorly for plants. Results: A circRNA prediction software for plants (termed PcircRNA_finder) was developed that is more sensitive in detecting circRNAs than other frequently used programs (such as find_circ and CIRCexplorer), Based on analysis of simulated and real rRNA-/RNAase R RNA-Seq data from Arabidopsis thaliana and rice PcircRNA_finder provides a more comprehensive sensitive, precise prediction method for plants circRNAs. Availability and Implementation:http://ibi.zju.edu.cn/bioinplant/tools/manual.htm. Contact:fanlj@zju.edu.cn Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Li Chen
- Institute of Crop Sciences & Institute of Bioinformatics
| | - Yongyi Yu
- Institute of Crop Sciences & Institute of Bioinformatics
| | - Xinchen Zhang
- Institute of Crop Sciences & Institute of Bioinformatics
| | - Chen Liu
- Institute of Crop Sciences & Institute of Bioinformatics
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics.,Research Center of Air Pollution and Health, Zhejiang University, Hangzhou 310058, China
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1639
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Li LJ, Huang Q, Pan HF, Ye DQ. Circular RNAs and systemic lupus erythematosus. Exp Cell Res 2016; 346:248-54. [DOI: 10.1016/j.yexcr.2016.07.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/20/2016] [Indexed: 01/01/2023]
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1640
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Zhang Q, Li H, Zhao XQ, Xue H, Zheng Y, Meng H, Jia Y, Bo SL. The evolution mechanism of intron length. Genomics 2016; 108:47-55. [DOI: 10.1016/j.ygeno.2016.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/20/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
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1641
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Filippenkov IB, Kalinichenko EO, Limborska SA, Dergunova LV. Circular RNAs—one of the enigmas of the brain. Neurogenetics 2016; 18:1-6. [DOI: 10.1007/s10048-016-0490-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
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1642
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Granados-Riveron JT, Aquino-Jarquin G. The complexity of the translation ability of circRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1245-51. [PMID: 27449861 DOI: 10.1016/j.bbagrm.2016.07.009] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/21/2016] [Accepted: 07/15/2016] [Indexed: 12/12/2022]
Abstract
Circular RNAs (circRNAs) are a new class of long non-coding RNAs that play a potential role in gene expression regulation, acting as efficient microRNAs sponges. The latest surprise concerning circRNAs is that we now know that they can serve as transcriptional activators in human cells, indicating that circRNAs are involved in important regulatory tasks. Recently, new insight has been gained about the coding potential of circular viroid RNAs, as well as the presence of Internal Ribosomal Entry Sites (IRES) allowing the formation of peptides or proteins from circular RNA. Here, we discuss the current state of our knowledge regarding evidence supporting the hypothesis that circRNAs serve as protein-coding sequences in vitro and in vivo. Also, we remark on the difficulties of their identification and highlight some tools currently available for exploring the coding potential of circRNA.
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Affiliation(s)
- Javier T Granados-Riveron
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, 4to Piso, Sección 2, Hospital Infantil de México, Federico Gómez, Mexico
| | - Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, 4to Piso, Sección 2, Hospital Infantil de México, Federico Gómez, Mexico.
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1643
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Chen W, Schuman E. Circular RNAs in Brain and Other Tissues: A Functional Enigma. Trends Neurosci 2016; 39:597-604. [PMID: 27445124 DOI: 10.1016/j.tins.2016.06.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 01/20/2023]
Abstract
Circular RNAs (circRNAs) are RNAs with a covalently closed loop structure that have recently regained the attention of biologists. Using deep RNA sequencing (RNA-seq) coupled with novel bioinformatic approaches, genome-wide studies have detected a large number of circRNAs, many of which are abundant, stable, and well conserved during evolution. With few exceptions, the function of most circRNAs remains elusive. Several recent studies have shown that circRNAs are more enriched in neuronal tissues and are often derived from genes specific for neuronal and synaptic function. Moreover, circRNA expression is regulated during neuronal development and by synaptic plasticity, suggesting specific neuronal functions. In this review, we discuss recent advances in the detection, biogenesis, and potential functions of circRNAs, with a particular focus on brain tissues.
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Affiliation(s)
- Wei Chen
- Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany; Department of Biology, South University of Science and Technology of China, Shenzhen, China.
| | - Erin Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany.
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1644
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Ma K, Guo L, Xu A, Cui S, Wang JH. Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal Cortex. PLoS One 2016; 11:e0159093. [PMID: 27427907 PMCID: PMC4948880 DOI: 10.1371/journal.pone.0159093] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/27/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Major depression is a prevalent mood disorder. Chronic stress is presumably main etiology that leads to the neuron and synapse atrophies in the limbic system. However, the intermediate molecules from stresses to neuronal atrophy remain elusive, which we have studied in the medial prefrontal cortices from depression mice. METHODS AND RESULTS The mice were treated by the chronic unpredictable mild stress (CUMS) until they expressed depression-like behaviors confirmed by the tests of sucrose preference, forced swimming and Y-maze. High-throughput sequencings of microRNA and mRNA in the medial prefrontal cortices were performed in CUMS-induced depression mice versus control mice to demonstrate the molecular profiles of major depression. In the medial prefrontal cortices of depression-like mice, the levels of mRNAs that translated the proteins for the GABAergic synapses, dopaminergic synapses, myelination, synaptic vesicle cycle and neuronal growth were downregulated. miRNAs of regulating these mRNAs are upregulated. CONCLUSION The deteriorations of GABAergic and dopaminergic synapses as well as axonal growth are associated with CUMS-induced depression.
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MESH Headings
- Animals
- Depressive Disorder, Major/etiology
- Depressive Disorder, Major/genetics
- Depressive Disorder, Major/pathology
- Disease Models, Animal
- Gene Expression Regulation
- Gene Regulatory Networks
- Male
- Mice, Inbred C57BL
- MicroRNAs/analysis
- MicroRNAs/genetics
- Prefrontal Cortex/metabolism
- Prefrontal Cortex/pathology
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Stress, Psychological/complications
- Stress, Psychological/genetics
- Stress, Psychological/pathology
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Affiliation(s)
- Ke Ma
- Qingdao University, School of Pharmacy, Shandong, China
| | - Li Guo
- State Key Lab of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Aiping Xu
- College of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Shan Cui
- State Key Lab of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jin-Hui Wang
- Qingdao University, School of Pharmacy, Shandong, China
- State Key Lab of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Science and Technology of China, Hefei, Anhui, China
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1645
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Filippenkov IB, Sudarkina OY, Limborska SA, Dergunova LV. Circular RNA of the human sphingomyelin synthase 1 gene: Multiple splice variants, evolutionary conservatism and expression in different tissues. RNA Biol 2016; 12:1030-42. [PMID: 26274505 DOI: 10.1080/15476286.2015.1076611] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The human sphingomyelin synthase 1 gene (SGMS1) encodes an essential enzyme that is involved in the synthesis of sphingomyelin and diacylglycerol from phosphatidylcholine and ceramide. Among the products of SGMS1, we found new transcripts, circular RNAs (circRNAs), that contain sequences of the gene's 5' untranslated region (5'UTR). Some of them include the gene's coding region and fragments of introns. An analysis of the abundance of circRNAs in human tissues showed that the largest transcripts were predominantly found in different parts of the brain. circRNAs of rat and mouse sphingomyelin synthase 1 orthologous genes were detected and are highly similar to the human SGMS1 gene transcripts. A quantitative analysis of the abundance of such transcripts also revealed their elevated amount in the brain. A computational analysis of sequences of human circRNAs showed their high potential of binding microRNAs (miRNAs), including the miRNAs that form complexes with Ago proteins and the mRNA of SGMS1. We assume that the circRNAs identified here participate in the regulation of the function of the SGMS1 gene in the brain.
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Affiliation(s)
- Ivan B Filippenkov
- a Human Molecular Genetics Department ; Institute of Molecular Genetics; Russian Academy of Sciences ; Moscow , Russia
| | - Olga Yu Sudarkina
- a Human Molecular Genetics Department ; Institute of Molecular Genetics; Russian Academy of Sciences ; Moscow , Russia
| | - Svetlana A Limborska
- a Human Molecular Genetics Department ; Institute of Molecular Genetics; Russian Academy of Sciences ; Moscow , Russia.,b Institute of Cerebrovascular Pathology and Stroke; Pirogov Russian National Research Medical University ; Moscow , Russia
| | - Lyudmila V Dergunova
- a Human Molecular Genetics Department ; Institute of Molecular Genetics; Russian Academy of Sciences ; Moscow , Russia.,b Institute of Cerebrovascular Pathology and Stroke; Pirogov Russian National Research Medical University ; Moscow , Russia
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1646
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Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res 2016; 26:1277-87. [PMID: 27365365 PMCID: PMC5052039 DOI: 10.1101/gr.202895.115] [Citation(s) in RCA: 733] [Impact Index Per Article: 81.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/28/2016] [Indexed: 01/16/2023]
Abstract
Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus can produce multiple circRNAs through alternative back-splice site selection and/or alternative splice site selection; however, a detailed map of alternative back-splicing/splicing in circRNAs is lacking. Here, with the upgraded CIRCexplorer2 pipeline, we systematically annotated different types of alternative back-splicing and alternative splicing events in circRNAs from various cell lines. Compared with their linear cognate RNAs, circRNAs exhibited distinct patterns of alternative back-splicing and alternative splicing. Alternative back-splice site selection was correlated with the competition of putative RNA pairs across introns that bracket alternative back-splice sites. In addition, all four basic types of alternative splicing that have been identified in the (linear) mRNA process were found within circRNAs, and many exons were predominantly spliced in circRNAs. Unexpectedly, thousands of previously unannotated exons were detected in circRNAs from the examined cell lines. Although these novel exons had similar splice site strength, they were much less conserved than known exons in sequences. Finally, both alternative back-splicing and circRNA-predominant alternative splicing were highly diverse among the examined cell lines. All of the identified alternative back-splicing and alternative splicing in circRNAs are available in the CIRCpedia database (http://www.picb.ac.cn/rnomics/circpedia). Collectively, the annotation of alternative back-splicing and alternative splicing in circRNAs provides a valuable resource for depicting the complexity of circRNA biogenesis and for studying the potential functions of circRNAs in different cells.
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Affiliation(s)
- Xiao-Ou Zhang
- Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Dong
- Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Lin Zhang
- Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zheng Luo
- Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Ling Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science, ShanghaiTech University, Shanghai 20003, China
| | - Li Yang
- Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science, ShanghaiTech University, Shanghai 20003, China
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1647
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Gao Y, Wang J, Zheng Y, Zhang J, Chen S, Zhao F. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nat Commun 2016; 7:12060. [PMID: 27350239 PMCID: PMC4931246 DOI: 10.1038/ncomms12060] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/20/2016] [Indexed: 02/06/2023] Open
Abstract
Although previous studies demonstrated circular RNAs (circRNAs) does not exclusively comprise mRNA exons, no study has extensively explored their internal structure. By combining an algorithm with long-read sequencing data and experimental validation, we, for the first time, comprehensively investigate internal components of circRNAs in 10 human cell lines and 62 fruit fly samples, and reveal the prevalence of alternative splicing (AS) events within circRNAs. Significantly, a large proportion of circRNA AS exons can hardly be detected in mRNAs and are enriched with binding sites of distinct splicing factors from those enriched in mRNA exons. We find that AS events in circRNAs have a preference towards nucleus localization and exhibit tissue- and developmental stage-specific expression patterns. This study suggests an independent regulation on the biogenesis or decay of AS events in circRNAs and the identified circular AS isoforms provide targets for future studies on circRNA formation and function.
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Affiliation(s)
- Yuan Gao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zheng
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyang Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Chen
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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1648
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Dang Y, Yan L, Hu B, Fan X, Ren Y, Li R, Lian Y, Yan J, Li Q, Zhang Y, Li M, Ren X, Huang J, Wu Y, Liu P, Wen L, Zhang C, Huang Y, Tang F, Qiao J. Tracing the expression of circular RNAs in human pre-implantation embryos. Genome Biol 2016; 17:130. [PMID: 27315811 PMCID: PMC4911693 DOI: 10.1186/s13059-016-0991-3] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 05/24/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND PolyA- RNAs have not been widely analyzed in human pre-implantation embryos due to the scarcity of materials. In particular, circular RNA (circRNA), a novel type of polyA- RNA, has not been characterized during human pre-implantation development. RESULTS We systematically analyze polyA+ messenger RNAs (mRNAs) and polyA- RNAs in individual human oocytes and pre-implantation embryos using SUPeR-seq. We de novo identify 10,032 circRNAs from 2974 hosting genes. Most of these circRNAs are developmentally stage-specific and dynamically regulated. Many of them are maternally expressed, implying their potentially important regulatory functions in oogenesis and the formation of totipotent zygotes. Comparison between human and mouse embryos reveals both high conservation and clear distinction between these two species. Human pre-implantation embryos generate more types of circRNA compared with mouse embryos and this is associated with a striking increase of the length of the circRNA flanking introns in humans. We also perform RNA de novo assembly and identify novel transcript units, many of which are potentially novel long non-coding RNAs. CONCLUSIONS This study reports the first analysis of the whole transcriptome comprising both polyA+ mRNAs and polyA- RNAs including circRNAs during human pre-implantation development. It provides an invaluable resource for analyzing the unique function and complex regulatory mechanisms of circRNAs during this process.
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Affiliation(s)
- Yujiao Dang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Liying Yan
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Boqiang Hu
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Xiaoying Fan
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Yixin Ren
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Rong Li
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Ying Lian
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Jie Yan
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Qingqing Li
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Yan Zhang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Min Li
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Xiulian Ren
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Jin Huang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Yuqi Wu
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Ping Liu
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Lu Wen
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Chen Zhang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China
| | - Yanyi Huang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- College of Engineering, Peking University, Beijing, 100871, China.
| | - Fuchou Tang
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Center for Molecular and Translational Medicine, Peking University Health Science Center, Beijing, 100191, China.
| | - Jie Qiao
- Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.
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1649
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Zhang C, Wu H, Wang Y, Zhu S, Liu J, Fang X, Chen H. Circular RNA of cattle casein genes are highly expressed in bovine mammary gland. J Dairy Sci 2016; 99:4750-4760. [DOI: 10.3168/jds.2015-10381] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/20/2016] [Indexed: 12/11/2022]
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1650
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Ayupe AC, Tahira AC, Camargo L, Beckedorff FC, Verjovski-Almeida S, Reis EM. Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome. RNA Biol 2016; 12:877-92. [PMID: 26151857 DOI: 10.1080/15476286.2015.1062960] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) that map to intragenic regions of the human genome with the same (intronic lncRNAs) or opposite orientation (antisense lncRNAs) relative to protein-coding mRNAs have been largely dismissed from biochemical and functional characterization due to the belief that they are mRNA precursors, byproducts of RNA splicing or simply transcriptional noise. In this work, we used a custom microarray to investigate aspects of the biogenesis, processing, stability, evolutionary conservation, and cellular localization of ∼ 6,000 intronic lncRNAs and ∼ 10,000 antisense lncRNAs. Most intronic (2,903 of 3,427, 85%) and antisense lncRNAs (4,945 of 5,214, 95%) expressed in HeLa cells showed evidence of 5' cap modification, compatible with their transcription by RNAP II. Antisense lncRNAs (median t1/2 = 3.9 h) were significantly (p < 0.0001) more stable than mRNAs (median t1/2 = 3.2 h), whereas intronic lncRNAs (median t1/2 = 2.1 h) comprised a more heterogeneous class that included both stable (t1/2 > 3 h) and unstable (t1/2 < 1 h) transcripts. Intragenic lncRNAs display evidence of evolutionary conservation, have little/no coding potential and were ubiquitously detected in the cytoplasm. Notably, a fraction of the intronic and antisense lncRNAs (13 and 15%, respectively) were expressed from loci at which the corresponding host mRNA was not detected. The abundances of a subset of intronic/antisense lncRNAs were correlated (r ≥ |0.8|) with those of genes encoding proteins involved in cell division and DNA replication. Taken together, the findings of this study contribute novel biochemical and genomic information regarding intronic and antisense lncRNAs, supporting the notion that these classes include independently transcribed RNAs with potentials for exerting regulatory functions in the cell.
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Affiliation(s)
- Ana C Ayupe
- a Departamento de Bioquímica ; Instituto de Química ; Universidade de São Paulo ; Sao Paulo , Brazil
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