1
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Das S, Zea Rojas MP, Tran EJ. Novel insights on the positive correlation between sense and antisense pairs on gene expression. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1864. [PMID: 39087253 PMCID: PMC11626863 DOI: 10.1002/wrna.1864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 08/02/2024]
Abstract
A considerable proportion of the eukaryotic genome undergoes transcription, leading to the generation of noncoding RNA molecules that lack protein-coding information and are not subjected to translation. These noncoding RNAs (ncRNAs) are well recognized to have essential roles in several biological processes. Long noncoding RNAs (lncRNAs) represent the most extensive category of ncRNAs found in the human genome. Much research has focused on investigating the roles of cis-acting lncRNAs in the regulation of specific target gene expression. In the majority of instances, the regulation of sense gene expression by its corresponding antisense pair occurs in a negative (discordant) manner, resulting in the suppression of the target genes. The notion that a negative correlation exists between sense and antisense pairings is, however, not universally valid. In fact, several recent studies have reported a positive relationship between corresponding cis antisense pairs within plants, budding yeast, and mammalian cancer cells. The positive (concordant) correlation between anti-sense and sense transcripts leads to an increase in the level of the sense transcript within the same genomic loci. In addition, mechanisms such as altering chromatin structure, the formation of R loops, and the recruitment of transcription factors can either enhance transcription or stabilize sense transcripts through their antisense pairs. The primary objective of this work is to provide a comprehensive understanding of both aspects of antisense regulation, specifically focusing on the positive correlation between sense and antisense transcripts in the context of eukaryotic gene expression, including its implications towards cancer progression. This article is categorized under: RNA Processing > 3' End Processing Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Subhadeep Das
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
- Purdue University Institute for Cancer Research, Purdue UniversityWest LafayetteIndianaUSA
| | | | - Elizabeth J. Tran
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
- Purdue University Institute for Cancer Research, Purdue UniversityWest LafayetteIndianaUSA
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2
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Liu M, Zhang S, Zhou H, Hu X, Li J, Fu B, Wei M, Huang H, Wu H. The interplay between non-coding RNAs and alternative splicing: from regulatory mechanism to therapeutic implications in cancer. Theranostics 2023; 13:2616-2631. [PMID: 37215575 PMCID: PMC10196821 DOI: 10.7150/thno.83920] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Alternative splicing (AS) is a common and conserved process in eukaryotic gene regulation. It occurs in approximately 95% of multi-exon genes, greatly enriching the complexity and diversity of mRNAs and proteins. Recent studies have found that in addition to coding RNAs, non-coding RNAs (ncRNAs) are also inextricably linked with AS. Multiple different types of ncRNAs are generated by AS of precursor long non-coding (pre-lncRNAs) or precursor messenger RNAs (pre-mRNAs). Furthermore, ncRNAs, as a novel class of regulators, can participate in AS regulation by interacting with the cis-acting elements or trans-acting factors. Several studies have implicated abnormal expression of ncRNAs and ncRNA-related AS events in the initiation, progression, and therapy resistance in various types of cancers. Therefore, owing to their roles in mediating drug resistance, ncRNAs, AS-related factors and AS-related novel antigens may serve as promising therapeutic targets in cancer treatment. In this review, we summarize the interaction between ncRNAs and AS processes, emphasizing their great influences on cancer, especially on chemoresistance, and highlighting their potential values in clinical treatment.
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Affiliation(s)
- Min Liu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Subo Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Heng Zhou
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P. R. China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Jianing Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Boshi Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Shenyang Kangwei Medical Laboratory Analysis Co. LTD, Shenyang, Liaoning, P. R. China
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
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3
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:2976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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Affiliation(s)
| | | | - Izabela Makałowska
- Institute of Human Biology and Evolution, Adam Mickiewicz University in Poznań, Uniwersytetu Ponańskiego 6, 61-614 Poznań, Poland
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4
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CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles. Sci Rep 2022; 12:15525. [PMID: 36109624 PMCID: PMC9477841 DOI: 10.1038/s41598-022-19782-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are transcribed from the same genomic locus as their partner gene but from the opposite DNA strand and overlap with the partner gene transcript. Here, we developed a simple and convenient program termed CCIVR (comprehensive cis-NATs identifier via RNA-seq data) that comprehensively identifies all kinds of cis-NATs based on genome annotation with expression data obtained from RNA-seq. Using CCIVR with genome databases, we demonstrated total cis-NAT pairs from 11 model organisms. CCIVR analysis with RNA-seq data from parthenogenetic and androgenetic embryonic stem cells identified well-known imprinted cis-NAT pair, KCNQ1/KCNQ1OT1, ensuring the availability of CCIVR. Finally, CCIVR identified cis-NAT pairs that demonstrate inversely correlated expression upon TGFβ stimulation including cis-NATs that functionally repress their partner genes by introducing epigenetic alteration in the promoters of partner genes. Thus, CCIVR facilitates the investigation of structural characteristics and functions of cis-NATs in numerous processes in various species.
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5
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Bychkov I, Baydakova G, Filatova A, Migiaev O, Marakhonov A, Pechatnikova N, Pomerantseva E, Konovalov F, Ampleeva M, Kaimonov V, Skoblov M, Zakharova E. Complex Transposon Insertion as a Novel Cause of Pompe Disease. Int J Mol Sci 2021; 22:ijms221910887. [PMID: 34639227 PMCID: PMC8509548 DOI: 10.3390/ijms221910887] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 11/22/2022] Open
Abstract
Pompe disease (OMIM#232300) is an autosomal recessive lysosomal storage disorder caused by mutations in the GAA gene. According to public mutation databases, more than 679 pathogenic variants have been described in GAA, none of which are associated with mobile genetic elements. In this article, we report a novel molecular genetic cause of Pompe disease, which could be hardly detected using routine molecular genetic analysis. Whole genome sequencing followed by comprehensive functional analysis allowed us to discover and characterize a complex mobile genetic element insertion deep in the intron 15 of the GAA gene in a patient with infantile onset Pompe disease.
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Affiliation(s)
- Igor Bychkov
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
- Correspondence:
| | - Galina Baydakova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | - Alexandra Filatova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | - Ochir Migiaev
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | - Andrey Marakhonov
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | | | - Ekaterina Pomerantseva
- Center of Genetics and Reproductive Medicine GENETICO, JSC, 119333 Moscow, Russia; (E.P.); (V.K.)
| | - Fedor Konovalov
- Independent Clinical Bioinformatics Laboratory, 123181 Moscow, Russia; (F.K.); (M.A.)
| | - Maria Ampleeva
- Independent Clinical Bioinformatics Laboratory, 123181 Moscow, Russia; (F.K.); (M.A.)
| | - Vladimir Kaimonov
- Center of Genetics and Reproductive Medicine GENETICO, JSC, 119333 Moscow, Russia; (E.P.); (V.K.)
| | - Mikhail Skoblov
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | - Ekaterina Zakharova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
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6
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Rosikiewicz W, Sikora J, Skrzypczak T, Kubiak MR, Makałowska I. Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends. Sci Rep 2021; 11:8984. [PMID: 33903630 PMCID: PMC8076222 DOI: 10.1038/s41598-021-87970-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/07/2021] [Indexed: 11/09/2022] Open
Abstract
Despite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5' ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.
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Affiliation(s)
- Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jarosław Sikora
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Tomasz Skrzypczak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- Center for Advanced Technology, Adam Mickiewicz University, Poznań, Poland
| | - Magdalena R Kubiak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Izabela Makałowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.
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7
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Rosikiewicz W, Suzuki Y, Makalowska I. OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes. Nucleic Acids Res 2019; 46:D186-D193. [PMID: 29069459 PMCID: PMC5753363 DOI: 10.1093/nar/gkx948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/20/2017] [Indexed: 01/24/2023] Open
Abstract
Gene overlap plays various regulatory functions on transcriptional and post-transcriptional levels. Most current studies focus on protein-coding genes overlapping with non-protein-coding counterparts, the so called natural antisense transcripts. Considerably less is known about the role of gene overlap in the case of two protein-coding genes. Here, we provide OverGeneDB, a database of human and mouse 5′ end protein-coding overlapping genes. The database contains 582 human and 113 mouse gene pairs that are transcribed using overlapping promoters in at least one analyzed library. Gene pairs were identified based on the analysis of the transcription start site (TSS) coordinates in 73 human and 10 mouse organs, tissues and cell lines. Beside TSS data, resources for 26 human lung adenocarcinoma cell lines also contain RNA-Seq and ChIP-Seq data for seven histone modifications and RNA Polymerase II activity. The collected data revealed that the overlap region is rarely conserved between the studied species and tissues. In ∼50% of the overlapping genes, transcription started explicitly in the overlap regions. In the remaining half of overlapping genes, transcription was initiated both from overlapping and non-overlapping TSSs. OverGeneDB is accessible at http://overgenedb.amu.edu.pl.
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Affiliation(s)
- Wojciech Rosikiewicz
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-712 Poznan, Poland
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 272-8562, Japan
| | - Izabela Makalowska
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-712 Poznan, Poland
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8
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Mei ZZ, Sun H, Ou X, Li L, Cai J, Hu S, Wang J, Luo H, Liu J, Jiang Y. The natural antisense transcript NATTD regulates the transcription of decapping scavenger (DcpS) enzyme. Int J Biochem Cell Biol 2019; 110:103-110. [PMID: 30858142 DOI: 10.1016/j.biocel.2019.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/25/2022]
Abstract
Natural antisense transcripts (NATs) are transcribed from the opposite strand of other genes. Most of them are noncoding RNAs. They have been reported to play important roles in a variety of biological processes. In this study, we identified a novel NAT, NATTD, which is partially complementary to both the TIRAP/Mal and DcpS genes. Interestingly, NATTD only positively regulates the expression of DcpS, a decapping scavenger enzyme which is a promising therapeutic target for spinal muscular atrophy. But it has no obvious effects on the expression of TIRAP/Mal gene. The NATTD transcript primarily resides in the nucleus and does not alter the mRNA stability of DcpS. Instead, it is required for the recruitment of RNA polymerase II at the mouse DcpS promoter. Chromatin immunoprecipitation assays revealed that knocking-down NATTD transcript with shRNA enhanced the H3K27-Me3 modification at the DcpS promoter. In summary, our studies identified NATTD as a regulator of DcpS transcription through epigenetic mechanisms.
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Affiliation(s)
- Zhu-Zhong Mei
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China.
| | - Hongwei Sun
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Xiaoli Ou
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Lei Li
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Junwei Cai
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Shuiwang Hu
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Juan Wang
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Haihua Luo
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China
| | - Jinghua Liu
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China.
| | - Yong Jiang
- From Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of Pathophysiology, Southern Medical University, Guangzhou 510515, China.
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9
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Serviss JT, Andrews N, Van den Eynden J, Richter FC, Houtman M, Vesterlund M, Schwarzmueller L, Johnsson P, Larsson E, Grandér D, Pokrovskaja Tamm K. An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-34a. Cell Death Dis 2018; 9:736. [PMID: 29970884 PMCID: PMC6030072 DOI: 10.1038/s41419-018-0777-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 01/25/2023]
Abstract
The microRNA-34a is a well-studied tumor suppressor microRNA (miRNA) and a direct downstream target of TP53 with roles in several pathways associated with oncogenesis, such as proliferation, cellular growth, and differentiation. Due to its broad tumor suppressive activity, it is not surprising that miR34a expression is altered in a wide variety of solid tumors and hematological malignancies. However, the mechanisms by which miR34a is regulated in these cancers is largely unknown. In this study, we find that a long noncoding RNA transcribed antisense to the miR34a host gene, is critical for miR34a expression and mediation of its cellular functions in multiple types of human cancer. We name this long noncoding RNA lncTAM34a, and characterize its ability to facilitate miR34a expression under different types of cellular stress in both TP53-deficient and wild-type settings.
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Affiliation(s)
- Jason T Serviss
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden.
| | - Nathanael Andrews
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Jimmy Van den Eynden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Felix Clemens Richter
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Miranda Houtman
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden.,Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Mattias Vesterlund
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Laura Schwarzmueller
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden.,Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center, Amsterdam, The Netherlands
| | - Per Johnsson
- Ludwig Institute for Cancer Research, Stockholm, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Dan Grandér
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Katja Pokrovskaja Tamm
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden
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10
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daSilva LF, Beckedorff FC, Ayupe AC, Amaral MS, Mesel V, Videira A, Reis EM, Setubal JC, Verjovski-Almeida S. Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs. Front Genet 2018; 9:132. [PMID: 29875794 PMCID: PMC5985396 DOI: 10.3389/fgene.2018.00132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/03/2018] [Indexed: 11/30/2022] Open
Abstract
Cell signaling events triggered by androgen hormone in prostate cells is dependent on activation of the androgen receptor (AR) transcription factor. Androgen hormone binding to AR promotes its displacement from the cytoplasm to the nucleus and AR binding to DNA motifs, thus inducing activatory and inhibitory transcriptional programs through a complex regulatory mechanism not yet fully understood. In this work, we performed RNA-seq deep-sequencing of LNCaP prostate cancer cells and found over 7000 expressed long intergenic non-coding RNAs (lincRNAs), of which ∼4000 are novel lincRNAs, and 258 lincRNAs have their expression activated by androgen. Immunoprecipitation of AR, followed by large-scale sequencing of co-immunoprecipitated RNAs (RIP-Seq) has identified in the LNCaP cell line a total of 619 lincRNAs that were significantly enriched (FDR < 10%, DESeq2) in the anti-Androgen Receptor (antiAR) fraction in relation to the control fraction (non-specific IgG), and we named them Androgen-Receptor-Associated lincRNAs (ARA-lincRNAs). A genome-wide analysis showed that protein-coding gene neighbors to ARA-lincRNAs had a significantly higher androgen-induced change in expression than protein-coding genes neighboring lincRNAs not associated to AR. To find relevant epigenetic signatures enriched at the ARA-lincRNAs’ transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.
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Affiliation(s)
- Lucas F daSilva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Felipe C Beckedorff
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Ana C Ayupe
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Murilo S Amaral
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Vinícius Mesel
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Alexandre Videira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Eduardo M Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
| | - Sergio Verjovski-Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
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11
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Brown T, Howe FS, Murray SC, Wouters M, Lorenz P, Seward E, Rata S, Angel A, Mellor J. Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. Mol Syst Biol 2018; 14:e8007. [PMID: 29440389 PMCID: PMC5810148 DOI: 10.15252/msb.20178007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/13/2018] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript degradation. At GAL1, high levels of antisense transcription alter sense transcription dynamics, reducing rates of transcript production and processing, while increasing transcript stability. This relationship with transcript stability is also observed as a genome-wide association. Establishing the antisense transcription-associated chromatin signature through disruption of the Set3C histone deacetylase activity is sufficient to similarly change these rates even in the absence of antisense transcription. Thus, antisense transcription alters sense transcription dynamics in a chromatin-dependent manner.
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Affiliation(s)
- Thomas Brown
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Struan C Murray
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Philipp Lorenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emily Seward
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Scott Rata
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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12
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Latgé G, Poulet C, Bours V, Josse C, Jerusalem G. Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers. Int J Mol Sci 2018; 19:ijms19010123. [PMID: 29301303 PMCID: PMC5796072 DOI: 10.3390/ijms19010123] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/07/2017] [Accepted: 12/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers.
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Affiliation(s)
- Guillaume Latgé
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Christophe Poulet
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Center of Genetics, University Hospital (CHU), 4500 Liège, Belgium.
| | - Claire Josse
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Guy Jerusalem
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
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13
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Napoli S, Piccinelli V, Mapelli SN, Pisignano G, Catapano CV. Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription. RNA Biol 2017; 14:1742-1755. [PMID: 28805496 PMCID: PMC5731802 DOI: 10.1080/15476286.2017.1356564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are long noncoding RNAs transcribed from the opposite strand and overlapping coding and noncoding genes on the sense strand. cis-NATs are widely present in the human genome and can be involved in multiple mechanisms of gene regulation. Here, we describe the presence of cis-NATs in the 3′ distal region of the c-MYC locus and investigate their impact on transcriptional regulation of this key oncogene in human cancers. We found that cis-NATs are produced as consequence of the activation of cryptic transcription initiation sites in the 3′ distal region downstream of the c-MYC 3′UTR. The process is tightly regulated and leads to the formation of two main transcripts, NAT6531 and NAT6558, which differ in their ability to fold into stem-loop secondary structures. NAT6531 acts as a substrate for DICER and as a source of small RNAs capable of modulating c-MYC transcription. This complex system, based on the interplay between cis-NATs and NAT-derived small RNAs, may represent an important layer of epigenetic regulation of the expression of c-MYC and other genes in human cells.
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Affiliation(s)
- Sara Napoli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Valentina Piccinelli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Sarah N Mapelli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Giuseppina Pisignano
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Carlo V Catapano
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland.,b Department of Oncology , Faculty of Biology and Medicine, University of Lausanne , Lausanne , Switzerland
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14
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Murray SC, Mellor J. Using both strands: The fundamental nature of antisense transcription. BIOARCHITECTURE 2016; 6:12-21. [PMID: 26760777 DOI: 10.1080/19490992.2015.1130779] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Non-coding transcription across the antisense strands of genes is an abundant, pervasive process in eukaryotes from yeast to humans, however its biological function remains elusive. Here, we provide commentary on a recent study of ours, which demonstrates a genome-wide role for antisense transcription: establishing a unique, dynamic chromatin architecture over genes. Antisense transcription increases the level of nucleosome occupancy and histone acetylation at the promoter and body of genes, without necessarily modulating the level of protein-coding sense transcription. It is also associated with high levels of histone turnover. By allowing genes to sample a wider range of chromatin configurations, antisense transcription could serve to make genes more sensitive to changing signals, priming them for responses to developmental programs or stressful cellular environments. Given the abundance of antisense transcription and the breadth of these chromatin changes, we propose that antisense transcription represents a fundamental, canonical feature of eukaryotic genes.
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Affiliation(s)
- Struan C Murray
- a Department of Biochemistry ; University of Oxford ; Oxford , UK
| | - Jane Mellor
- a Department of Biochemistry ; University of Oxford ; Oxford , UK
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15
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Mellor J, Woloszczuk R, Howe FS. The Interleaved Genome. Trends Genet 2016; 32:57-71. [DOI: 10.1016/j.tig.2015.10.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 09/29/2015] [Accepted: 10/23/2015] [Indexed: 12/25/2022]
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16
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Yuan C, Wang J, Harrison AP, Meng X, Chen D, Chen M. Genome-wide view of natural antisense transcripts in Arabidopsis thaliana. DNA Res 2015; 22:233-43. [PMID: 25922535 PMCID: PMC4463847 DOI: 10.1093/dnares/dsv008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/06/2015] [Indexed: 01/19/2023] Open
Abstract
Natural antisense transcripts (NATs) are endogenous transcripts that can form double-stranded RNA structures. Many protein-coding genes (PCs) and non-protein-coding genes (NPCs) tend to form cis-NATs and trans-NATs, respectively. In this work, we identified 4,080 cis-NATs and 2,491 trans-NATs genome-widely in Arabidopsis. Of these, 5,385 NAT-siRNAs were detected from the small RNA sequencing data. NAT-siRNAs are typically 21nt, and are processed by Dicer-like 1 (DCL1)/DCL2 and RDR6 and function in epigenetically activated situations, or 24nt, suggesting these are processed by DCL3 and RDR2 and function in environment stress. NAT-siRNAs are significantly derived from PC/PC pairs of trans-NATs and NPC/NPC pairs of cis-NATs. Furthermore, NAT pair genes typically have similar pattern of epigenetic status. Cis-NATs tend to be marked by euchromatic modifications, whereas trans-NATs tend to be marked by heterochromatic modifications.
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Affiliation(s)
- Chunhui Yuan
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China
| | - Jingjing Wang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Andrew P Harrison
- Department of Mathematical Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
| | - Xianwen Meng
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China
| | - Dijun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Gatersleben, Germany
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou 310058, China James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
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17
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Carrieri C, Forrest ARR, Santoro C, Persichetti F, Carninci P, Zucchelli S, Gustincich S. Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease. Front Cell Neurosci 2015; 9:114. [PMID: 25883552 PMCID: PMC4381646 DOI: 10.3389/fncel.2015.00114] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/12/2015] [Indexed: 01/04/2023] Open
Abstract
Antisense (AS) transcripts are RNA molecules that are transcribed from the opposite strand to sense (S) genes forming S/AS pairs. The most prominent configuration is when a lncRNA is antisense to a protein coding gene. Increasing evidences prove that antisense transcription may control sense gene expression acting at distinct regulatory levels. However, its contribution to brain function and neurodegenerative diseases remains unclear. We have recently identified AS Uchl1 as an antisense to the mouse Ubiquitin carboxy-terminal hydrolase L1 (Uchl1) gene (AS Uchl1), the synthenic locus of UCHL1/PARK5. This is mutated in rare cases of early-onset familial Parkinson's Disease (PD) and loss of UCHL1 activity has been reported in many neurodegenerative diseases. Importantly, manipulation of UchL1 expression has been proposed as tool for therapeutic intervention. AS Uchl1 induces UchL1 expression by increasing its translation. It is the representative member of SINEUPs (SINEB2 sequence to UP-regulate translation), a new functional class of natural antisense lncRNAs that activate translation of their sense genes. Here we take advantage of FANTOM5 dataset to identify the transcription start sites associated to S/AS pair at Uchl1 locus. We show that AS Uchl1 expression is under the regulation of Nurr1, a major transcription factor involved in dopaminergic cells' differentiation and maintenance. Furthermore, AS Uch1 RNA levels are strongly down-regulated in neurochemical models of PD in vitro and in vivo. This work positions AS Uchl1 RNA as a component of Nurr1-dependent gene network and target of cellular stress extending our understanding on the role of antisense transcription in the brain.
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Affiliation(s)
- Claudia Carrieri
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy
| | - Alistair R R Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan
| | - Claudio Santoro
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Francesca Persichetti
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan
| | - Silvia Zucchelli
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy ; Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Stefano Gustincich
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy
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18
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Nishiyama MY, Ferreira SS, Tang PZ, Becker S, Pörtner-Taliana A, Souza GM. Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes. PLoS One 2014; 9:e107351. [PMID: 25222706 PMCID: PMC4164538 DOI: 10.1371/journal.pone.0107351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022] Open
Abstract
Sugarcane is a major crop used for food and bioenergy production. Modern cultivars are hybrids derived from crosses between Saccharum officinarum and Saccharum spontaneum. Hybrid cultivars combine favorable characteristics from ancestral species and contain a genome that is highly polyploid and aneuploid, containing 100–130 chromosomes. These complex genomes represent a huge challenge for molecular studies and for the development of biotechnological tools that can facilitate sugarcane improvement. Here, we describe full-length enriched cDNA libraries for Saccharum officinarum, Saccharum spontaneum, and one hybrid genotype (SP803280) and analyze the set of open reading frames (ORFs) in their genomes (i.e., their ORFeomes). We found 38,195 (19%) sugarcane-specific transcripts that did not match transcripts from other databases. Less than 1.6% of all transcripts were ancestor-specific (i.e., not expressed in SP803280). We also found 78,008 putative new sugarcane transcripts that were absent in the largest sugarcane expressed sequence tag database (SUCEST). Functional annotation showed a high frequency of protein kinases and stress-related proteins. We also detected natural antisense transcript expression, which mapped to 94% of all plant KEGG pathways; however, each genotype showed different pathways enriched in antisense transcripts. Our data appeared to cover 53.2% (17,563 genes) and 46.8% (937 transcription factors) of all sugarcane full-length genes and transcription factors, respectively. This work represents a significant advancement in defining the sugarcane ORFeome and will be useful for protein characterization, single nucleotide polymorphism and splicing variant identification, evolutionary and comparative studies, and sugarcane genome assembly and annotation.
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Affiliation(s)
| | | | - Pei-Zhong Tang
- ThermoFisher Scientific, Carlsbad, California, United States of America
| | - Scott Becker
- ThermoFisher Scientific, Carlsbad, California, United States of America
| | | | - Glaucia Mendes Souza
- Departamento de Bioquímica, Universidade de São Paulo, São Paulo, SP, Brazil
- * E-mail:
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19
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Kadakkuzha BM, Liu XA, Narvaez M, Kaye A, Akhmedov K, Puthanveettil SV. Asymmetric localization of natural antisense RNA of neuropeptide sensorin in Aplysia sensory neurons during aging and activity. Front Genet 2014; 5:84. [PMID: 24795747 PMCID: PMC4001032 DOI: 10.3389/fgene.2014.00084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 03/29/2014] [Indexed: 11/21/2022] Open
Abstract
Despite the advances in our understanding of transcriptome, regulation and function of its non-coding components continue to be poorly understood. Here we searched for natural antisense transcript for sensorin (NAT-SRN), a neuropeptide expressed in the presynaptic sensory neurons of gill-withdrawal reflex of the marine snail Aplysia californica. Sensorin (SRN) has a key role in learning and long-term memory storage in Aplysia. We have now identified NAT-SRN in the central nervous system (CNS) and have confirmed its expression by northern blotting and fluorescent RNA in situ hybridization. Quantitative analysis of NAT-SRN in micro-dissected cell bodies and processes of sensory neurons suggest that NAT-SRN is present in the distal neuronal processes along with sense transcripts. Importantly, aging is associated with reduction in levels of NAT-SRN in sensory neuron processes. Furthermore, we find that forskolin, an activator of CREB signaling, differentially alters the distribution of SRN and NAT-SRN. These studies reveal novel insights into physiological regulation of natural antisense RNAs.
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Affiliation(s)
- Beena M Kadakkuzha
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Xin-An Liu
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Maria Narvaez
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Alexandra Kaye
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
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20
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Villegas VE, Rahman MFU, Fernandez-Barrena MG, Diao Y, Liapi E, Sonkoly E, Ståhle M, Pivarcsi A, Annaratone L, Sapino A, Ramírez Clavijo S, Bürglin TR, Shimokawa T, Ramachandran S, Kapranov P, Fernandez-Zapico ME, Zaphiropoulos PG. Identification of novel non-coding RNA-based negative feedback regulating the expression of the oncogenic transcription factor GLI1. Mol Oncol 2014; 8:912-26. [PMID: 24726458 PMCID: PMC4082767 DOI: 10.1016/j.molonc.2014.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 02/18/2014] [Accepted: 03/11/2014] [Indexed: 12/01/2022] Open
Abstract
Non‐coding RNAs are a complex class of nucleic acids, with growing evidence supporting regulatory roles in gene expression. Here we identify a non‐coding RNA located head‐to‐head with the gene encoding the Glioma‐associated oncogene 1 (GLI1), a transcriptional effector of multiple cancer‐associated signaling pathways. The expression of this three‐exon GLI1 antisense (GLI1AS) RNA in cancer cells was concordant with GLI1 levels. siRNAs knockdown of GLI1AS up‐regulated GLI1 and increased cellular proliferation and tumor growth in a xenograft model system. Conversely, GLI1AS overexpression decreased the levels of GLI1, its target genes PTCH1 and PTCH2, and cellular proliferation. Additionally, we demonstrate that GLI1 knockdown reduced GLI1AS, while GLI1 overexpression increased GLI1AS, supporting the role of GLI1AS as a target gene of the GLI1 transcription factor. Activation of TGFβ and Hedgehog signaling, two known regulators of GLI1 expression, conferred a concordant up‐regulation of GLI1 and GLI1AS in cancer cells. Finally, analysis of the mechanism underlying the interplay between GLI1 and GLI1AS indicates that the non‐coding RNA elicits a local alteration of chromatin structure by increasing the silencing mark H3K27me3 and decreasing the recruitment of RNA polymerase II to this locus. Taken together, the data demonstrate the existence of a novel non‐coding RNA‐based negative feedback loop controlling GLI1 levels, thus expanding the repertoire of mechanisms regulating the expression of this oncogenic transcription factor. A novel negative feedback loop on Hedgehog signaling is demonstrated. The mechanism involves a non‐coding RNA antisense to the GLI1 gene, GLI1AS. GLI1AS is shown to be a target gene of the GLI1 transcription factor. GLI1AS represses gene expression at the GLI1/GLI1AS locus. GLI1AS acts as an epigenetic modifier eliciting repressive chromatin marks.
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Affiliation(s)
- Victoria E Villegas
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Faculty of Natural Sciences and Mathematics & Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Yumei Diao
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Eleni Liapi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Enikö Sonkoly
- Unit of Dermatology and Venereology, Department of Medicine, Karolinska Institutet, Solna, Sweden
| | - Mona Ståhle
- Unit of Dermatology and Venereology, Department of Medicine, Karolinska Institutet, Solna, Sweden
| | - Andor Pivarcsi
- Unit of Dermatology and Venereology, Department of Medicine, Karolinska Institutet, Solna, Sweden
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sandra Ramírez Clavijo
- Faculty of Natural Sciences and Mathematics & Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Thomas R Bürglin
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Takashi Shimokawa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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21
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Subudhi AK, Boopathi PA, Garg S, Middha S, Acharya J, Pakalapati D, Saxena V, Aiyaz M, Orekondy HB, Mugasimangalam RC, Sirohi P, Kochar SK, Kochar DK, Das A. Natural antisense transcripts in Plasmodium falciparum isolates from patients with complicated malaria. Exp Parasitol 2014; 141:39-54. [PMID: 24657575 DOI: 10.1016/j.exppara.2014.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 02/17/2014] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
Abstract
Mechanisms regulating gene expression in malaria parasites are not well understood. Little is known about how the parasite regulates its gene expression during transition from one developmental stage to another and in response to various environmental conditions. Parasites in a diseased host face environments which differ from the static, well adapted in vitro conditions. Parasites thus need to adapt quickly and effectively to these conditions by establishing transcriptional states which are best suited for better survival. With the discovery of natural antisense transcripts (NATs) in this parasite and considering the various proposed mechanisms by which NATs might regulate gene expression, it has been speculated that these might be playing a critical role in gene regulation. We report here the diversity of NATs in this parasite, using isolates taken directly from patients with differing clinical symptoms caused by malaria infection. Using a custom designed strand specific whole genome microarray, a total of 797 NATs targeted against annotated loci have been detected. Out of these, 545 NATs are unique to this study. The majority of NATs were positively correlated with the expression pattern of the sense transcript. However, 96 genes showed a change in sense/antisense ratio on comparison between uncomplicated and complicated disease conditions. The antisense transcripts map to a broad range of biochemical/metabolic pathways, especially pathways pertaining to the central carbon metabolism and stress related pathways. Our data strongly suggests that a large group of NATs detected here are unannotated transcription units antisense to annotated gene models. The results reveal a previously unknown set of NATs that prevails in this parasite, their differential regulation in disease conditions and mapping to functionally well annotated genes. The results detailed here call for studies to deduce the possible mechanism of action of NATs, which would further help in understanding the in vivo pathological adaptations of these parasites.
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Affiliation(s)
- Amit Kumar Subudhi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - P A Boopathi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Shilpi Garg
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Sheetal Middha
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Jyoti Acharya
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Deepak Pakalapati
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Vishal Saxena
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | | | | | | | - Paramendra Sirohi
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Sanjay K Kochar
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Dhanpat K Kochar
- Rajasthan University of Health Sciences, Jaipur, Rajasthan, India.
| | - Ashis Das
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
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22
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Boopathi P, Subudhi AK, Garg S, Middha S, Acharya J, Pakalapati D, Saxena V, Aiyaz M, Chand B, Mugasimangalam RC, Kochar SK, Sirohi P, Kochar DK, Das A. Revealing natural antisense transcripts from Plasmodium vivax isolates: Evidence of genome regulation in complicated malaria. INFECTION GENETICS AND EVOLUTION 2013; 20:428-43. [DOI: 10.1016/j.meegid.2013.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 01/08/2023]
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23
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Varela MA, Roberts TC, Wood MJA. Epigenetics and ncRNAs in brain function and disease: mechanisms and prospects for therapy. Neurotherapeutics 2013; 10:621-31. [PMID: 24068583 PMCID: PMC3805859 DOI: 10.1007/s13311-013-0212-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The most fundamental roles of non-coding RNAs (ncRNAs) and epigenetic mechanisms are the guidance of cellular differentiation in development and the regulation of gene expression in adult tissues. In brain, both ncRNAs and the various epigenetic gene regulatory mechanisms play a fundamental role in neurogenesis and normal neuronal function. Thus, epigenetic chromatin remodelling can render coding sites transcriptionally inactive by DNA methylation, histone modifications or antisense RNA interactions. On the other hand, microRNAs (miRNAs) are ncRNA molecules that can regulate the expression of hundreds of genes post-transcriptionally, typically recognising binding sites in the 3' untranslated region (UTR) of mRNA transcripts. Furthermore, there are a myriad of interactions in the interface of miRNAs and epigenetics. For example, epigenetic mechanisms can silence miRNA coding sites, and miRNAs can be the effectors of transcriptional gene silencing, targeting complementary promoters or silencing the expression of epigenetic modifier genes like MECP2 and EZH2 leading to global changes in the epigenome. Alterations in this regulatory machinery play a key role in the pathology of complex disorders including cancer and neurological diseases. For example, miRNA genes are frequently inactivated by epimutations in gliomas. Here we describe the interactions between epigenetic and ncRNA regulatory systems and discuss therapeutic potential, with an emphasis on tumors, cognitive disorders and neurodegenerative diseases.
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Affiliation(s)
- Miguel A. Varela
- />Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Thomas C. Roberts
- />Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
- />Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Matthew J. A. Wood
- />Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
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Vadaie N, Morris KV. Long antisense non-coding RNAs and the epigenetic regulation of gene expression. Biomol Concepts 2013; 4:411-5. [DOI: 10.1515/bmc-2013-0014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/17/2013] [Indexed: 01/08/2023] Open
Abstract
AbstractShortly after the completion of the human genome project in 2003, the Encode project was launched. The project was set out to identify the functional elements in the human genome, and unexpectedly it was found that >80% of the genome is transcribed. The Encode project identified those transcribed regions of the genome to be encoded by non-coding RNAs (ncRNAs). With only 2% of the genome carrying gene-encoding proteins, the conundrum was then, what is the function, if any, of these non-coding regions of the genome? These ncRNAs included both short and long RNAs. The focus of this review will be on antisense long non-coding RNAs (lncRNAs), as these transcripts have been observed to play a role in gene expression of protein-coding genes. Some lncRNAs have been found to regulate protein-coding gene transcription at the epigenetic level, whereby they suppress transcription through the recruitment of protein complexes to target loci in the genome. Conversely, there are lncRNAs that have a positive role in gene expression with less known about mechanism, and some lncRNAs have been shown to be involved in post-transcriptional processes. Additionally, lncRNAs have been observed to regulate their own expression in a positive feedback loop by functioning as a decoy. The biological significance of lncRNAs is only just now becoming evident, with many lncRNAs found to play a significant role in several human diseases.
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Affiliation(s)
- Nadia Vadaie
- 1Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res 2013; 23:1730-9. [PMID: 23816784 PMCID: PMC3787269 DOI: 10.1101/gr.149310.112] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cis-NATs using ssRNA-seq, we developed a new computational method based on a model comparison framework that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole-root and cell-type–specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified 918 additional cis-NAT pairs. Newly identified cis-NAT pairs are supported by polyadenylation data, alternative splicing patterns, and RT-PCR validation. We found 209 cis-NAT pairs that have opposite expression levels in neighboring cell types, implying cell-type–specific roles for cis-NATs. By integrating a genome-wide epigenetic profile of Arabidopsis, we identified a unique chromatin signature of cis-NATs, suggesting a connection between cis-NAT transcription and chromatin modification in plants. An analysis of small-RNA sequencing data showed that ∼4% of cis-NAT pairs produce putative cis-NAT–induced siRNAs. Taken together, our data and analyses illustrate the potential for multifaceted regulatory roles of plant cis-NATs.
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Affiliation(s)
- Song Li
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA
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Perez P, Jang SI, Alevizos I. Emerging landscape of non-coding RNAs in oral health and disease. Oral Dis 2013; 20:226-35. [PMID: 23781896 DOI: 10.1111/odi.12142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022]
Abstract
The world of non-coding RNAs has only recently started being discovered. For the past 40 years, coding genes, mRNA, and proteins have been the center of cellular and molecular biology, and pathologic alterations were attributed to either the aberration of gene sequence or altered promoter activity. It was only after the completion of the human genome sequence that the scientific community started seriously wondering why only a very small portion of the genome corresponded to protein-coding genes. New technologies such as the whole-genome and whole-transcriptome sequencing demonstrated that at least 90% of the genome is actively transcribed. The identification and cataloguing of multiple kinds of non-coding RNA (ncRNA) have exponentially increased, and it is now widely accepted that ncRNAs play major biological roles in cellular physiology, development, metabolism, and are also implicated in a variety of diseases. The aim of this review is to describe the two major classes (long and short forms) of non-coding RNAs and describe their subclasses in terms of function and their relevance and potential in oral diseases.
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Affiliation(s)
- P Perez
- Sjögren's Clinic, Molecular Physiology & Therapeutics, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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Ling MHT, Ban Y, Wen H, Wang SM, Ge SX. Conserved expression of natural antisense transcripts in mammals. BMC Genomics 2013; 14:243. [PMID: 23577827 PMCID: PMC3635984 DOI: 10.1186/1471-2164-14-243] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/06/2013] [Indexed: 02/03/2023] Open
Abstract
Background Recent studies had found thousands of natural antisense transcripts originating from the same genomic loci of protein coding genes but from the opposite strand. It is unclear whether the majority of antisense transcripts are functional or merely transcriptional noise. Results Using the Affymetrix Exon array with a modified cDNA synthesis protocol that enables genome-wide detection of antisense transcription, we conducted large-scale expression analysis of antisense transcripts in nine corresponding tissues from human, mouse and rat. We detected thousands of antisense transcripts, some of which show tissue-specific expression that could be subjected to further study for their potential function in the corresponding tissues/organs. The expression patterns of many antisense transcripts are conserved across species, suggesting selective pressure on these transcripts. When compared to protein-coding genes, antisense transcripts show a lesser degree of expression conservation. We also found a positive correlation between the sense and antisense expression across tissues. Conclusion Our results suggest that natural antisense transcripts are subjected to selective pressure but to a lesser degree compared to sense transcripts in mammals.
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Affiliation(s)
- Maurice H T Ling
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57007, USA
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Zhang J, Mujahid H, Hou Y, Nallamilli BR, Peng Z. Plant Long ncRNAs: A New Frontier for Gene Regulatory Control. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.45128] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Natural Antisense Makes Sense for Gene-specific Activation in Brain. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e24. [PMID: 23344004 PMCID: PMC3393518 DOI: 10.1038/mtna.2012.17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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