1
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Gong J, Hu S, Shan Q, Qin J, Han N, Xie F, Lu H. Bone metastasis in non-small-cell lung cancer: genomic characterization and exploration of potential targets. Ther Adv Med Oncol 2024; 16:17588359241239293. [PMID: 38510678 PMCID: PMC10953105 DOI: 10.1177/17588359241239293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Background Bone metastasis (BM) seriously affects the quality of life and reduces the survival time of patients with non-small-cell lung cancer (NSCLC). The genomic characteristics and potential targets of BMs are yet to be fully explored. Objective To explore the genetic characteristics and potential targets of BM in NSCLC. Design In all, 83 patients with NSCLC were retrospectively selected in this study. Genomic characterization of BMs was explored with the analysis of NGS results from primary tumors and BMs in 6 patients, then combined with NGS results of lung tumors in 16 patients with initial recurrence in bone to analyze mutations potentially associated with BMs, and finally, the correlation was further validated in 61 postoperative patients. Methods The next generation sequencing (NGS) was performed to identify genomic differences between pulmonary primary tumors and BM. Fluorescence in situ hybridization and immunohistochemistry were performed in postoperative tumor tissues from patients who had undergone radical surgery to validate the predictive role of molecular targets for BM. The correlation between cyclin-dependent kinase 4 (CDK4) and BM was evaluated by Pearson's chi-square test. The university of alabama at birminghan cancer data analysis portal (UALCAN) was carried out for the detection of CDK4 expression in lung cancer and the relationship between CDK4 and clinicopathological parameters. The relationship between prognosis and CDK4 expression was analyzed by the Kaplan-Meier plotter. Results The rate of gene amplification was increased (24% versus 36%) while gene substitution/indel was decreased (64% versus 52%) in BMs. The BM-specific mutations were analyzed in 16 recurrent patients which revealed the highest incidence of CDK4 amplification (18.8%). According to the Kaplan-Meier plotter database, the NSCLC patients with high CDK4 gene expression showed poor overall survival (OS) and recurrence-free survival (RFS) (p < 0.05). The incidence of CDK4 amplification tended to be higher in recurrent patients compared to the patients without BM (18.8% versus 4.7%, p = 0.118). Conclusion Compared to the primary tumors of NSCLC, the genome of BMs showed an increased proportion of amplification and a decreased proportion of gene substitution/indel. Furthermore, the CDK4 amplification ratio seemed to be elevated in NSCLC patients with BM which may be associated with poor OS and RFS.
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Affiliation(s)
- Jiali Gong
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
- Department of Hematology and Oncology, Ningbo No. 2 Hospital, Ningbo, Zhejiang, P.R. China
| | - Shumin Hu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
| | - Qianyun Shan
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
| | - Jing Qin
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
| | - Na Han
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
| | - Fajun Xie
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou, P.R. China
| | - Hongyang Lu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, No. 1 East Banshan Road, Gongshu, Hangzhou 310022, P.R. China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic and Cancer Medicine, Gongshu, Hangzhou 310022, P.R. China
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2
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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: 0] [Impact Index Per Article: 0] [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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3
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Korneev S, Garaliene J, Taylor G, Kemenes I, Kemenes G. Time dependent differential regulation of a novel long non-coding natural antisense RNA during long-term memory formation. Sci Rep 2021; 11:3594. [PMID: 33574420 PMCID: PMC7878882 DOI: 10.1038/s41598-021-83190-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/28/2021] [Indexed: 11/17/2022] Open
Abstract
Long natural antisense transcripts (NATs) have been demonstrated in significant numbers in a variety of eukaryotic organisms. They are particularly prevalent in the nervous system suggesting their importance in neural functions. However, the precise physiological roles of the overwhelming majority of long NATs remain unclear. Here we report on the characterization of a novel molluscan nitric oxide synthase (NOS)-related long non-coding NAT (Lym-NOS1AS). This NAT is spliced and polyadenylated and is transcribed from the non-template strand of the Lym-NOS1 gene. We demonstrate that the Lym-NOS1AS is co-expressed with the sense Lym-NOS1 mRNA in a key neuron of memory network. Also, we report that the Lym-NOS1AS is temporally and spatially regulated by one-trial conditioning leading to long term memory (LTM) formation. Specifically, in the cerebral, but not in the buccal ganglia, the temporal pattern of changes in Lym-NOS1AS expression after training correlates with the alteration of memory lapse and non-lapse periods. Our data suggest that the Lym-NOS1AS plays a role in the consolidation of nitric oxide-dependent LTM.
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Affiliation(s)
- Sergei Korneev
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.
| | - Jekaterina Garaliene
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Gabriella Taylor
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Ildikó Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - György Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
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4
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Xia Y, Deng Y, Zhou Y, Li D, Sun X, Gu L, Chen Z, Zhao Q. TSPAN31 suppresses cell proliferation in human cervical cancer through down-regulation of its antisense pairing with CDK4. Cell Biochem Funct 2020; 38:660-668. [PMID: 32207169 DOI: 10.1002/cbf.3526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 01/08/2023]
Abstract
Natural antisense transcripts (NAT) are prevalent phenomena in the mammalian genome and play significant regulatory roles in gene expression. While new insights into NAT continue to be revealed, their exact function and their underlying mechanisms in human cancer remain largely unclear. We identified a NAT of CDK4, referred to TSPAN31, which inhibits CDK4 mRNA and protein expression in human cervical cancer by targeting the 3'-untranslated region (3'-UTR) of the CDK4 mRNA. Furthermore, silencing the expression of the TSPAN31 mRNA rescued the TSPAN31 3'-UTR- or the TSPAN31 full-length-induced decrease in CDK4 expression. Noteworthy, we discovered that TSPAN31, as a member of the tetraspanin family, suppressed cell proliferation by down-regulating its antisense pairing with CDK4 and decreasing retinoblastoma protein phosphorylation in human cervical cancer. Therefore, the results of the present study suggest that TSPAN31 may serve as a potential molecular target for the development of novel anti-cancer agents. SIGNIFICANCE OF THE STUDY: Natural antisense transcripts are widely found in the genome and play an important role in the growth and development of cells. TSPAN31 is natural antisense transcript, and CDK4 is an important gene in the regulation of the cell cycle. Therefore, TSPAN31 and CDK4 have great significance in the study of tumour therapeutic targets.
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Affiliation(s)
- Yingjie Xia
- Department of Biochemistry and Molecular Biology, GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, PR China
| | - Yuanfei Deng
- Department of Biochemistry and Molecular Biology, GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, PR China
| | - Yuting Zhou
- Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Dan Li
- Department of Biochemistry and Molecular Biology, GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, PR China
| | - Xuemeng Sun
- Department of Biochemistry and Molecular Biology, GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, PR China
| | - Lei Gu
- Department of Clinical Medical, Guangzhou Medical University, Guangdong, PR China
| | - Zipeng Chen
- Department of Clinical Medical, Guangzhou Medical University, Guangdong, PR China
| | - Qing Zhao
- Department of Biochemistry and Molecular Biology, GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, PR China
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5
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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: 0.8] [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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6
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PTB-AS, a Novel Natural Antisense Transcript, Promotes Glioma Progression by Improving PTBP1 mRNA Stability with SND1. Mol Ther 2019; 27:1621-1637. [PMID: 31253583 DOI: 10.1016/j.ymthe.2019.05.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 05/14/2019] [Accepted: 05/29/2019] [Indexed: 01/31/2023] Open
Abstract
Glioma, the most common primary malignancy in the brain, has high recurrence and lethality rates, and thus, elucidation of the molecular mechanisms of this incurable disease is urgently needed. Poly-pyrimidine tract binding protein (PTBP1, also known as hnRNP I), an RNA-binding protein, has various mechanisms to promote gliomagenesis. However, the mechanisms regulating PTBP1 expression are unclear. Herein, we report a novel natural antisense noncoding RNA, PTB-AS, whose expression correlated positively with PTBP1 mRNA. We found that PTB-AS significantly promoted the proliferation and migration in vivo and in vitro of glioma cells. PTB-AS substantially increased the PTBP1 level by directly binding to its 3' UTR and stabilizing the mRNA. Furthermore, staphylococcal nuclease domain-containing 1 (SND1) dramatically increased the binding capacity between PTB-AS and PTBP1 mRNA. Mechanistically, PTB-AS could mask the binding site of miR-9 in the PTBP1-3' UTR; miR-9 negatively regulates PTBP1. To summarize, we revealed that PTB-AS, which maintains the PTBP1 level through extended base pairing to the PTBP1 3' UTR with the assistance of SND1, could significantly promote gliomagenesis.
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7
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Abstract
One of the most important resources for researchers of noncoding RNAs is the information available in public databases spread over the internet. However, the effective exploration of this data can represent a daunting task, given the large amount of databases available and the variety of stored data. This chapter describes a classification of databases based on information source, type of RNA, source organisms, data formats, and the mechanisms for information retrieval, detailing the relevance of each of these classifications and its usability by researchers. This classification is used to update a 2012 review, indexing now more than 229 public databases. This review will include an assessment of the new trends for ncRNA research based on the information that is being offered by the databases. Additionally, we will expand the previous analysis focusing on the usability and application of these databases in pathogen and disease research. Finally, this chapter will analyze how currently available database schemas can help the development of new and improved web resources.
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8
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Chavez GG, Taylor G, Garaliene J, Richardson GP, Korneev SA. The temporal expression profile of a Nos3-related natural antisense RNA in the brain suggests a possible role in neurogenesis. Nitric Oxide 2017; 71:27-31. [PMID: 29031735 PMCID: PMC5714617 DOI: 10.1016/j.niox.2017.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/22/2017] [Accepted: 10/11/2017] [Indexed: 12/15/2022]
Abstract
Experimental work over the past several years has revealed an unexpected abundance of long natural antisense transcripts (NATs) in eukaryotic species. In light of the proposed role of such RNA molecules in the regulation of gene expression in the brain, attention is now focused on specific examples of neuronal NATs. Of particular interest are NATs that are complementary to mRNAs encoding nitric oxide synthase (NOS), the enzyme responsible for production of the important gaseous neurotransmitter nitric oxide (NO). Here we study the temporal expression profile of murine Nos3as NAT in the brain. Notably, Nos3as NAT is known to act as a negative regulator of Nos3 gene expression. The results of our quantitative analysis reveal differential expression of Nos3as NAT during embryonic and post-embryonic stages of development of the brain. Also, they show that the low levels of Nos3as NAT coincides with active neurogenesis. In addition we report on an inverse correlation between the relative expression level of Nos3as NAT and the level of Nos3 protein. Thus our data raise the hypothesis that the Nos3as NAT regulates neurogenesis through suppression of Nos3 gene activity. This idea is further supported by experiments conducted on the olfactory bulbs and cultured neuroblastoma cells.
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Affiliation(s)
- Gabriela G Chavez
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton, BN1 9QG, UK
| | - Gabriella Taylor
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton, BN1 9QG, UK
| | - Jekaterina Garaliene
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton, BN1 9QG, UK
| | - Guy P Richardson
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton, BN1 9QG, UK
| | - Sergei A Korneev
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton, BN1 9QG, UK.
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9
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Wang J, Zhou Y, Li D, Sun X, Deng Y, Zhao Q. TSPAN
31 is a critical regulator on transduction of survival and apoptotic signals in hepatocellular carcinoma cells. FEBS Lett 2017; 591:2905-2918. [DOI: 10.1002/1873-3468.12737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Jianglin Wang
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
| | - Yuting Zhou
- Department of Molecular & Cellular Biochemistry College of Medicine University of Kentucky Lexington KY USA
| | - Dan Li
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
| | - Xuemeng Sun
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
| | - Yuanfei Deng
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
| | - Qing Zhao
- Department of Biochemistry and Molecular Biology GMU‐GIBH Joint School of Life Sciences Guangzhou Medical University China
- Sino‐French Hoffmann Institute Guangzhou Medical University China
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10
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Strategies to identify natural antisense transcripts. Biochimie 2017; 132:131-151. [DOI: 10.1016/j.biochi.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022]
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11
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Yu D, Meng Y, Zuo Z, Xue J, Wang H. NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes. Sci Rep 2016; 6:21666. [PMID: 26858106 PMCID: PMC4746697 DOI: 10.1038/srep21666] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/28/2016] [Indexed: 12/12/2022] Open
Abstract
Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip.
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Affiliation(s)
- Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Ziwei Zuo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Jie Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
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12
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Zhou Z, Liu H, Wang C, Lu Q, Huang Q, Zheng C, Lei Y. Long non-coding RNAs as novel expression signatures modulate DNA damage and repair in cadmium toxicology. Sci Rep 2015; 5:15293. [PMID: 26472689 PMCID: PMC4607885 DOI: 10.1038/srep15293] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 09/22/2015] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence suggests that long non-coding RNAs (lncRNAs) are involved in a variety of physiological and pathophysiological processes. Our study was to investigate whether lncRNAs as novel expression signatures are able to modulate DNA damage and repair in cadmium(Cd) toxicity. There were aberrant expression profiles of lncRNAs in 35th Cd-induced cells as compared to untreated 16HBE cells. siRNA-mediated knockdown of ENST00000414355 inhibited the growth of DNA-damaged cells and decreased the expressions of DNA-damage related genes (ATM, ATR and ATRIP), while increased the expressions of DNA-repair related genes (DDB1, DDB2, OGG1, ERCC1, MSH2, RAD50, XRCC1 and BARD1). Cadmium increased ENST00000414355 expression in the lung of Cd-exposed rats in a dose-dependent manner. A significant positive correlation was observed between blood ENST00000414355 expression and urinary/blood Cd concentrations, and there were significant correlations of lncRNA-ENST00000414355 expression with the expressions of target genes in the lung of Cd-exposed rats and the blood of Cd exposed workers. These results indicate that some lncRNAs are aberrantly expressed in Cd-treated 16HBE cells. lncRNA-ENST00000414355 may serve as a signature for DNA damage and repair related to the epigenetic mechanisms underlying the cadmium toxicity and become a novel biomarker of cadmium toxicity.
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Affiliation(s)
- Zhiheng Zhou
- School of Public Health, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
| | - Haibai Liu
- School of Public Health, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
| | - Caixia Wang
- Department of Internal Medicine of Guangzhou First People’s Hospital, Guangzhou Medical University, Guangzhou 510180, P.R. China
| | - Qian Lu
- Shenzhen Longgang District Center for Disease Control & Prevention, Shenzhen 518108, P.R. China
| | - Qinhai Huang
- School of Public Health, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
| | - Chanjiao Zheng
- School of Public Health, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
| | - Yixiong Lei
- School of Public Health, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
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13
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Esposito F, De Martino M, Forzati F, Fusco A. HMGA1-pseudogene overexpression contributes to cancer progression. Cell Cycle 2015; 13:3636-9. [PMID: 25483074 DOI: 10.4161/15384101.2014.974440] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Two pseudogenes for HMGA1, whose overexpression has a critical role in cancer progression, have been identified. They act as decoy for miRNAs that are able to target the HMGA1 gene then enhancing cell proliferation and migration. Moreover, these pseudogenes contain sequences that are potential target sites for cancer-related miRNAs. Interestingly, HMGA1 pseudogenes are highly expressed in human anaplastic thyroid carcinomas, that is one of the most aggressive tumor in mankind, but almost undetectable in well differentiated thyroid carcinomas.
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Affiliation(s)
- Francesco Esposito
- a Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli ; Università degli Studi di Napoli "Federico II," ; Naples , Italy
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14
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Korneev SA, Maconochie M, Naskar S, Korneeva EI, Richardson GP, O'Shea M. A novel long non-coding natural antisense RNA is a negative regulator of Nos1 gene expression. Sci Rep 2015; 5:11815. [PMID: 26154151 PMCID: PMC4495418 DOI: 10.1038/srep11815] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/19/2015] [Indexed: 11/09/2022] Open
Abstract
Long non-coding natural antisense transcripts (NATs) are widespread in eukaryotic species. Although recent studies indicate that long NATs are engaged in the regulation of gene expression, the precise functional roles of the vast majority of them are unknown. Here we report that a long NAT (Mm-antiNos1 RNA) complementary to mRNA encoding the neuronal isoform of nitric oxide synthase (Nos1) is expressed in the mouse brain and is transcribed from the non-template strand of the Nos1 locus. Nos1 produces nitric oxide (NO), a major signaling molecule in the CNS implicated in many important functions including neuronal differentiation and memory formation. We show that the newly discovered NAT negatively regulates Nos1 gene expression. Moreover, our quantitative studies of the temporal expression profiles of Mm-antiNos1 RNA in the mouse brain during embryonic development and postnatal life indicate that it may be involved in the regulation of NO-dependent neurogenesis.
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Affiliation(s)
- Sergei A Korneev
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | - Mark Maconochie
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Souvik Naskar
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | - Elena I Korneeva
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | - Guy P Richardson
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | - Michael O'Shea
- Sussex Neuroscience, School of Life Science, University of Sussex, Brighton BN1 9QG, UK
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15
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Beltran M, Aparicio-Prat E, Mazzolini R, Millanes-Romero A, Massó P, Jenner RG, Díaz VM, Peiró S, de Herreros AG. Splicing of a non-coding antisense transcript controls LEF1 gene expression. Nucleic Acids Res 2015; 43:5785-97. [PMID: 25990740 PMCID: PMC4499130 DOI: 10.1093/nar/gkv502] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/04/2015] [Indexed: 12/14/2022] Open
Abstract
In this report we have analyzed the role of antisense transcription in the control of LEF1 transcription factor expression. A natural antisense transcript (NAT) is transcribed from a promoter present in the first intron of LEF1 gene and undergoes splicing in mesenchymal cells. Although this locus is silent in epithelial cells, and neither NAT transcript nor LEF1 mRNA are expressed, in cell lines with an intermediate epithelial-mesenchymal phenotype presenting low LEF1 expression, the NAT is synthesized and remains unprocessed. Contrarily to the spliced NAT, this unspliced NAT down-regulates the main LEF1 promoter activity and attenuates LEF1 mRNA transcription. Unspliced LEF1 NAT interacts with LEF1 promoter and facilitates PRC2 binding to the LEF1 promoter and trimethylation of lysine 27 in histone 3. Expression of the spliced form of LEF1 NAT in trans prevents the action of unspliced NAT by competing for interaction with the promoter. Thus, these results indicate that LEF1 gene expression is attenuated by an antisense non-coding RNA and that this NAT function is regulated by the balance between its spliced and unspliced forms.
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Affiliation(s)
- Manuel Beltran
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, 08003 Barcelona, Spain UCL Cancer Institute, University College London, London, WC1E6BT, UK
| | - Estel Aparicio-Prat
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, 08003 Barcelona, Spain
| | - Rocco Mazzolini
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, 08003 Barcelona, Spain
| | - Alba Millanes-Romero
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, 08003 Barcelona, Spain
| | - Pere Massó
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, 08003 Barcelona, Spain
| | - Richard G Jenner
- UCL Cancer Institute, University College London, London, WC1E6BT, UK
| | - Víctor M Díaz
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, 08003 Barcelona, Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Sandra Peiró
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, 08003 Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, 08003 Barcelona, Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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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: 31] [Impact Index Per Article: 3.4] [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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Paschoal AR, Maracaja-Coutinho V, Setubal JC, Simões ZLP, Verjovski-Almeida S, Durham AM. Non-coding transcription characterization and annotation. RNA Biol 2014; 9:274-82. [DOI: 10.4161/rna.19352] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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18
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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: 0.6] [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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19
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Werner A, Cockell S, Falconer J, Carlile M, Alnumeir S, Robinson J. Contribution of natural antisense transcription to an endogenous siRNA signature in human cells. BMC Genomics 2014; 15:19. [PMID: 24410956 PMCID: PMC3898206 DOI: 10.1186/1471-2164-15-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 12/15/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Eukaryotic cells express a complex layer of noncoding RNAs. An intriguing family of regulatory RNAs includes transcripts from the opposite strand of protein coding genes, so called natural antisense transcripts (NATs). Here, we test the hypothesis that antisense transcription triggers RNA interference and gives rise to endogenous short RNAs (endo-siRNAs). RESULTS We used cloned human embryonic kidney cells (HEK293) followed by short RNAseq to investigate the small genic RNA transcriptome. 378 genes gave rise to short RNA reads that mapped to exons of RefSeq genes. The length profile of short RNAs showed a broad peak of 20-24 nucleotides, indicative of endo-siRNAs. Collapsed reads mapped predominantly to the first and the last exon of genes (74%). RNAs reads were intersected with sequences occupied by RNAPII or bound to Argonaute (AGO1 by crosslinking, ligation, and sequencing of hybrids, CLASH). In the first exon, 94% of the reads correlated with RNAPII occupancy with an average density of 130 (relative units); this decreased to 65%/20 in middle exons and 54%/12 in the last exon. CLASH reads mapping to multi-exon genes showed little distribution bias with an average of about 5 CLASH reads overlapping with 60% of the endo-siRNA reads. However, endo-siRNAs (21-25 nt) intersecting with CLASH reads were enriched at the 5'end and decreased towards the 3'end.We then investigated the 378 genes with particular focus on features indicative for short RNA production; however, found that endo-siRNA numbers did not correlate with gene structures that favor convergent transcription. In contrast, our gene set was found notably over-represented in the NATsDB sense/antisense group as compared to non-overlapping and non-bidirectional groups. Moreover, read counts showed no correlation with the steady-state levels of the related mRNAs and the pattern of endo-siRNAs proved reproducible after an induced mutagenic insult. CONCLUSIONS Our results suggest that antisense transcripts contribute to low levels of endo-siRNAs in fully differentiated human cells. A characteristic endo-siRNA footprint is being produced at sites of RNAPII transcription which is also related to AGO1. This endo-siRNA signature represents an intriguing finding and its reproducibility suggests that the production of endo-siRNAs is a regulated process with potential homoeostatic impact.
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Affiliation(s)
- Andreas Werner
- RNA Biology Group, Institute of Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle NE2 4HH, UK.
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20
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Spicuglia S, Maqbool MA, Puthier D, Andrau JC. An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function. Methods 2013; 63:3-17. [DOI: 10.1016/j.ymeth.2013.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/02/2013] [Accepted: 04/04/2013] [Indexed: 12/17/2022] Open
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21
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Yang L, Zou M, Fu B, He S. Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. BMC Genomics 2013; 14:65. [PMID: 23368736 PMCID: PMC3599513 DOI: 10.1186/1471-2164-14-65] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 01/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genomic basis of teleost phenotypic complexity remains obscure, despite increasing availability of genome and transcriptome sequence data. Fish-specific genome duplication cannot provide sufficient explanation for the morphological complexity of teleosts, considering the relatively large number of extinct basal ray-finned fishes. RESULTS In this study, we performed comparative genomic analysis to discover the Conserved Teleost-Specific Genes (CTSGs) and orphan genes within zebrafish and found that these two sets of lineage-specific genes may have played important roles during zebrafish embryogenesis. Lineage-specific genes within zebrafish share many of the characteristics of their counterparts in other species: shorter length, fewer exon numbers, higher GC content, and fewer of them have transcript support. Chromosomal location analysis indicated that neither the CTSGs nor the orphan genes were distributed evenly in the chromosomes of zebrafish. The significant enrichment of immunity proteins in CTSGs annotated by gene ontology (GO) or predicted ab initio may imply that defense against pathogens may be an important reason for the diversification of teleosts. The evolutionary origin of the lineage-specific genes was determined and a very high percentage of lineage-specific genes were generated via gene duplications. The temporal and spatial expression profile of lineage-specific genes obtained by expressed sequence tags (EST) and RNA-seq data revealed two novel properties: in addition to being highly tissue-preferred expression, lineage-specific genes are also highly temporally restricted, namely they are expressed in narrower time windows than evolutionarily conserved genes and are specifically enriched in later-stage embryos and early larval stages. CONCLUSIONS Our study provides the first systematic identification of two different sets of lineage-specific genes within zebrafish and provides valuable information leading towards a better understanding of the molecular mechanisms of the genomic basis of teleost phenotypic complexity for future studies.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China
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22
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Zhang YE, Landback P, Vibranovski M, Long M. New genes expressed in human brains: implications for annotating evolving genomes. Bioessays 2012; 34:982-91. [PMID: 23001763 DOI: 10.1002/bies.201200008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage-specific genes. It was recently reported that an excess of primate-specific and human-specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination.
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Affiliation(s)
- Yong E Zhang
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, P.R. China
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23
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Sartor GC, St Laurent G, Wahlestedt C. The Emerging Role of Non-Coding RNAs in Drug Addiction. Front Genet 2012; 3:106. [PMID: 22737160 PMCID: PMC3381216 DOI: 10.3389/fgene.2012.00106] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 05/23/2012] [Indexed: 12/02/2022] Open
Abstract
Prolonged drug use causes long-lasting neuroadaptations in reward-related brain areas that contribute to addiction. Despite significant amount of research dedicated to understanding the underlying mechanisms of addiction, the molecular underpinnings remain unclear. At the same time, much of the pervasive transcription that encompasses the human genome occurs in the nervous system and contributes to its heterogeneity and complexity. Recent evidence suggests that non-coding RNAs (ncRNAs) play an important and dynamic role in transcriptional regulation, epigenetic signaling, stress response, and plasticity in the nervous system. Dysregulation of ncRNAs are thought to contribute to many, and perhaps all, neurological disorders, including addiction. Here, we review recent insights in the functional relevance of ncRNAs, including both microRNAs (miRNAs), and long non-coding RNAs, and then illustrate specific examples of ncRNA regulation in the context of drug addiction. We conclude that ncRNAs are importantly involved in the persistent neuroadaptations associated with addiction-related behaviors, and that therapies that target specific ncRNAs may represent new avenues for the treatment of drug addiction.
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Affiliation(s)
- Gregory C Sartor
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami, FL, USA
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24
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Kim Guisbert KS, Zhang Y, Flatow J, Hurtado S, Staley JP, Lin S, Sontheimer EJ. Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. RNA (NEW YORK, N.Y.) 2012; 18:1142-53. [PMID: 22539527 PMCID: PMC3358637 DOI: 10.1261/rna.030510.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Changes in transcript architecture can have powerful effects on protein expression. Regulation of the transcriptome is often dramatically revealed during dynamic conditions such as development. To examine changes in transcript architecture we analyzed the expression and transcript boundaries of protein-coding and noncoding RNAs over the developmental process of meiosis in Saccharomyces cerevisiae. Custom-designed, high-resolution tiling arrays were used to define the time-resolved transcriptome of cells undergoing meiosis and sporulation. These arrays were specifically designed for the S. cerevisiae strain SK1 that sporulates with high efficiency and synchrony. In addition, new methods were created to define transcript boundaries and to identify dynamic changes in transcript expression and architecture over time. Of 8407 total segments, 699 (8.3%) were identified by our algorithm as regions containing potential transcript architecture changes. Our analyses reveal extensive changes to both the coding and noncoding transcriptome, including altered 5' ends, 3' ends, and splice sites. Additionally, 3910 (46.5%) unannotated expressed segments were identified. Interestingly, subsets of unannotated RNAs are located across from introns (anti-introns) or across from the junction between two genes (anti-intergenic junctions). Many of these unannotated RNAs are abundant and exhibit sporulation-specific changes in expression patterns. All work, including heat maps of the tiling array, annotation for the SK1 strain, and phastCONS conservation analysis, is available at http://groups.molbiosci.northwestern.edu/sontheimer/sk1meiosis.php. Our high-resolution transcriptome analyses reveal that coding and noncoding transcript architectures are exceptionally dynamic in S. cerevisiae and suggest a vast array of novel transcriptional and post-transcriptional control mechanisms that are activated upon meiosis and sporulation.
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Affiliation(s)
- Karen S. Kim Guisbert
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Yong Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Jared Flatow
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Sara Hurtado
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Jonathan P. Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Simon Lin
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Erik J. Sontheimer
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
- Corresponding author.E-mail .
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25
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Fan J, Papadopoulos V. Transcriptional regulation of translocator protein (Tspo) via a SINE B2-mediated natural antisense transcript in MA-10 Leydig cells. Biol Reprod 2012; 86:147, 1-15. [PMID: 22378763 DOI: 10.1095/biolreprod.111.097535] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Translocator protein (18 kDa; TSPO) is a mitochondrial cholesterol- and drug-binding protein involved in cholesterol import into mitochondria, the rate-limiting step in steroidogenesis. TSPO is expressed at high levels in Leydig cells of the testis, and its expression levels dictate the ability of the cells to form androgen. In search of mechanisms that regulate Tspo expression, a number of transcription factors acting on its promoter region have been identified. We report herein the presence of a mechanism of regulation of Tspo expression via complementation with a natural antisense transcript (NAT). At the Tspo locus, a short interspersed repetitive element (SINE) of the SINE B2 family has the potential for high transcriptional activity. The extension of the SINE B2 element-mediated transcript overlapped with exon 3 of the Tspo gene and formed a NAT specific for Tspo (Tspo-NAT) in MA-10 mouse tumor Leydig cells. The identified Tspo-NAT was also found in testis and kidney tissues. Overexpression of the Tspo-NAT regulated Tspo gene expression and its function in steroid formation in MA-10 cells. Time-course studies have indicated that Tspo-NAT expression is regulated by cAMP and could regulate TSPO levels to maintain optimal steroid production by MA-10 Leydig cells. Taken together, these results suggest a new micro-transcriptional mechanism that regulates Tspo expression and thus steroidogenesis via an intron-based SINE B2-driven NAT specific for the Tspo gene.
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Affiliation(s)
- Jinjiang Fan
- The Research Institute of the McGill University Health Centre, McGill University, Montréal, Québec, Canada
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26
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Bidirectional regulation between WDR83 and its natural antisense transcript DHPS in gastric cancer. Cell Res 2012; 22:1374-89. [PMID: 22491477 DOI: 10.1038/cr.2012.57] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Natural antisense transcripts (NATs) exist ubiquitously in mammalian genomes and play roles in the regulation of gene expression. However, both the existence of bidirectional antisense RNA regulation and the possibility of protein-coding genes that function as antisense RNAs remain speculative. Here, we found that the protein-coding gene, deoxyhypusine synthase (DHPS), as the NAT of WDR83, concordantly regulated the expression of WDR83 mRNA and protein. Conversely, WDR83 also regulated DHPS by antisense pairing in a concordant manner. WDR83 and DHPS were capable of forming an RNA duplex at overlapping 3' untranslated regions and this duplex increased their mutual stability, which was required for the bidirectional regulation. As a pair of protein-coding cis-sense/antisense transcripts, WDR83 and DHPS were upregulated simultaneously and correlated positively in gastric cancer (GC), driving GC pathophysiology by promoting cell proliferation. Furthermore, the positive relationship between WDR83 and DHPS was also observed in other cancers. The bidirectional regulatory relationship between WDR83 and DHPS not only enriches our understanding of antisense regulation, but also provides a more complete understanding of their functions in tumor development.
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Abstract
We determined the genome-wide digital gene expression (DGE) profiles of primary acute lymphoblastic leukemia (ALL) cells from 21 patients taking advantage of ‘second-generation' sequencing technology. Patients included in this study represent four cytogenetically distinct subtypes of B-cell precursor (BCP) ALL and T-cell lineage ALL (T-ALL). The robustness of DGE combined with supervised classification by nearest shrunken centroids (NSC) was validated experimentally and by comparison with published expression data for large sets of ALL samples. Genes that were differentially expressed between BCP ALL subtypes were enriched to distinct signaling pathways with dic(9;20) enriched to TP53 signaling, t(9;22) to interferon signaling, as well as high hyperdiploidy and t(12;21) to apoptosis signaling. We also observed antisense tags expressed from the non-coding strand of ∼50% of annotated genes, many of which were expressed in a subtype-specific pattern. Antisense tags from 17 gene regions unambiguously discriminated between the BCP ALL and T-ALL subtypes, and antisense tags from 76 gene regions discriminated between the 4 BCP subtypes. We observed a significant overlap of gene regions with alternative polyadenylation and antisense transcription (P<1 × 10−15). Our study using DGE profiling provided new insights into the RNA expression patterns in ALL cells.
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28
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Yang Z, Jin X, Rao X, Hu F. A natural antisense transcript regulates mucD gene expression and biofilm biosynthesis in Pseudomonas aeruginosa. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711060245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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29
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Chen D, Yuan C, Zhang J, Zhang Z, Bai L, Meng Y, Chen LL, Chen M. PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res 2011; 40:D1187-93. [PMID: 22058132 PMCID: PMC3245084 DOI: 10.1093/nar/gkr823] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a ‘Gene Set Analysis’ module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/.
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Affiliation(s)
- Dijun Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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30
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Faure E, Delaye L, Tribolo S, Levasseur A, Seligmann H, Barthélémy RM. Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene. Biol Direct 2011; 6:56. [PMID: 22024028 PMCID: PMC3214167 DOI: 10.1186/1745-6150-6-56] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 10/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondria mediate most of the energy production that occurs in the majority of eukaryotic organisms. These subcellular organelles contain a genome that differs from the nuclear genome and is referred to as mitochondrial DNA (mtDNA). Despite a disparity in gene content, all mtDNAs encode at least two components of the mitochondrial electron transport chain, including cytochrome c oxidase I (Cox1). PRESENTATION OF THE HYPOTHESIS A positionally conserved ORF has been found on the complementary strand of the cox1 genes of both eukaryotic mitochondria (protist, plant, fungal and animal) and alpha-proteobacteria. This putative gene has been named gau for gene antisense ubiquitous in mtDNAs. The length of the deduced protein is approximately 100 amino acids. In vertebrates, several stop codons have been found in the mt gau region, and potentially functional gau regions have been found in nuclear genomes. However, a recent bioinformatics study showed that several hypothetical overlapping mt genes could be predicted, including gau; this involves the possible import of the cytosolic AGR tRNA into the mitochondria and/or the expression of mt antisense tRNAs with anticodons recognizing AGR codons according to an alternative genetic code that is induced by the presence of suppressor tRNAs. Despite an evolutionary distance of at least 1.5 to 2.0 billion years, the deduced Gau proteins share some conserved amino acid signatures and structure, which suggests a possible conserved function. Moreover, BLAST analysis identified rare, sense-oriented ESTs with poly(A) tails that include the entire gau region. Immunohistochemical analyses using an anti-Gau monoclonal antibody revealed strict co-localization of Gau proteins and a mitochondrial marker. TESTING THE HYPOTHESIS This hypothesis could be tested by purifying the gau gene product and determining its sequence. Cell biological experiments are needed to determine the physiological role of this protein. IMPLICATIONS OF THE HYPOTHESIS Studies of the gau ORF will shed light on the origin of novel genes and their functions in organelles and could also have medical implications for human diseases that are caused by mitochondrial dysfunction. Moreover, this strengthens evidence for mitochondrial genes coded according to an overlapping genetic code.
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Affiliation(s)
- Eric Faure
- Université de Provence, Marseille cedex 3, France.
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Zhang YE, Landback P, Vibranovski MD, Long M. Accelerated recruitment of new brain development genes into the human genome. PLoS Biol 2011; 9:e1001179. [PMID: 22028629 PMCID: PMC3196496 DOI: 10.1371/journal.pbio.1001179] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 09/08/2011] [Indexed: 11/24/2022] Open
Abstract
How the human brain evolved has attracted tremendous interests for decades. Motivated by case studies of primate-specific genes implicated in brain function, we examined whether or not the young genes, those emerging genome-wide in the lineages specific to the primates or rodents, showed distinct spatial and temporal patterns of transcription compared to old genes, which had existed before primate and rodent split. We found consistent patterns across different sources of expression data: there is a significantly larger proportion of young genes expressed in the fetal or infant brain of humans than in mouse, and more young genes in humans have expression biased toward early developing brains than old genes. Most of these young genes are expressed in the evolutionarily newest part of human brain, the neocortex. Remarkably, we also identified a number of human-specific genes which are expressed in the prefrontal cortex, which is implicated in complex cognitive behaviors. The young genes upregulated in the early developing human brain play diverse functional roles, with a significant enrichment of transcription factors. Genes originating from different mechanisms show a similar expression bias in the developing brain. Moreover, we found that the young genes upregulated in early brain development showed rapid protein evolution compared to old genes also expressed in the fetal brain. Strikingly, genes expressed in the neocortex arose soon after its morphological origin. These four lines of evidence suggest that positive selection for brain function may have contributed to the origination of young genes expressed in the developing brain. These data demonstrate a striking recruitment of new genes into the early development of the human brain.
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Affiliation(s)
- Yong E. Zhang
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Patrick Landback
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Maria D. Vibranovski
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
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Thiagarajan RD, Cloonan N, Gardiner BB, Mercer TR, Kolle G, Nourbakhsh E, Wani S, Tang D, Krishnan K, Georgas KM, Rumballe BA, Chiu HS, Steen JA, Mattick JS, Little MH, Grimmond SM. Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling. BMC Genomics 2011; 12:441. [PMID: 21888672 PMCID: PMC3180702 DOI: 10.1186/1471-2164-12-441] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 09/05/2011] [Indexed: 12/29/2022] Open
Abstract
Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. Results To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. Conclusion The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events.
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Affiliation(s)
- Rathi D Thiagarajan
- Institute for Molecular Bioscience, The University of Queensland, St, Lucia QLD 4072, Australia.
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Gan H, Lin X, Zhang Z, Zhang W, Liao S, Wang L, Han C. piRNA profiling during specific stages of mouse spermatogenesis. RNA (NEW YORK, N.Y.) 2011; 17:1191-203. [PMID: 21602304 PMCID: PMC3138557 DOI: 10.1261/rna.2648411] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/01/2011] [Indexed: 05/19/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small RNAs abundantly expressed in animal gonads. piRNAs that map to retrotransposons are generated by a "ping-pong" amplification loop to suppress the activity of retrotransposons. However, the biogenesis and function of other categories of piRNAs have yet to be investigated. In this study, we first profiled the expression of small RNAs in type A spermatogonia, pachytene spermatocytes, and round spermatids by deep sequencing. We then focused on the computational analysis of the potential piRNAs generated in the present study as well as other published sets. piRNAs mapping to retrotransposons, mRNAs, and intergenic regions had different length distributions and were differentially regulated in spermatogenesis. piRNA-generating mRNAs (PRMRs), whose expression positively correlated with their piRNA products, constituted one-third of the protein-coding genes and were evolutionarily conserved and enriched with splicing isoforms and antisense transcripts. PRMRs with piRNAs preferentially mapped to CDSs and 3' UTRs partitioned into three clusters differentially expressed during spermatogenesis and enriched with unique sets of functional annotation terms related to housekeeping activities as well as spermatogenesis-specific processes. Intergenic piRNAs were divided into 2992 clusters probably representing novel transcriptional units that have not been reported. The transcripts of a large number of genes involved in spermatogenesis are the precursors of piRNAs, and these genes are intricately regulated by alternative splicing and antisense transcripts. piRNAs, whose regulatory role in gene expression awaits to be identified, are clearly products of a novel regulatory process that needs to be defined.
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Affiliation(s)
- Haiyun Gan
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiwen Lin
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuqiang Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Shangying Liao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Lixian Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunsheng Han
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
- Corresponding author.E-mail .
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Zhang YE, Vibranovski MD, Krinsky BH, Long M. A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes. ACTA ACUST UNITED AC 2011; 27:1749-53. [PMID: 21551137 DOI: 10.1093/bioinformatics/btr280] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Retrocopies are important genes in the genomes of almost all higher eukaryotes. However, the annotation of such genes is a non-trivial task. Intronless genes have often been considered to be retroposed copies of intron-containing paralogs. Such categorization relies on the implicit premise that alignable regions of the duplicates should be long enough to cover exon-exon junctions of the intron-containing genes, and thus intron loss events can be inferred. Here, we examined the alternative possibility that intronless genes could be generated by partial DNA-based duplication of intron-containing genes in the fruitfly genome. RESULTS By building pairwise protein-, transcript- and genome-level DNA alignments between intronless genes and their corresponding intron-containing paralogs, we found that alignments do not cover exon-exon junctions in 40% of cases and thus no intron loss could be inferred. For these cases, the candidate parental proteins tend to be partially duplicated, and intergenic sequences or neighboring genes are included in the intronless paralog. Moreover, we observed that it is significantly less likely for these paralogs to show inter-chromosomal duplication and testis-dominant transcription, compared to the remaining 60% of cases with evidence of clear intron loss (retrogenes). These lines of analysis reveal that DNA-based duplication contributes significantly to the 40% of cases of single exon gene duplication. Finally, we performed an analogous survey in the human genome and the result is similar, wherein 34% of the cases do not cover exon-exon junctions. Thus, genome annotation for retrogene identification should discard candidates without clear evidence of intron loss. CONTACT mlong@uchicago.edu; zhangy@uchicago.edu
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Affiliation(s)
- Yong E Zhang
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA.
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Natural antisense transcripts regulate gene expression in an epigenetic manner. Biochem Biophys Res Commun 2010; 396:177-81. [PMID: 20438699 DOI: 10.1016/j.bbrc.2010.04.147] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 04/27/2010] [Indexed: 12/15/2022]
Abstract
Cytosine DNA methylation, covalent histone modifications, and RNA-mediated gene regulation are the major aspects of epigenetic regulation. Natural antisense transcripts (NATs), as a new member of regulatory RNAs, occur ubiquitously in prokaryote and eukaryote, and play significant roles in physiological or pathological processes. NATs, mostly non-coding RNAs, are involved in transcriptional interference, genomic imprinting, X inactivation, RNA editing, translational regulation, RNA export, DNA methylation, histone modifications, and so on. NATs regulate gene expression through direct interaction with the sense transcripts or indirect interaction with other targets, such as DNA methyltransferases, histone acetylases and histone deacetylases. There may be a direct link among NATs, DNA methylaton and histone modifications. Through formation of sense-antisense duplex structures, NATs exert a widespread impact on conventional gene expression at the mRNA and/or protein level and regulate sense transcripts in a concordant or discordant manner. As one of the important components in epigenetics, NATs could be a potentially rich source for scientists to exploit in the therapy of cancers and other diseases.
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Zhu Z, Zhang Y, Long M. Extensive structural renovation of retrogenes in the evolution of the Populus genome. PLANT PHYSIOLOGY 2009; 151:1943-51. [PMID: 19789289 PMCID: PMC2785971 DOI: 10.1104/pp.109.142984] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Retroposition, as an important copy mechanism for generating new genes, was believed to play a negligible role in plants. As a representative dicot, the genomic sequences of Populus (poplar; Populus trichocarpa) provide an opportunity to investigate this issue. We identified 106 retrogenes and found the majority (89%) of them are associated with functional signatures in sequence evolution, transcription, and (or) translation. Remarkably, examination of gene structures revealed extensive structural renovation of these retrogenes: we identified 18 (17%) of them undergoing either chimerization to form new chimerical genes and (or) intronization (transformation into intron sequences of previously exonic sequences) to generate new intron-containing genes. Such a change might occur at a high speed, considering eight out of 18 such cases occurred recently after divergence between Arabidopsis (Arabidopsis thaliana) and Populus. This pattern also exists in Arabidopsis, with 15 intronized retrogenes occurring after the divergence between Arabidopsis and papaya (Carica papaya). Thus, the frequency of intronization in dicots revealed its importance as a mechanism in the evolution of exon-intron structure. In addition, we also examined the potential impact of the Populus nascent sex determination system on the chromosomal distribution of retrogenes and did not observe any significant effects of the extremely young sex chromosomes.
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Grinchuk OV, Jenjaroenpun P, Orlov YL, Zhou J, Kuznetsov VA. Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns. Nucleic Acids Res 2009; 38:534-47. [PMID: 19906709 PMCID: PMC2811022 DOI: 10.1093/nar/gkp954] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cis-antisense gene pairs (CASGPs) can transcribe mRNAs from an opposite strand of a given locus. To classify and understand diverse CASGP phenomena in the human we compiled a genome-wide catalog of CASGPs and integrated these sequences with microarray, SAGE and miRNA data. Using the concept of overlapping regions and clustering of SA transcripts by chromosome coordinates, we identified up to 9000 overlapping antisense loci. Four thousand three hundred and seventy-four of these CASGPs form 1759 complex gene architectures. We found that ∼35% (6347/18160) of RefSeq genes are overlapped with the antisense transcripts. About 30% of Affymetrix U133 microarray initial sequences map transcripts of ∼35% CASGPs and reveal mostly concordant expression in CASGPs. We found strong significant overrepresentation of human miRNA genes in loci of CASGPs. We developed a data-driven model of cross-talk between co-expressed CASGPs and DICER1-mediated miRNA pathway in normal spermatogenesis and in severe teratozoospermia. Specifically, we revealed complex SA structural–functional gene module composing the protein-coding genes, WDR6, DALRD3, NDUFAF3 and ncRNA precursors, mir-425 and mir-191, which could provide downregulation of ncRNA pathway via direct targeting DICER1 and basonuclin 2 transcripts by mir-425 and mir-191 in normal spermatogenesis, but this mechanism is switched off in severe teratozoospermia. The database is available from http://globalisland.bii.a-star.edu.sg/∼jiangtao/sas/index3.php?link =about
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Affiliation(s)
- Oleg V Grinchuk
- Bioinformatics Institute, 30 Biopolis Street #07-01, Singapore 138672, Singapore
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Grigoriadis A, Oliver GR, Tanney A, Kendrick H, Smalley MJ, Jat P, Neville AM. Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues. BMC Genomics 2009; 10:324. [PMID: 19615061 PMCID: PMC2721853 DOI: 10.1186/1471-2164-10-324] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 07/17/2009] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts--NATs), some of which may play a key role in a range of human diseases. To date, several databases of in silico defined human sense-antisense (SAS) pairs have appeared, however no study has focused on differential expression of SAS pairs in breast tissue. We therefore investigated the expression levels of sense and antisense transcripts in normal and malignant human breast epithelia using the Affymetrix HG-U133 Plus 2.0 and Almac Diagnostics Breast Cancer DSA microarray technologies as well as massively parallel signature sequencing (MPSS) data. RESULTS The expression of more than 2500 antisense transcripts were detected in normal breast duct luminal cells and in primary breast tumors substantially enriched for their epithelial cell content by DSA microarray. Expression of 431 NATs were confirmed by either of the other two technologies. A corresponding sense transcript could be identified on DSA for 257 antisense transcripts. Of these SAS pairs, 163 have not been previously reported. A positive correlation of differential expression between normal and malignant breast samples was observed for most SAS pairs. Orientation specific RT-QPCR of selected SAS pairs validated their expression in several breast cancer cell lines and solid breast tumours. CONCLUSION Disease-focused and antisense enriched microarray platforms (such as Breast Cancer DSA) confirm the assumption that antisense transcription in the human breast is more prevalent than previously anticipated. Expression of a proportion of these NATs has already been confirmed by other technologies while the true existence of the remaining ones has to be validated. Nevertheless, future studies will reveal whether the relative abundances of antisense and sense transcripts have regulatory influences on the translation of these mRNAs.
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Affiliation(s)
- Anita Grigoriadis
- Ludwig Institute for Cancer Research, 605 Third Avenue, New York, NY 10158, USA
- Breakthrough Breast Cancer Research Unit, Guy's Hospital, King's Health Partners AHSC, London, UK
| | - Gavin R Oliver
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, BT63 5QD, UK
| | - Austin Tanney
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, BT63 5QD, UK
| | - Howard Kendrick
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | | | - Parmjit Jat
- Department of Neurodegenerative Disease, Institute of Neurology, London, WC1N 3BG, UK
| | - A Munro Neville
- Ludwig Institute for Cancer Research, 605 Third Avenue, New York, NY 10158, USA
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Soldà G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A. An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. Brief Bioinform 2009; 10:475-89. [PMID: 19383843 DOI: 10.1093/bib/bbp022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-protein coding RNAs (ncRNAs) have emerged as a vast and heterogeneous portion of eukaryotic transcriptomes. Several ncRNA families, either short (<200 nucleotides, nt) or long (>200 nt), have been described and implicated in a variety of biological processes, from translation to gene expression regulation and nuclear trafficking. Most probably, other families are still to be discovered. Computational methods for ncRNA research require different approaches from the ones normally used in the prediction of protein-coding genes. Indeed, primary sequence alone is often insufficient to infer ncRNA functionality, whereas secondary structure and local conservation of portions of the transcript could provide useful information for both the prediction and the functional annotation of ncRNAs. Here we present an overview of computational methods and bioinformatics resources currently available for studying ncRNA genes, introducing the common themes as well as the different approaches required for long and short ncRNA identification and annotation.
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Affiliation(s)
- Giulia Soldà
- Department of Biology and Genetics for Medical Sciences, University of Milano, 20133 Milan, Italy.
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Korneev SA, Korneeva EI, Lagarkova MA, Kiselev SL, Critchley G, O'Shea M. Novel noncoding antisense RNA transcribed from human anti-NOS2A locus is differentially regulated during neuronal differentiation of embryonic stem cells. RNA 2008; 14:2030-7. [PMID: 18820242 PMCID: PMC2553742 DOI: 10.1261/rna.1084308] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here, we report on the discovery of a locus in the human genome, which evolved by gene duplication followed by an internal DNA inversion. This locus exhibits high sequence similarity to the gene for the inducible isoform of NOS protein (NOS2A) and is transcribed into a noncoding RNA containing a region of significant antisense homology with the NOS2A mRNA. We show that this antisense transcript (anti-NOS2A RNA) is expressed in different types of brain tumors, including meningiomas and glioblastomas. More importantly, we demonstrate that the expression profiles of the anti-NOS2A RNA and the NOS2A mRNA exhibit concurrent reciprocal changes in undifferentiated human embryonic stem cells (hESCs) and in hESCs induced to differentiate into neurogenic precursors such as neurospheres. As NOS2A has a role in neurogenesis, our results suggest that the anti-NOS2A RNA is involved in the regulation of neuronal differentiation of hESCs through the modulation of NOS2A gene expression.
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Affiliation(s)
- Sergei A Korneev
- Sussex Centre for Neuroscience, School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom.
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The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Curr Genet 2008; 54:241-69. [PMID: 18813928 DOI: 10.1007/s00294-008-0215-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 12/25/2022]
Abstract
Naturally occurring Antisense Transcripts (NATs) compose an emerging group of regulatory RNAs. These regulatory elements appear in all organisms examined, but little is known about global expression of NATs in fungi. Analysis of currently available EST sequences suggests that 352 cis NATs are present in Aspergillus flavus. An Affymetrix GeneChip microarray containing probes for these cis NATs, as well as all predicted genes in A. flavus, allowed a whole genome expression analysis of these elements in response to two ecologically important temperatures for the fungus. RNA expression analysis showed that 32 NATs and 2,709 genes were differentially expressed between 37 degrees C, the optimum temperature for growth, and 28 degrees C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. These NATs correspond to sense genes with diverse functions including transcription initiation, carbohydrate processing and binding, temperature sensitive morphogenesis, and secondary metabolism. This is the first report of a whole genome transcriptional analysis of NAT expression in a fungus.
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Schnütgen F, Hansen J, De-Zolt S, Horn C, Lutz M, Floss T, Wurst W, Noppinger PR, von Melchner H. Enhanced gene trapping in mouse embryonic stem cells. Nucleic Acids Res 2008; 36:e133. [PMID: 18812397 PMCID: PMC2582619 DOI: 10.1093/nar/gkn603] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene trapping is used to introduce insertional mutations into genes of mouse embryonic stem cells (ESCs). It is performed with gene trap vectors that simultaneously mutate and report the expression of the endogenous gene at the site of insertion and provide a DNA tag for rapid identification of the disrupted gene. Gene traps have been employed worldwide to assemble libraries of mouse ESC lines harboring mutations in single genes, which can be used to make mutant mice. However, most of the employed gene trap vectors require gene expression for reporting a gene trap event and therefore genes that are poorly expressed may be under-represented in the existing libraries. To address this problem, we have developed a novel class of gene trap vectors that can induce gene expression at insertion sites, thereby bypassing the problem of intrinsic poor expression. We show here that the insertion of the osteopontin enhancer into several conventional gene trap vectors significantly increases the gene trapping efficiency in high-throughput screens and facilitates the recovery of poorly expressed genes.
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Affiliation(s)
- Frank Schnütgen
- Department of Molecular Hematology, University of Frankfurt Medical School, Frankfurt am Main, Germany
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Li CY, Liu QR, Zhang PW, Li XM, Wei L, Uhl GR. OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. Nucleic Acids Res 2008; 37:D251-60. [PMID: 18790807 PMCID: PMC2686464 DOI: 10.1093/nar/gkn568] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
‘Cell adhesion molecules’ (CAMs) are essential elements of cell/cell communication that are important for proper development and plasticity of a variety of organs and tissues. In the brain, appropriate assembly and tuning of neuronal connections is likely to require appropriate function of many cell adhesion processes. Genetic studies have linked and/or associated CAM variants with psychiatric, neurologic, neoplastic, immunologic and developmental phenotypes. However, despite increasing recognition of their functional and pathological significance, no systematic study has enumerated CAMs or documented their global features. We now report compilation of 496 human CAM genes in six gene families based on manual curation of protein domain structures, Gene Ontology annotations, and 1487 NCBI Entrez annotations. We map these genes onto a cell adhesion molecule ontology that contains 850 terms, up to seven levels of depth and provides a hierarchical description of these molecules and their functions. We develop OKCAM, a CAM knowledgebase that provides ready access to these data and ontologic system at http://okcam.cbi.pku.edu.cn. We identify global CAM properties that include: (i) functional enrichment, (ii) over-represented regulation modes and expression patterns and (iii) relationships to human Mendelian and complex diseases, and discuss the strengths and limitations of these data.
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Affiliation(s)
- Chuan-Yun Li
- Molecular Neurobiology Branch, NIH-IRP (NIDA), Baltimore, MD 21224, USA
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Li JT, Zhang Y, Kong L, Liu QR, Wei L. Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res 2008; 36:4833-44. [PMID: 18653530 PMCID: PMC2528163 DOI: 10.1093/nar/gkn470] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs in human and nine other animals, using ESTs to increase coverage significantly over previous studies. The percentage of transcriptional units (TUs) involved in trans-SAs among all TUs was as high as 4.13%. Particularly 2896 human TUs (or 2.89% of all human TUs) were involved in 3327 trans-SAs. Sequence complementarities over multiple segments with predicted RNA hybridization indicated that some trans-SAs might have sophisticated RNA-RNA pairing patterns. One-fourth of human trans-SAs involved noncoding TUs, suggesting that many noncoding RNAs may function by a trans-acting antisense mechanism. TUs in trans-SAs were statistically significantly enriched in nucleic acid binding, ion/protein binding and transport and signal transduction functions and pathways; a significant number of human trans-SAs showed concordant or reciprocal expression pattern; a significant number of human trans-SAs were conserved in mouse. This evidence suggests important regulatory functions of trans-SAs. In 30 cases, trans-SAs were related to cis-SAs through paralogues, suggesting a possible mechanism for the origin of trans-SAs. All trans-SAs are available at http://trans.cbi.pku.edu.cn/.
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Affiliation(s)
- Jiong-Tang Li
- Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, 100871, PR China
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Yin Y, Zhao Y, Wang J, Liu C, Chen S, Chen R, Zhao H. antiCODE: a natural sense-antisense transcripts database. BMC Bioinformatics 2007; 8:319. [PMID: 17760969 PMCID: PMC1997216 DOI: 10.1186/1471-2105-8-319] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 08/30/2007] [Indexed: 01/03/2023] Open
Abstract
Background Natural antisense transcripts (NATs) are endogenous RNA molecules that exhibit partial or complete complementarity to other RNAs, and that may contribute to the regulation of molecular functions at various levels. In recent years, large-scale NAT screens in several model organisms have produced much data, but there is no database to assemble all these data. AntiCODE intends to function as an integrated NAT database for this purpose. Results This release of antiCODE contains more than 30,000 non-redundant natural sense-antisense transcript pairs from 12 eukaryotic model organisms. In order to provide an integrated NAT research platform, efficient browser, search and Blast functions have been included to enable users to easily access information through parameters such as species, accession number, overlapping patterns, coding potential etc. In addition to the collected information, antiCODE also introduces a simple classification system to facilitate the study of natural antisense transcripts. Conclusion Though a few similar databases also dealing with NATs have appeared lately, antiCODE is the most comprehensive among these, comprising almost all currently detected NAT pairs.
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Affiliation(s)
- Yifei Yin
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, CAMS & PUMC, Beijing 100730, China
- Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
| | - Yi Zhao
- Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
| | - Jie Wang
- Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Changning Liu
- Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Shuguang Chen
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, CAMS & PUMC, Beijing 100730, China
| | - Runsheng Chen
- Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, CAMS & PUMC, Beijing 100730, China
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Zhang Y, Luoh SM, Hon LS, Baertsch R, Wood WI, Zhang Z. GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acids Res 2007; 35:W152-8. [PMID: 17545196 PMCID: PMC1933245 DOI: 10.1093/nar/gkm381] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
GeneHub-GEPIS is a web application that performs digital expression analysis in human and mouse tissues based on an integrated gene database. Using aggregated expressed sequence tag (EST) library information and EST counts, the application calculates the normalized gene expression levels across a large panel of normal and tumor tissues, thus providing rapid expression profiling for a given gene. The backend GeneHub component of the application contains pre-defined gene structures derived from mRNA transcript sequences from major databases and includes extensive cross references for commonly used gene identifiers. ESTs are then linked to genes based on their precise genomic locations as determined by GMAP. This genome-based approach reduces incorrect matches between ESTs and genes, thus minimizing the noise seen with previous tools. In addition, the gene-centric design makes it possible to add several important features, including text searching capabilities, the ability to accept diverse input values, expression analysis for microRNAs, basic gene annotation, batch analysis and linking between mouse and human genes. GeneHub-GEPIS is available at http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/ or http://www.gepis.org/.
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Affiliation(s)
- Yan Zhang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA and Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Shiuh-Ming Luoh
- Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA and Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Lawrence S. Hon
- Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA and Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Robert Baertsch
- Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA and Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - William I. Wood
- Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA and Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Zemin Zhang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA and Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
- *To whom correspondence should be addressed. +1 650 225 4293650 225 5389
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The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. BMC Genomics 2007; 8:74. [PMID: 17362513 PMCID: PMC1831481 DOI: 10.1186/1471-2164-8-74] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 03/15/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutations in the PTEN induced putative kinase 1 (PINK1) are implicated in early-onset Parkinson's disease. PINK1 is expressed abundantly in mitochondria rich tissues, such as skeletal muscle, where it plays a critical role determining mitochondrial structural integrity in Drosophila. RESULTS Herein we characterize a novel splice variant of PINK1 (svPINK1) that is homologous to the C-terminus regulatory domain of the protein kinase. Naturally occurring non-coding antisense provides sophisticated mechanisms for diversifying genomes and we describe a human specific non-coding antisense expressed at the PINK1 locus (naPINK1). We further demonstrate that PINK1 varies in vivo when human skeletal muscle mitochondrial content is enhanced, supporting the idea that PINK1 has a physiological role in mitochondrion. The observation of concordant regulation of svPINK1 and naPINK1 during in vivo mitochondrial biogenesis was confirmed using RNAi, where selective targeting of naPINK1 results in loss of the PINK1 splice variant in neuronal cell lines. CONCLUSION Our data presents the first direct observation that a mammalian non-coding antisense molecule can positively influence the abundance of a cis-transcribed mRNA under physiological abundance conditions. While our analysis implies a possible human specific and dsRNA-mediated mechanism for stabilizing the expression of svPINK1, it also points to a broader genomic strategy for regulating a human disease locus and increases the complexity through which alterations in the regulation of the PINK1 locus could occur.
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