1
|
Yang WY, Liu ZY, Zhu Y, Xiao Y, Xiao WF, Tang L, Dong ZQ, Pan MH, Lu C, Chen P. MicroRNA bmo-miR-31-5p inhibits apoptosis and promotes BmNPV proliferation by targeting the CYP9e2 gene of Bombyx mori. PEST MANAGEMENT SCIENCE 2024; 80:4564-4574. [PMID: 38742692 DOI: 10.1002/ps.8162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/24/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Bombyx mori nuclear polyhedrosis virus (BmNPV), as a typical baculovirus, is the primary pathogen that infects the silkworm B. mori, a lepidopteran species. Owing to the high biological safety of BmNPV in infecting insects, it is commonly utilized as a biological insecticide for pest control. Apoptosis is important in the interaction between the host and pathogenic microorganisms. MicroRNAs (miRNAs) influence immune responses and promote stability of the immune system via apoptosis. Therefore, the study of apoptosis-related miRNA in silkworms during virus infection can not only provide support for standardizing the prevention and control of diseases and insect pests, but also reduce the economic losses to sericulture caused by the misuse of biological pesticides. RESULTS Through transcriptome sequencing, we identified a miRNA, miR-31-5p, and demonstrated that it can inhibit apoptosis in silkworm cells and promote the proliferation of BmNPV in BmE-SWU1 cells. We identified a target gene of miR-31-5p, B. mori cytochrome P450 9e2 (BmCYP9e2), and demonstrated that it can promote apoptosis in silkworm cells and inhibit the proliferation of BmNPV. Moreover, we constructed transgenic silkworm strains with miR-31-5p knockout and confirmed that they can inhibit the proliferation of BmNPV. CONCLUSION These data indicate that miR-31-5p may exert functions of inhibiting apoptosis and promoting virus proliferation by regulating BmCYP9e2. The findings demonstrate how miRNAs influence host cell apoptosis and how they are involved in the host immune system response to viruses, providing important insights into the applications of biological insecticides for pest control. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Wen-Yu Yang
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei, China
| | - Zhen-Ye Liu
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei, China
| | - Yan Zhu
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei, China
| | - Yu Xiao
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei, China
| | - Wen-Fu Xiao
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong, China
| | - Liang Tang
- Sericulture Technology Promotion Station of Guangxi, Nanning, China
| | - Zhan-Qi Dong
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei, China
| | - Min-Hui Pan
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei, China
| | - Cheng Lu
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei, China
| | - Peng Chen
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei, China
| |
Collapse
|
2
|
Guan X, Pavani KC, Chunduru J, Broeckx BJG, Van Soom A, Peelman L. Hsa-miR-665 Is a Promising Biomarker in Cancer Prognosis. Cancers (Basel) 2023; 15:4915. [PMID: 37894282 PMCID: PMC10605552 DOI: 10.3390/cancers15204915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Biomarkers are biomolecules used to identify or predict the presence of a specific disease or condition. They play an important role in early diagnosis and may be crucial for treatment. MicroRNAs (miRNAs), a group of small non-coding RNAs, are more and more regarded as promising biomarkers for several reasons. Dysregulation of miRNAs has been linked with development of several diseases, including many different types of cancer, and abnormal levels can be present in early stages of tumor development. Because miRNAs are stable molecules secreted and freely circulating in blood and urine, they can be sampled with little or no invasion. Here, we present an overview of the current literature, focusing on the types of cancers for which dysregulation of miR-665 has been associated with disease progression, recurrence, and/or prognosis. It needs to be emphasized that the role of miR-665 sometimes seems ambiguous, in the sense that it can be upregulated in one cancer type and downregulated in another and can even change during the progression of the same cancer. Caution is thus needed before using miR-665 as a biomarker, and extrapolation between different cancer types is not advisable. Moreover, more detailed understanding of the different roles of miR-665 will help in determining its potential as a diagnostic and prognostic biomarker.
Collapse
Affiliation(s)
- Xuefeng Guan
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium; (X.G.); (B.J.G.B.)
| | - Krishna Chaitanya Pavani
- Department of Internal Medicine, Reproduction and Population Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (K.C.P.); (A.V.S.)
- Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Gent, Belgium
| | - Jayendra Chunduru
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Bart J. G. Broeckx
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium; (X.G.); (B.J.G.B.)
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (K.C.P.); (A.V.S.)
| | - Luc Peelman
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium; (X.G.); (B.J.G.B.)
| |
Collapse
|
3
|
Fajardo D, Saint Jean R, Lyons PJ. Acquisition of new function through gene duplication in the metallocarboxypeptidase family. Sci Rep 2023; 13:2512. [PMID: 36781897 PMCID: PMC9925722 DOI: 10.1038/s41598-023-29800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Gene duplication is a key first step in the process of expanding the functionality of a multigene family. In order to better understand the process of gene duplication and its role in the formation of new enzymes, we investigated recent duplication events in the M14 family of proteolytic enzymes. Within vertebrates, four of 23 M14 genes were frequently found in duplicate form. While AEBP1, CPXM1, and CPZ genes were duplicated once through a large-scale, likely whole-genome duplication event, the CPO gene underwent many duplication events within fish and Xenopus lineages. Bioinformatic analyses of enzyme specificity and conservation suggested a greater amount of neofunctionalization and purifying selection in CPO paralogs compared with other CPA/B enzymes. To examine the functional consequences of evolutionary changes on CPO paralogs, the four CPO paralogs from Xenopus tropicalis were expressed in Sf9 and HEK293T cells. Immunocytochemistry showed subcellular distribution of Xenopus CPO paralogs to be similar to that of human CPO. Upon activation with trypsin, the enzymes demonstrated differential activity against three substrates, suggesting an acquisition of new function following duplication and subsequent mutagenesis. Characteristics such as gene size and enzyme activation mechanisms are possible contributors to the evolutionary capacity of the CPO gene.
Collapse
Affiliation(s)
- Daniel Fajardo
- Department of Biology, Andrews University, Berrien Springs, MI, 49104, USA
| | - Ritchie Saint Jean
- Department of Biology, Andrews University, Berrien Springs, MI, 49104, USA
| | - Peter J Lyons
- Department of Biology, Andrews University, Berrien Springs, MI, 49104, USA.
| |
Collapse
|
4
|
Yang K, Niu Y, Cui Z, Jin L, Peng S, Dong Z. Long noncoding RNA TFAP2A-AS1 promotes oral squamous cell carcinoma cell growth and movement via competitively binding miR-1297 and regulating TFAP2A expression. Mol Carcinog 2022; 61:865-875. [PMID: 35730908 DOI: 10.1002/mc.23438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/23/2022] [Accepted: 06/02/2022] [Indexed: 01/17/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is an aggressive and common malignancy in the head and neck, characterized by poor prognosis and high incidence. This study aimed to investigate the role of long noncoding RNA TFAP2A-AS1 in OSCC. The competing endogenous RNA network of TFAP2A-AS1 was constructed by bioinformatics analysis. The expressions of miR-1297, TFAP2A-AS1, and TFAP2A were measured by quantitative reverse transcription-polymerase chain reaction. The correlations of TFAP2A-AS1, miR-1297, and TFAP2A with clinicopathological characteristics of OSCC were assessed. RNA immunoprecipitation and dual-luciferase reporter assay were used to identify the target of miR-1297. Cell proliferation was measured by colony formation assay and [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay. Transwell assay and wound healing assay were performed to assess cell movement. TFAP2A-AS1 and TFAP2A were upregulated in OSCC and their expression levels were positively correlated. The levels of TFAP2A-AS1, miR-1297, and TFAP2A were also associated with lymphatic metastasis and the tumor-node-metastasis (TNM) stage of OSCC patients. TFAP2A-AS1 acted as a miR-1297 sponge. OSCC cell growth and movement were inhibited by miR-1297. Changes in the miR-1297 expression abolished the effects of TFAP2A-AS1 on OSCC cells. Additionally, TFAP2A was a target of miR-1297. TFAP2A promoted OSCC cell growth and migration/invasion, indicating that TFAP2A mediated the effects of TFAP2A-AS1 and miR-1297. TFAP2A-AS1 exerts an oncogenic effect in OSCC via the TFAP2A-AS1/miR-1297/TFAP2A axis, which may provide new targets and strategies for OSCC treatments.
Collapse
Affiliation(s)
- Kaicheng Yang
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Yunfeng Niu
- Department of Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Zifeng Cui
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Linyu Jin
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Shixiong Peng
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Zhiming Dong
- Department of Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| |
Collapse
|
5
|
Sabaie H, Gharesouran J, Asadi MR, Farhang S, Ahangar NK, Brand S, Arsang-Jang S, Dastar S, Taheri M, Rezazadeh M. Downregulation of miR-185 is a common pathogenic event in 22q11.2 deletion syndrome-related and idiopathic schizophrenia. Metab Brain Dis 2022; 37:1175-1184. [PMID: 35075501 DOI: 10.1007/s11011-022-00918-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/20/2022] [Indexed: 10/19/2022]
Abstract
Schizophrenia (SCZ) is known as a complicated mental disease with an unknown etiology. The microdeletion of 22q11.2 is the most potent genetic risk factor. Researchers are still trying to find which genes in the deletion region are linked to SCZ. MIR185, encoding microRNA (miR)-185, is present in the minimal 1.5 megabase deletion. Nonetheless, the miR-185 expression profile and its corresponding target genes in animal models and patients with 22q11.2 deletion syndrome (22q11.2DS) imply that more study is required about miR-185 and its corresponding downstream pathways within idiopathic SCZ. The expression of hsa-miR-185-5p and its corresponding target gene, shisa family member 7 (SHISA7), sometimes called CKAMP59, were evaluated in the peripheral blood (PB) samples of Iranian Azeri patients with idiopathic SCZ and healthy subjects, matched by gender and age as control groups by quantitative polymerase chain reaction (qPCR). Fifty SCZ patients (male/female: 22/28, age (mean ± standard deviation (SD)): 35.9 ± 5.6) and 50 matched healthy controls (male/female: 23/27, age (mean ± SD): 34.7 ± 5.4) were enrolled. The expression of hsa-miR-185-5p in the PB samples from subjects with idiopathic SCZ was substantially lower than in that of control groups (posterior beta = -0.985, adjusted P-value < 0.0001). There was also a difference within the expression profile between female and male subgroups (posterior beta = -0.86, adjusted P-value = 0.046 and posterior beta = -1.015, adjusted P-value = 0.004, in turn). Nevertheless, no significant difference was present in the expression level of CKAMP59 between PB samples from patients and control groups (adjusted P-value > 0.999). The analysis of the receiver operating characteristic (ROC) curve suggested that hsa-miR-185-5p may correctly distinguish subjects with idiopathic SCZ from healthy people (the area under curve (AUC) value: 0.722). Furthermore, there was a strong positive correlation between the expression pattern of the abovementioned genes in patients with SCZ and healthy subjects (r = 0.870, P < 0.001 and r = 0.812, P < 0.001, respectively), indicating that this miR works as an enhancer. More research is needed to determine if the hsa-miR-185-5p has an enhancer activity. In summary, this is the first research to highlight the expression of the miR-185 and CKAMP59 genes in the PB from subjects with idiopathic SCZ. Our findings suggest that gene expression alterations mediated by miR-185 may play a role in the pathogenesis of idiopathic and 22q11.2DS SCZ. It is worth noting that, despite a substantial and clear relationship between CKAMP59 and hsa-miR-185-5p, indicating an interactive network, their involvement in the development of SCZ should be reconsidered based on the whole blood sample since the changed expression level of CKAMP59 was not significant. Further research with greater sample sizes and particular leukocyte subsets can greatly make these results stronger.
Collapse
Affiliation(s)
- Hani Sabaie
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Gharesouran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Asadi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sara Farhang
- Research Center of Psychiatry and Behavioral Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Rob Giel Research Center, University Medical Center Groningen, University Center for Psychiatry, University of Groningen, Groningen, Netherlands
| | - Noora Karim Ahangar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Serge Brand
- Psychiatric Clinics, Center for Affective, Stress and Sleep Disorders, University of Basel, Basel, Switzerland
| | - Shahram Arsang-Jang
- Cancer Gene Therapy Research Center, Zanjan University of Medical Science, Zanjan, Iran
| | - Saba Dastar
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Fatih, Istanbul, Turkey
| | - Mohammad Taheri
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
6
|
Najari-Hanjani P, Farazmandfar T, Golalipour M. PER3P1 pseudogene modulates PER3 oscillation: a new player in the molecular clock network. BIOL RHYTHM RES 2022. [DOI: 10.1080/09291016.2022.2050978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Parisa Najari-Hanjani
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
| | - Touraj Farazmandfar
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
| | - Masoud Golalipour
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
| |
Collapse
|
7
|
Zhang M, Xiong F, Zhang S, Guo W, He Y. Crucial Roles of miR-625 in Human Cancer. Front Med (Lausanne) 2022; 9:845094. [PMID: 35308517 PMCID: PMC8931282 DOI: 10.3389/fmed.2022.845094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/09/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic and epigenetic characteristics are core factors of cancer. MicroRNAs (miRNAs) are small non-coding RNAs which regulate gene expression at the post-transcriptional level via binding to corresponding mRNAs. Recently, increasing evidence has proven that miRNAs regulate the occurrence and development of human cancer. Here, we mainly review the abnormal expression of miR-625 in a variety of cancers. In summarizing the role and potential molecular mechanisms of miR-625 in various tumors in detail, we reveal that miR-625 is involved in a variety of biological processes, such as cell proliferation, invasion, migration, apoptosis, cell cycle regulation, and drug resistance. In addition, we discuss the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks and briefly explain the specific mechanisms of competing endogenous RNAs. In conclusion, we reveal the potential value of miR-625 in cancer diagnosis, treatment, and prognosis and hope to provide new ideas for the clinical application of miR-625.
Collapse
Affiliation(s)
- Menggang Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Fei Xiong
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| |
Collapse
|
8
|
Sabaie H, Talebi M, Gharesouarn J, Asadi MR, Jalaiei A, Arsang-Jang S, Hussen BM, Taheri M, Jalili Khoshnoud R, Rezazadeh M. Identification and Analysis of BCAS4/hsa-miR-185-5p/SHISA7 Competing Endogenous RNA Axis in Late-Onset Alzheimer’s Disease Using Bioinformatic and Experimental Approaches. Front Aging Neurosci 2022; 14:812169. [PMID: 35264942 PMCID: PMC8899724 DOI: 10.3389/fnagi.2022.812169] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/18/2022] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease (AD) is a heterogeneous degenerative brain disorder with a rising prevalence worldwide. SHISA7 (CKAMP59) has emerged as one of the most intriguing new members of the SHISA family, in that, unlike other CKAMP counterparts, it exhibits a direct function in inhibitory synaptic GABAAR regulation. We used bioinformatics and experimental methods in this research to explore competing endogenous RNA (ceRNA) regulation of BCAS4 and SHISA7 in tau pathogenesis and their capacity as peripheral biomarkers linked to an abnormal inflammatory response in AD. The Gene Expression Omnibus database included two microarray datasets, including information on mRNAs (GSE106241) and miRNAs (GSE157239) from individuals with AD with different degrees of AD-associated neurofibrillary pathology in the temporal cortex (TC) tissue specimens and corresponding controls were downloaded from the Gene Expression Omnibus database. The limma package in the R software was used to identify differently expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) associated with AD-related neurofibrillary pathology. Additionally, we used the quantitative polymerase chain reaction technique to examine the expression of the BCAS4/hsa-miR-185-5p/SHISA7 ceRNA axis in the peripheral blood (PB) of fifty AD patients and fifty control subjects. BCAS4 was shown to act as a ceRNA to control the SHISA7 expression throughout AD-associated neurofibrillary pathology in TC tissue specimens by sponging hsa-miR-185-5p, based on our bioinformatics study. Furthermore, in PB specimens from individuals suffering from AD and normal controls, we found no substantial differences in BCAS4 expression patterns. SHISA7 expression in AD patients’ PB was found to be reduced, as was the case in the TC. On the other hand, we discovered reduced amounts of hsa-miR-185-5p in AD patients’ PB samples compared to control subjects, unlike in TC tissue, where it had been demonstrated to be overexpressed. BCAS4 and SHISA7 expression levels showed a strong positive correlation, suggesting the presence of an interconnected network, most likely as a result of ceRNA regulation among PB specimens. The present study is the first evidence to highlight the expression of the BCAS4/miR-185-5p/SHISA7 ceRNA axis in the brain and PB of AD patients, and offers a new viewpoint on molecular processes underlying AD pathogenic mechanisms.
Collapse
Affiliation(s)
- Hani Sabaie
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahnaz Talebi
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Gharesouarn
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Asadi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Jalaiei
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahram Arsang-Jang
- Cancer Gene Therapy Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- *Correspondence: Mohammad Taheri,
| | - Reza Jalili Khoshnoud
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Functional Neurosurgery Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Reza Jalili Khoshnoud,
| | - Maryam Rezazadeh
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Maryam Rezazadeh,
| |
Collapse
|
9
|
Sun M, Wang Y, Zheng C, Wei Y, Hou J, Zhang P, He W, Lv X, Ding Y, Liang H, Hon CC, Chen X, Xu H, Chen Y. Systematic functional interrogation of human pseudogenes using CRISPRi. Genome Biol 2021; 22:240. [PMID: 34425866 PMCID: PMC8381491 DOI: 10.1186/s13059-021-02464-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert important functions. However, to what extent human pseudogenes are functionally relevant remains unclear. There has been no large-scale characterization of pseudogene function because of technical challenges, including high sequence similarity between pseudogene and parent genes, and poor annotation of transcription start sites. RESULTS To overcome these technical obstacles, we develop an integrated computational pipeline to design the first genome-wide library of CRISPR interference (CRISPRi) single-guide RNAs (sgRNAs) that target human pseudogene promoter-proximal regions. We perform the first pseudogene-focused CRISPRi screen in luminal A breast cancer cells and reveal approximately 70 pseudogenes that affect breast cancer cell fitness. Among the top hits, we identify a cancer-testis unitary pseudogene, MGAT4EP, that is predominantly localized in the nucleus and interacts with FOXA1, a key regulator in luminal A breast cancer. By enhancing the promoter binding of FOXA1, MGAT4EP upregulates the expression of oncogenic transcription factor FOXM1. Integrative analyses of multi-omic data from the Cancer Genome Atlas (TCGA) reveal many unitary pseudogenes whose expressions are significantly dysregulated and/or associated with overall/relapse-free survival of patients in diverse cancer types. CONCLUSIONS Our study represents the first large-scale study characterizing pseudogene function. Our findings suggest the importance of nuclear function of unitary pseudogenes and underscore their underappreciated roles in human diseases. The functional genomic resources developed here will greatly facilitate the study of human pseudogene function.
Collapse
Affiliation(s)
- Ming Sun
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Present affiliation: Department of Oncology Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Baita west road #16, Suzhou, 215001, China
| | - Yunfei Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Present affiliation: Clinical Science Lab, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Caishang Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jiakai Hou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Present affiliation: Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Present affiliation: Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Genetics and Epigenetics Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Xiangdong Lv
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yao Ding
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chung-Chau Hon
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Han Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Genetics and Epigenetics Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
| |
Collapse
|
10
|
Garewal N, Goyal N, Pathania S, Kaur J, Singh K. Gauging the trends of pseudogenes in plants. Crit Rev Biotechnol 2021; 41:1114-1129. [PMID: 33993808 DOI: 10.1080/07388551.2021.1901648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pseudogenes, the debilitated parts of ancient genes, were previously scrapped off as junk or discarded genes with no functional significance. Pseudogenes have come under scrutiny for their functionality, since recent studies have unveiled their importance in the regulation of their corresponding parent genes and various biological mechanisms. Despite the enormous occurrence of pseudogenes in plants, the lack of experimental validation has contributed toward their unresolved roles in gene regulation. Contrarily, most of the studies associated with gene regulation have been mainly reported for humans, mice, and other mammalian genomes. Consequently, in order to present a cumulative report on plant-based pseudogenes research, an attempt has been made to assemble multiple studies presenting the pseudogene classification, the prediction and the determination of comparative accuracies of various computational pipelines, and recent trends in analyzing their biological functions, and regulatory mechanisms. This review represents the classical, as well as the recent advances on pseudogene identification and their potential roles in transcriptional regulation, which could possibly invigorate the quality of genome annotation, evolutionary analysis, and complexity surrounding the regulatory pathways in plants. Thus, when the ambiguous boundary girdling the pseudogenes eventually recedes on account of their explicit orchestration role, research in flora would no longer saunter compared to that on fauna.
Collapse
Affiliation(s)
- Naina Garewal
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Neetu Goyal
- Department of Biotechnology, Panjab University, Chandigarh, India
| | | | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
| |
Collapse
|
11
|
Lee HE, Park SJ, Huh JW, Imai H, Kim HS. Enhancer Function of MicroRNA-3681 Derived from Long Terminal Repeats Represses the Activity of Variable Number Tandem Repeats in the 3' UTR of SHISA7. Mol Cells 2020; 43:607-618. [PMID: 32655015 PMCID: PMC7398795 DOI: 10.14348/molcells.2020.0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 01/03/2023] Open
Abstract
microRNAs (miRNAs) are non-coding RNA molecules involved in the regulation of gene expression. miRNAs inhibit gene expression by binding to the 3' untranslated region (UTR) of their target gene. miRNAs can originate from transposable elements (TEs), which comprise approximately half of the eukaryotic genome and one type of TE, called the long terminal repeat (LTR) is found in class of retrotransposons. Amongst the miRNAs derived from LTR, hsa-miR-3681 was chosen and analyzed using bioinformatics tools and experimental analysis. Studies on hsa-miR-3681 have been scarce and this study provides the relative expression analysis of hsa-miR-3681-5p from humans, chimpanzees, crab-eating monkeys, and mice. Luciferase assay for hsa-miR-3681-5p and its target gene SHISA7 supports our hypothesis that the number of miRNA binding sites affects target gene expression. Especially, the variable number tandem repeat (VNTR) and hsa-miR-3681-5p share the binding sites in the 3' UTR of SHISA7, which leads the enhancer function of hsa-miR-3681-5p to inhibit the activity of VNTR. In conclusion, hsa-miR-3681-5p acts as a super-enhancer and the enhancer function of hsa-miR-3681-5p acts as a repressor of VNTR activity in the 3' UTR of SHISA7.
Collapse
Affiliation(s)
- Hee-Eun Lee
- Department of Integrated Biological Science, Pusan National University, Busan 4624, Korea
- Institute of Systems Biology, Pusan National University, Busan 4641, Korea
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon 3113, Korea
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama 484-806, Japan
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 4641, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 4241, Korea
| |
Collapse
|
12
|
Transcriptional activity and strain-specific history of mouse pseudogenes. Nat Commun 2020; 11:3695. [PMID: 32728065 PMCID: PMC7392758 DOI: 10.1038/s41467-020-17157-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 06/08/2020] [Indexed: 01/07/2023] Open
Abstract
Pseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional data. Here, combining both manual curation and automatic pipelines, we present a genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains (available via the mouse.pseudogene.org resource). We also annotate 165 unitary pseudogenes in mouse, and 303, in human. The overall pseudogene repertoire in mouse is similar to that in human in terms of size, biotype distribution, and family composition (e.g. with GAPDH and ribosomal proteins being the largest families). Notable differences arise in the pseudogene age distribution, with multiple retro-transpositional bursts in mouse evolutionary history and only one in human. Furthermore, in each strain about a fifth of all pseudogenes are unique, reflecting strain-specific evolution. Finally, we find that ~15% of the mouse pseudogenes are transcribed, and that highly transcribed parent genes tend to give rise to many processed pseudogenes.
Collapse
|
13
|
Chen X, Wan L, Wang W, Xi WJ, Yang AG, Wang T. Re-recognition of pseudogenes: From molecular to clinical applications. Theranostics 2020; 10:1479-1499. [PMID: 32042317 PMCID: PMC6993246 DOI: 10.7150/thno.40659] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Pseudogenes were initially regarded as "nonfunctional" genomic elements that did not have protein-coding abilities due to several endogenous inactivating mutations. Although pseudogenes are widely expressed in prokaryotes and eukaryotes, for decades, they have been largely ignored and classified as gene "junk" or "relics". With the widespread availability of high-throughput sequencing analysis, especially omics technologies, knowledge concerning pseudogenes has substantially increased. Pseudogenes are evolutionarily conserved and derive primarily from a mutation or retrotransposon, conferring the pseudogene with a "gene repository" role to store and expand genetic information. In contrast to previous notions, pseudogenes have a variety of functions at the DNA, RNA and protein levels for broadly participating in gene regulation to influence the development and progression of certain diseases, especially cancer. Indeed, some pseudogenes have been proven to encode proteins, strongly contradicting their "trash" identification, and have been confirmed to have tissue-specific and disease subtype-specific expression, indicating their own value in disease diagnosis. Moreover, pseudogenes have been correlated with the life expectancy of patients and exhibit great potential for future use in disease treatment, suggesting that they are promising biomarkers and therapeutic targets for clinical applications. In this review, we summarize the natural properties, functions, disease involvement and clinical value of pseudogenes. Although our knowledge of pseudogenes remains nascent, this field deserves more attention and deeper exploration.
Collapse
|
14
|
Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet 2019; 21:102-117. [DOI: 10.1038/s41576-019-0184-5] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/14/2022]
|
15
|
Zhang P, Wu W, Chen Q, Chen M. Non-Coding RNAs and their Integrated Networks. J Integr Bioinform 2019; 16:/j/jib.2019.16.issue-3/jib-2019-0027/jib-2019-0027.xml. [PMID: 31301674 PMCID: PMC6798851 DOI: 10.1515/jib-2019-0027] [Citation(s) in RCA: 351] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/02/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs' essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.
Collapse
Affiliation(s)
- Peijing Zhang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenyi Wu
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
16
|
Wang X, Wan J, Xu Z, Jiang S, Ji L, Liu Y, Zhai S, Cui R. Identification of competitive endogenous RNAs network in breast cancer. Cancer Med 2019; 8:2392-2403. [PMID: 30932362 PMCID: PMC6536941 DOI: 10.1002/cam4.2099] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 02/08/2019] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND MiRNAs can regulate gene expression directly or indirectly, and long noncoding RNAs as competing endogenous RNA (ceRNAs) can bind to miRNAs competitively and affect mRNA expression. The ceRNA network is still unclear in breast cancer. In this study, a ceRNA network was constructed, and new treatment and prognosis targets and biomarkers for breast cancer were explored. METHODS A total of 1 096 cancer tissues and 112 adjacent normal tissues to cancer from the TCGA database were used to screen out significant differentially expressed mRNAs (DEMs), lncRNAs (DELs), and miRNAs (DEMis) to construct a ceRNA network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to predict potential functions. Survival analysis was performed to predict which functions were significant for prognosis. RESULTS From the analysis, 2 139 DEMs, 1 059 DELs, and 84 DEMis were obtained. Targeting predictions for DEMis-DELs and DEMis-DEMs can yield 26 DEMs, 90 DELs, and 18 DEMis. We performed GO enrichment analysis, and the results showed that the upregulated DEMs were involved in nucleosomes, extracellular regions, and nucleosome assembly, while the downregulated DEMs were mainly involved in Z disk, muscle contraction, and structural constituents of muscle. KEGG pathway analysis was performed on all DEMs, and the pathways were enriched in retinol metabolism, steroid hormone biosynthesis, and tyrosine metabolism. Through survival analysis of the ceRNA network, we identified four DEMs, two DELs, and two DEMis that were significant for poor prognosis. CONCLUSIONS This study suggested that constructing a ceRNA network and performing survival analysis on the network could screen out new significant treatment and prognosis targets and biomarkers.
Collapse
Affiliation(s)
- Xiaojin Wang
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Jiahui Wan
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Zhanxiang Xu
- Department of Cardiovascular MedicineHongqi Hospital Affiliated to Mudanjiang Medical UniversityMudanjiangChina
| | - Shijun Jiang
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Lin Ji
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Yutian Liu
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Shuwen Zhai
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Rongjun Cui
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| |
Collapse
|
17
|
Ma G, Liu H, Du M, Zhang G, Lin Y, Ge Y, Wang M, Jin G, Zhao Q, Chu H, Gong W, Zhang Z. A genetic variation in the CpG island of pseudogene GBAP1 promoter is associated with gastric cancer susceptibility. Cancer 2019; 125:2465-2473. [PMID: 30951202 DOI: 10.1002/cncr.32081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 01/31/2023]
Abstract
BACKGROUND Previous genome-wide association studies (GWASs) have identified that several single nucleotide polymorphisms (SNPs) are implicated in gastric cancer (GC) risk. However, the multiple statistical comparisons of GWASs may reject some true biological positives with subthreshold P values. METHODS This study annotated the genomic locations of all CpG islands in the genome using the Encyclopedia of DNA Elements (ENCODE). The SNPs in the regions were then genotyped using the Illumina 660W Quad chip. The effects of the prominent variations on GC risk were further confirmed in the other independent cohorts. RESULTS SNP rs2990245, which is located in the promoter of pseudogene GBAP1, was associated with GC risk using GWASs data. An additional cohort of 1275 GC patients and 1424 controls validated that individuals with the CC genotype had a 62% decreased risk of GC compared with those who carried the TT genotype (P = 2.01E-04) in the codominant model. The significant association was observed in the additive, dominant, and recessive models. A meta-analysis combining the results from the GWASs and replication studies revealed that rs2990245 was significantly associated with decreased GC risk (P = 5.59E-12). Importantly, rs2990245 can regulate the expression of GBAP1 by influencing the methylation status of the GBAP1 promoter. GBAP1 can act as a competing endogenous RNA by binding competitively with micro-RNA-212-3p and then promoting GBA expression. CONCLUSION rs2990245 is significantly associated with a decreased risk of GC. Pseudogene GBAP1 contributes to the development and progression of GC by sequestering the miR-212-3p from binding to GBA.
Collapse
Affiliation(s)
- Gaoxiang Ma
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hanting Liu
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Gang Zhang
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yadi Lin
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuqiu Ge
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qinghong Zhao
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haiyan Chu
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Weida Gong
- Department of General Surgery, Yixing Cancer Hospital, Yixing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Center for Global Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| |
Collapse
|
18
|
Glenfield C, McLysaght A. Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis. Mol Biol Evol 2018; 35:2886-2899. [PMID: 30252115 PMCID: PMC6278865 DOI: 10.1093/molbev/msy183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The competitive endogenous RNA (ceRNA) hypothesis is an attractively simple model to explain the biological role of many putatively functionless noncoding RNAs. Under this model, there exist transcripts in the cell whose role is to titrate out microRNAs such that the expression level of another target sequence is altered. That it is logistically possible for expression of one microRNA recognition element (MRE)-containing transcript to affect another is seen in the multiple examples of pathogenic effects of inappropriate expression of MRE-containing RNAs. However, the role, if any, of ceRNAs in normal biological processes and at physiological levels is disputed. By comparison of parent genes and pseudogenes we show, both for a specific example and genome-wide, that the pseudo-3' untranslated regions (3'UTRs) of expressed pseudogenes are frequently retained and are under selective constraint in mammalian genomes. We found that the pseudo-3'UTR of BRAFP1, a previously described oncogenic ceRNA, has reduced substitutions relative to its pseudo-coding sequence, and we show sequence constraint on MREs shared between the parent gene, BRAF, and the pseudogene. Investigation of RNA-seq data reveals expression of BRAFP1 in normal somatic tissues in human and in other primates, consistent with biological ceRNA functionality of this pseudogene in nonpathogenic cellular contexts. Furthermore, we find that on a genome-wide scale pseudo-3'UTRs of mammalian pseudogenes (n = 1,629) are under stronger selective constraint than their pseudo-coding sequence counterparts, and are more often retained and expressed. Our results suggest that many human pseudogenes, often considered nonfunctional, may have an evolutionarily constrained role, consistent with the ceRNA hypothesis.
Collapse
Affiliation(s)
- Cian Glenfield
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
19
|
Zhao H, Gao Z, Wang L, Wang J, Wang S, Fei B, Chen C, Shi C, Liu X, Zhang H, Lou Y, Chen L, Sun H, Zhou X, Wang S, Zhang C, Xu H, Li L, Yang Y, Wei Y, Yang W, Gao Q, Yang H, Zhao S, Jiang Z. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis). Gigascience 2018; 7:5092772. [PMID: 30202850 PMCID: PMC6204424 DOI: 10.1093/gigascience/giy115] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022] Open
Abstract
Background Bamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies. Results Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo. Conclusions These fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.
Collapse
Affiliation(s)
- Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Zhimin Gao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Le Wang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China.,Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Jiongliang Wang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Songbo Wang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, No. 7 PengFei Rd, Dapeng District, Shenzhen 518120, China
| | - Benhua Fei
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Chengcheng Shi
- BGI-Qingdao, No. 2877, Tuanjie Rd, Sino-German Ecopark, Qingdao, Shandong Province, 266555, China
| | - Xiaochuan Liu
- BGI-Qingdao, No. 2877, Tuanjie Rd, Sino-German Ecopark, Qingdao, Shandong Province, 266555, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Yongfeng Lou
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - LianFu Chen
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Huayu Sun
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Xianqiang Zhou
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Sining Wang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Hao Xu
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Lichao Li
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Yihong Yang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Yanli Wei
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Wei Yang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Huanming Yang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, No. 7 PengFei Rd, Dapeng District, Shenzhen 518120, China
| | - Zehui Jiang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| |
Collapse
|
20
|
Liu F, Gong R, He B, Chen F, Hu Z. TUSC2P suppresses the tumor function of esophageal squamous cell carcinoma by regulating TUSC2 expression and correlates with disease prognosis. BMC Cancer 2018; 18:894. [PMID: 30219035 PMCID: PMC6139140 DOI: 10.1186/s12885-018-4804-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
Background Pseudogenes are RNA transcripts with high homology with its parent protein-coding genes. Although pseudogenes lost the ability to produce protein, it still exert import biological function, and play important role in the pathogenesis of a wide varity of tumors; However, the role of pseudogenes in esophageal squamous cell carcinoma (ESCC) is poorly understood. Methods TUSC2P function in ESCC were explored using both in vitro and in vivo experiments cell proliferation, invasion and apoptosis assay was performed to evaluated the effect of TUSC2P on the tumor biology of ESCC. Expression of relative genes was assessed by quantitative real-time PCR (qRT-PCR) and western blotting in EC109 and TE-1 cell, as well as ESCC patients. 3’UTR luciferase assay was used to confirm the direct binding of miRNAs with TUSC2 and TUSC2P 3’UTR. Relation betweenTUSC2P, TUSC2 and ESCC prognosis was predicted by survival analysis (n = 56). Results Pseudogene TUSC2P was down regulated in ESCC tissues compared with paired normal adjacent tissues, and the expression of TUSC2P was significantly correlated with survivalof ESCC patients. Over expression of TUSC2P in EC109 and TE-1 cells resulted in altered expression of TUSC2, thus inhibited proliferation, invasion and promoted apoptosis. Dual luciferase assay demonstrated that TUSC2P 3’UTR decoyed miR-17-5p, miR-520a-3p, miR-608, miR-661 from binding to TUSC2. Conclusions TUSC2P can suppresses the tumor function of esophageal squamous cell carcinoma by regulating TUSC2 expression and may also serve as a prognostic factor for ESCC patients. Electronic supplementary material The online version of this article (10.1186/s12885-018-4804-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Fengqiong Liu
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China.,Department of Epidemiology and Health Statistic, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China
| | - Ruijie Gong
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China
| | - Baochang He
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China.,Department of Epidemiology and Health Statistic, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China
| | - Fa Chen
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China.,Department of Epidemiology and Health Statistic, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China
| | - Zhijian Hu
- Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, 350108, People's Republic of China. .,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China. .,Department of Epidemiology and Health Statistic, School of Public Health, Fujian Medical University, 1 Xuefubei Road, Fuzhou, Fujian, China.
| |
Collapse
|
21
|
Smillie CL, Sirey T, Ponting CP. Complexities of post-transcriptional regulation and the modeling of ceRNA crosstalk. Crit Rev Biochem Mol Biol 2018; 53:231-245. [PMID: 29569941 PMCID: PMC5935048 DOI: 10.1080/10409238.2018.1447542] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 01/09/2023]
Abstract
Control of gene and protein expression is required for cellular homeostasis and is disrupted in disease. Following transcription, mRNA turnover and translation is modulated, most notably by microRNAs (miRNAs). This modulation is controlled by transcriptional and post-transcriptional events that alter the availability of miRNAs for target binding. Recent studies have proposed that some transcripts - termed competitive endogenous RNAs (ceRNAs) - sequester a miRNA and diminish its repressive effects on other transcripts. Such ceRNAs thus mutually alter each other's abundance by competing for binding to a common set of miRNAs. Some question the relevance of ceRNA crosstalk, arguing that an individual transcript, when its abundance lies within a physiological range of gene expression, will fail to compete for miRNA binding due to the high abundance of other miRNA binding sites across the transcriptome. Despite this, some experimental evidence is consistent with the ceRNA hypothesis. In this review, we draw upon existing data to highlight mechanistic and theoretical aspects of ceRNA crosstalk. Our intent is to propose how understanding of ceRNA crosstalk mechanisms can be improved and what evidence is required to demonstrate a ceRNA mechanism. A greater understanding of factors affecting ceRNA crosstalk should shed light on its relevance in physiological states.
Collapse
Affiliation(s)
- Claire L. Smillie
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tamara Sirey
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Chris P. Ponting
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
22
|
Yamamura S, Imai-Sumida M, Tanaka Y, Dahiya R. Interaction and cross-talk between non-coding RNAs. Cell Mol Life Sci 2018; 75:467-484. [PMID: 28840253 PMCID: PMC5765200 DOI: 10.1007/s00018-017-2626-6] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023]
Abstract
Non-coding RNA (ncRNA) has been shown to regulate diverse cellular processes and functions through controlling gene expression. Long non-coding RNAs (lncRNAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites. Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation. These interactions form complicated and intertwined networks. Certain lncRNAs encode miRNAs and small nucleolar RNAs (snoRNAs), and may regulate expression of these small RNAs as precursors. SnoRNAs have also been reported to be precursors for PIWI-interacting RNAs (piRNAs) and thus may regulate the piRNAs as a precursor. These miRNAs and piRNAs target messenger RNAs (mRNAs) and regulate gene expression. In this review, we will present and discuss these interactions, cross-talk, and co-regulation of ncRNAs and gene regulation due to these interactions.
Collapse
Affiliation(s)
- Soichiro Yamamura
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA.
| | - Mitsuho Imai-Sumida
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Yuichiro Tanaka
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Rajvir Dahiya
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| |
Collapse
|
23
|
De Martino M, Forzati F, Arra C, Fusco A, Esposito F. HMGA1-pseudogenes and cancer. Oncotarget 2017; 7:28724-35. [PMID: 26895108 PMCID: PMC5053758 DOI: 10.18632/oncotarget.7427] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/05/2016] [Indexed: 12/25/2022] Open
Abstract
Pseudogenes are DNA sequences with high homology to the corresponding functional gene, but, because of the accumulation of various mutations, they have lost their initial functions to code for proteins. Consequently, pseudogenes have been considered until few years ago dysfunctional relatives of the corresponding ancestral genes, and then useless in the course of genome evolution. However, several studies have recently established that pseudogenes are owners of key biological functions. Indeed, some pseudogenes control the expression of functional genes by competitively binding to the miRNAs, some of them generate small interference RNAs to negatively modulate the expression of functional genes, and some of them even encode functional mutated proteins. Here, we concentrate our attention on the pseudogenes of the HMGA1 gene, that codes for the HMGA1a and HMGA1b proteins having a critical role in development and cancer progression. In this review, we analyze the family of HMGA1 pseudogenes through three aspects: classification, characterization, and their possible function and involvement in cancer.
Collapse
Affiliation(s)
- Marco De Martino
- 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
| | - Floriana Forzati
- 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
| | - Claudio Arra
- Istituto Nazionale dei Tumori, Fondazione Pascale, Naples, Italy
| | - Alfredo Fusco
- 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
| | - Francesco Esposito
- 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
| |
Collapse
|
24
|
Hezroni H, Ben-Tov Perry R, Meir Z, Housman G, Lubelsky Y, Ulitsky I. A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes. Genome Biol 2017; 18:162. [PMID: 28854954 PMCID: PMC5577775 DOI: 10.1186/s13059-017-1293-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/31/2017] [Indexed: 12/04/2022] Open
Abstract
Background Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs. Results We systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality. Conclusions We estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1293-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hadas Hezroni
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Zohar Meir
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Gali Housman
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Yoav Lubelsky
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel.
| |
Collapse
|
25
|
Li LJ, Zhao W, Tao SS, Leng RX, Fan YG, Pan HF, Ye DQ. Competitive endogenous RNA network: potential implication for systemic lupus erythematosus. Expert Opin Ther Targets 2017; 21:639-648. [DOI: 10.1080/14728222.2017.1319938] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
26
|
A Macro View of MicroRNAs: The Discovery of MicroRNAs and Their Role in Hematopoiesis and Hematologic Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 334:99-175. [PMID: 28838543 DOI: 10.1016/bs.ircmb.2017.03.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MicroRNAs (MiRNAs) are a class of endogenously encoded ~22 nucleotide, noncoding, single-stranded RNAs that contribute to development, body planning, stem cell differentiation, and tissue identity through posttranscriptional regulation and degradation of transcripts. Given their importance, it is predictable that dysregulation of MiRNAs, which target a wide variety of transcripts, can result in malignant transformation. In this review, we explore the discovery of MiRNAs, their mechanism of action, and the tools that aid in their discovery and study. Strikingly, many of the studies that have expanded our understanding of the contributions of MiRNAs to normal physiology and in the development of diseases have come from studies in the hematopoietic system and hematologic malignancies, with some of the earliest identified functions for mammalian MiRNAs coming from observations made in leukemias. So, with a special focus on the hematologic system, we will discuss how MiRNAs contribute to differentiation of stem cells and how dysregulation of MiRNAs contributes to the development of malignancy, by providing examples of specific MiRNAs that function as oncogenes or tumor suppressors, as well as of defects in MiRNA processing. Finally, we will discuss the promise of MiRNA-based therapeutics and challenges for the future study of disease-causing MiRNAs.
Collapse
|
27
|
Conte F, Fiscon G, Chiara M, Colombo T, Farina L, Paci P. Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer. PLoS One 2017; 12:e0171661. [PMID: 28187158 PMCID: PMC5302781 DOI: 10.1371/journal.pone.0171661] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/24/2017] [Indexed: 12/14/2022] Open
Abstract
Recent findings have identified competing endogenous RNAs (ceRNAs) as the drivers in many disease conditions, including cancers. The ceRNAs indirectly regulate each other by reducing the amount of microRNAs (miRNAs) available to target messenger RNAs (mRNAs). The ceRNA interactions mediated by miRNAs are modulated by a titration mechanism, i.e. large changes in the ceRNA expression levels either overcome, or relieve, the miRNA repression on competing RNAs; similarly, a very large miRNA overexpression may abolish competition. The ceRNAs are also called miRNA "decoys" or miRNA "sponges" and encompass different RNAs competing with each other to attract miRNAs for interactions: mRNA, long non-coding RNAs (lncRNAs), pseudogenes, or circular RNAs. Recently, we developed a computational method for identifying ceRNA-ceRNA interactions in breast invasive carcinoma. We were interested in unveiling which lncRNAs could exert the ceRNA activity. We found a drastic rewiring in the cross-talks between ceRNAs from the physiological to the pathological condition. The main actor of this dysregulated lncRNA-associated ceRNA network was the lncRNA PVT1, which revealed a net biding preference towards the miR-200 family members in normal breast tissues. Despite its up-regulation in breast cancer tissues, mimicked by the miR-200 family members, PVT1 stops working as ceRNA in the cancerous state. The specific conditions required for a ceRNA landscape to occur are still far from being determined. Here, we emphasized the importance of the relative concentration of the ceRNAs, and their related miRNAs. In particular, we focused on the withdrawal in breast cancer tissues of the PVT1 ceRNA activity and performed a gene expression and sequence analysis of its multiple isoforms. We found that the PVT1 isoform harbouring the binding site for a representative miRNA of the miR-200 family shows a drastic decrease in its relative concentration with respect to the miRNA abundance in breast cancer tissues, providing a plausibility argument to the breakdown of the sponge program orchestrated by the oncogene PVT1.
Collapse
Affiliation(s)
- Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Milan, Italy
| | - Teresa Colombo
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, “Sapienza” University, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
- * E-mail:
| |
Collapse
|
28
|
An Y, Furber KL, Ji S. Pseudogenes regulate parental gene expression via ceRNA network. J Cell Mol Med 2017; 21:185-192. [PMID: 27561207 PMCID: PMC5192809 DOI: 10.1111/jcmm.12952] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/14/2016] [Indexed: 12/14/2022] Open
Abstract
The concept of competitive endogenous RNA (ceRNA) was first proposed by Salmena and colleagues. Evidence suggests that pseudogene RNAs can act as a 'sponge' through competitive binding of common miRNA, releasing or attenuating repression through sequestering miRNAs away from parental mRNA. In theory, ceRNAs refer to all transcripts such as mRNA, tRNA, rRNA, long non-coding RNA, pseudogene RNA and circular RNA, because all of them may become the targets of miRNA depending on spatiotemporal situation. As binding of miRNA to the target RNA is not 100% complementary, it is possible that one miRNA can bind to multiple target RNAs and vice versa. All RNAs crosstalk through competitively binding to miRNAvia miRNA response elements (MREs) contained within the RNA sequences, thus forming a complex regulatory network. The ratio of a subset of miRNAs to the corresponding number of MREs determines repression strength on a given mRNA translation or stability. An increase in pseudogene RNA level can sequester miRNA and release repression on the parental gene, leading to an increase in parental gene expression. A massive number of transcripts constitute a complicated network that regulates each other through this proposed mechanism, though some regulatory significance may be mild or even undetectable. It is possible that the regulation of gene and pseudogene expression occurring in this manor involves all RNAs bearing common MREs. In this review, we will primarily discuss how pseudogene transcripts regulate expression of parental genes via ceRNA network and biological significance of regulation.
Collapse
Affiliation(s)
- Yang An
- Department of Biochemistry and Molecular BiologyMedical SchoolHenan UniversityHenan ProvinceChina
| | - Kendra L. Furber
- College of Pharmacy and NutritionUniversity of SaskatchewanSaskatchewanSKCanada
| | - Shaoping Ji
- Department of Biochemistry and Molecular BiologyMedical SchoolHenan UniversityHenan ProvinceChina
| |
Collapse
|
29
|
Xiao J, Sekhwal MK, Li P, Ragupathy R, Cloutier S, Wang X, You FM. Pseudogenes and Their Genome-Wide Prediction in Plants. Int J Mol Sci 2016; 17:E1991. [PMID: 27916797 PMCID: PMC5187791 DOI: 10.3390/ijms17121991] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/20/2016] [Accepted: 11/22/2016] [Indexed: 11/17/2022] Open
Abstract
Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes). Pseudogenes are primarily identified by comparison to their parent genes. Bioinformatics tools for pseudogene prediction have been developed, among which PseudoPipe, PSF and Shiu's pipeline are publicly available. We compared these three tools using the well-annotated Arabidopsis thaliana genome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu's pipeline identified ~80% of A. thaliana pseudogenes, of which 94% were shared, while PSF failed to generate adequate results. A need for improvement of the bioinformatics tools for pseudogene prediction accuracy in plant genomes was thus identified, with the ultimate goal of improving the quality of genome annotation in plants.
Collapse
Affiliation(s)
- Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manoj Kumar Sekhwal
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Raja Ragupathy
- Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada.
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Xiue Wang
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| |
Collapse
|
30
|
Sardina DS, Alaimo S, Ferro A, Pulvirenti A, Giugno R. A novel computational method for inferring competing endogenous interactions. Brief Bioinform 2016; 18:1071-1081. [DOI: 10.1093/bib/bbw084] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 12/14/2022] Open
|
31
|
Le TD, Zhang J, Liu L, Li J. Computational methods for identifying miRNA sponge interactions. Brief Bioinform 2016; 18:577-590. [DOI: 10.1093/bib/bbw042] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 12/14/2022] Open
|
32
|
Abstract
The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for long non-coding RNAs, pseudogene transcripts and circular RNAs, as well as an alternative function for messenger RNAs. Empirical evidence supporting the hypothesis is accumulating but not without attracting scepticism. Recent studies that model transcriptome-wide binding-site abundance suggest that physiological changes in expression of most individual transcripts will not compromise miRNA activity. In this Review, we critically evaluate the evidence for and against the ceRNA hypothesis to assess the impact of endogenous miRNA-sponge interactions.
Collapse
Affiliation(s)
- Daniel W Thomson
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Kensington NSW 2052, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Kensington NSW 2052, Australia
| |
Collapse
|
33
|
Abstract
By definition, pseudogenes are relics of former genes that no longer possess biological functions. Operationally, they are identified based on disruptions of open reading frames (ORFs) or presumed losses of promoter activities. Intriguingly, a recent human proteomic study reported peptides encoded by 107 pseudogenes. These peptides may play currently unrecognized physiological roles. Alternatively, they may have resulted from accidental translations of pseudogene transcripts and possess no function. Comparing between human and macaque orthologs, we show that the nonsynonymous to synonymous substitution rate ratio (ω) is significantly smaller for translated pseudogenes than other pseudogenes. In particular, five of 34 translated pseudogenes amenable to evolutionary analysis have ω values significantly lower than 1, indicative of the action of purifying selection. This and other findings demonstrate that some but not all translated pseudogenes have selected functions at the protein level. Hence, neither ORF disruption nor presence of protein product disproves or proves gene functionality at the protein level.
Collapse
Affiliation(s)
- Jinrui Xu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor
| |
Collapse
|
34
|
Mahmudi O, Sennblad B, Arvestad L, Nowick K, Lagergren J. Gene-pseudogene evolution: a probabilistic approach. BMC Genomics 2015; 16 Suppl 10:S12. [PMID: 26449131 PMCID: PMC4602177 DOI: 10.1186/1471-2164-16-s10-s12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Over the last decade, methods have been developed for the reconstruction of gene trees that take into account the species tree. Many of these methods have been based on the probabilistic duplication-loss model, which describes how a gene-tree evolves over a species-tree with respect to duplication and losses, as well as extension of this model, e.g., the DLRS (Duplication, Loss, Rate and Sequence evolution) model that also includes sequence evolution under relaxed molecular clock. A disjoint, almost as recent, and very important line of research has been focused on non protein-coding, but yet, functional DNA. For instance, DNA sequences being pseudogenes in the sense that they are not translated, may still be transcribed and the thereby produced RNA may be functional. We extend the DLRS model by including pseudogenization events and devise an MCMC framework for analyzing extended gene families consisting of genes and pseudogenes with respect to this model, i.e., reconstructing gene-trees and identifying pseudogenization events in the reconstructed gene-trees. By applying the MCMC framework to biologically realistic synthetic data, we show that gene-trees as well as pseudogenization points can be inferred well. We also apply our MCMC framework to extended gene families belonging to the Olfactory Receptor and Zinc Finger superfamilies. The analysis indicate that both these super families contains very old pseudogenes, perhaps so old that it is reasonable to suspect that some are functional. In our analysis, the sub families of the Olfactory Receptors contains only lineage specific pseudogenes, while the sub families of the Zinc Fingers contains pseudogene lineages common to several species.
Collapse
|
35
|
Poliseno L, Marranci A, Pandolfi PP. Pseudogenes in Human Cancer. Front Med (Lausanne) 2015; 2:68. [PMID: 26442270 PMCID: PMC4585173 DOI: 10.3389/fmed.2015.00068] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/03/2015] [Indexed: 12/14/2022] Open
Abstract
Recent advances in the analysis of RNA sequencing data have shown that pseudogenes are highly specific markers of cell identity and can be used as diagnostic and prognostic markers. Furthermore, genetically engineered mouse models have recently provided compelling support for a causal link between altered pseudogene expression and cancer. In this review, we discuss the most recent milestones reached in the pseudogene field and the use of pseudogenes as cancer classifiers.
Collapse
Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori , Pisa , Italy ; Institute of Clinical Physiology, Consiglio Nazionale delle Ricerche , Pisa , Italy
| | - Andrea Marranci
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori , Pisa , Italy ; University of Siena , Siena , Italy
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, MA , USA
| |
Collapse
|
36
|
Dai Q, Li J, Zhou K, Liang T. Competing endogenous RNA: A novel posttranscriptional regulatory dimension associated with the progression of cancer. Oncol Lett 2015; 10:2683-2690. [PMID: 26722227 DOI: 10.3892/ol.2015.3698] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 07/07/2015] [Indexed: 12/19/2022] Open
Abstract
The existence of artificial sponges and antisense oligonucleotides designed to decrease the availability of microRNAs (miRNAs), a family of small non-coding RNAs that target RNA transcripts through miRNA response elements (MREs) involved in gene expression, suggests that miRNAs may also be regulated. The wide range of RNA transcripts harboring MREs, termed competing endogenous RNAs (ceRNAs), includes protein-coding messenger RNAs (mRNAs) and non-coding RNAs, for example long non-coding RNAs, pseudogenes and circular RNAs, which compete for a common pool of miRNAs as natural decoys. These ceRNAs are co-regulated and produce large, complex posttranscriptional regulatory networks, which have been implicated in numerous biological processes. The present review discusses recent discoveries that implicate natural microRNA decoys in the development of cancer.
Collapse
Affiliation(s)
- Qingsong Dai
- Key Laboratory for Medical Molecule Activity Research, Guangdong Medical College, Dongguan, Guangdong 523000, P.R. China ; Department of Biochemistry and Molecular Biology, Guangdong Medical College, Dongguan, Guangdong 523000, P.R. China
| | - Jixia Li
- Department of Biochemistry and Molecular Biology, Guangdong Medical College, Dongguan, Guangdong 523000, P.R. China
| | - Keyuan Zhou
- Key Laboratory for Medical Molecule Activity Research, Guangdong Medical College, Dongguan, Guangdong 523000, P.R. China
| | - Tong Liang
- Key Laboratory for Medical Molecule Activity Research, Guangdong Medical College, Dongguan, Guangdong 523000, P.R. China
| |
Collapse
|
37
|
Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B. Extensive identification and analysis of conserved small ORFs in animals. Genome Biol 2015; 16:179. [PMID: 26364619 PMCID: PMC4568590 DOI: 10.1186/s13059-015-0742-x] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/05/2015] [Indexed: 02/06/2023] Open
Abstract
Background There is increasing evidence that transcripts or transcript regions annotated as non-coding can harbor functional short open reading frames (sORFs). Loss-of-function experiments have identified essential developmental or physiological roles for a few of the encoded peptides (micropeptides), but genome-wide experimental or computational identification of functional sORFs remains challenging. Results Here, we expand our previously developed method and present results of an integrated computational pipeline for the identification of conserved sORFs in human, mouse, zebrafish, fruit fly, and the nematode C. elegans. Isolating specific conservation signatures indicative of purifying selection on amino acid (rather than nucleotide) sequence, we identify about 2,000 novel small ORFs located in the untranslated regions of canonical mRNAs or on transcripts annotated as non-coding. Predicted sORFs show stronger conservation signatures than those identified in previous studies and are sometimes conserved over large evolutionary distances. The encoded peptides have little homology to known proteins and are enriched in disordered regions and short linear interaction motifs. Published ribosome profiling data indicate translation of more than 100 novel sORFs, and mass spectrometry data provide evidence for more than 70 novel candidates. Conclusions Taken together, we identify hundreds of previously unknown conserved sORFs in major model organisms. Our computational analyses and integration with experimental data show that these sORFs are expressed, often translated, and sometimes widely conserved, in some cases even between vertebrates and invertebrates. We thus provide an integrated resource of putatively functional micropeptides for functional validation in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0742-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sebastian D Mackowiak
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Henrik Zauber
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Chris Bielow
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany. .,Berlin Institute of Health, Kapelle-Ufer 2, 10117, Berlin, Germany.
| | - Denise Thiel
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Kamila Kutz
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Lorenzo Calviello
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Guido Mastrobuoni
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Stefan Kempa
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Matthias Selbach
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Benedikt Obermayer
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| |
Collapse
|
38
|
Ye X, Fan F, Bhattacharya R, Bellister S, Boulbes DR, Wang R, Xia L, Ivan C, Zheng X, Calin GA, Wang J, Lu X, Ellis LM. VEGFR-1 Pseudogene Expression and Regulatory Function in Human Colorectal Cancer Cells. Mol Cancer Res 2015; 13:1274-82. [PMID: 26041938 DOI: 10.1158/1541-7786.mcr-15-0061] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/17/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED A large number of pseudogenes have been found to be transcribed in human cancers. However, only a few pseudogenes are functionally characterized. Here, we identified a transcribed pseudogene of VEGFR1, or fms-related tyrosine kinase 1 (FLT1), in human colorectal cancer cells. Interestingly, this pseudogene (designated as FLT1P1) was found to be transcribed bidirectionally and functionally modulated cognate VEGFR1 protein expression in the cells. Mechanistically, expression of FLT1P1 antisense transcript not only inhibited the VEGFR1 expression, but also inhibited non-cognate VEGF-A expression through interaction with miR-520a. Perturbation of FLT1P1 expression by RNA interference (RNAi) markedly inhibited tumor cell proliferation and xenograft tumor growth. This study identifies FLT1P1 antisense as a critical regulator of VEGFR1 and VEGF-A expression in colorectal cancer cells, and highlights its role in regulation of the pathogenesis of colorectal cancer. IMPLICATIONS The VEGFR1 pseudogene, FLT1P1, is a novel and functional regulator of VEGF signaling and its targeting could be an alternative strategy to modulate its cognate/target gene expression and downstream activity in cancer.
Collapse
Affiliation(s)
- Xiangcang Ye
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Fan Fan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajat Bhattacharya
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Seth Bellister
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Delphine R Boulbes
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rui Wang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ling Xia
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cristina Ivan
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiongbin Lu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lee M Ellis
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
39
|
Zhao Y, Tang L, Li Z, Jin J, Luo J, Gao G. Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics. BMC Evol Biol 2015; 15:66. [PMID: 25927997 PMCID: PMC4425925 DOI: 10.1186/s12862-015-0345-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/31/2015] [Indexed: 11/24/2022] Open
Abstract
Background Long-established protein-coding genes may lose their coding potential during evolution (“unitary gene loss”). Members of the Poaceae family are a major food source and represent an ideal model clade for plant evolution research. However, the global pattern of unitary gene loss in Poaceae genomes as well as the evolutionary fate of lost genes are still less-investigated and remain largely elusive. Results Using a locally developed pipeline, we identified 129 unitary gene loss events for long-established protein-coding genes from four representative species of Poaceae, i.e. brachypodium, rice, sorghum and maize. Functional annotation suggested that the lost genes in all or most of Poaceae species are enriched for genes involved in development and response to endogenous stimulus. We also found that 44 mutated genomic loci of lost genes, which we referred as relics, were still actively transcribed, and of which 84% (37 of 44) showed significantly differential expression across different tissues. More interestingly, we found that there were totally five expressed relics may function as competitive endogenous RNA in brachypodium, rice and sorghum genome. Conclusions Based on comparative genomics and transcriptome data, we firstly compiled a comprehensive catalogue of unitary gene loss events in Poaceae species and characterized a statistically significant functional preference for these lost genes as well showed the potential of relics functioning as competitive endogenous RNAs in Poaceae genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0345-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yi Zhao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.
| | - Liang Tang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China. .,Current address: College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, People's Republic of China.
| | - Zhe Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
| | - Jinpu Jin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.
| | - Jingchu Luo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.
| |
Collapse
|
40
|
Sanchez-Mejias A, Tay Y. Competing endogenous RNA networks: tying the essential knots for cancer biology and therapeutics. J Hematol Oncol 2015; 8:30. [PMID: 25888444 PMCID: PMC4381443 DOI: 10.1186/s13045-015-0129-1] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/16/2015] [Indexed: 12/14/2022] Open
Abstract
A recently discovered dimension of post-transcriptional gene regulation involves co-regulatory crosstalk between RNA transcripts, which compete for common pools of microRNA (miRNA) molecules. These competing endogenous RNAs (ceRNAs), or natural miRNA sponges, have an active role in regulating miRNA availability within the cell and form intertwined regulatory networks. Recent reports have implicated diverse RNA species including protein-coding messenger RNAs and non-coding RNAs as ceRNAs in human development and diseases including human cancer. In this review, we discuss the most recent discoveries that implicate natural miRNA decoys in human cancer biology, as well as exciting advances in the study of ceRNA networks and dynamics. The structure and topology of intricate genome-scale ceRNA networks can be predicted computationally, and their dynamic response to fluctuations in ceRNA and miRNA levels can be studied via mathematical modeling. Additionally, the development of new methods to quantitatively determine absolute expression levels of miRNA and ceRNA molecules have expanded the capacity to accurately study the efficiency of ceRNA crosstalk in diverse biological models. These major milestones are of critical importance to identify key components of ceRNA regulatory networks that could aid the development of new approaches to cancer diagnostics and oligonucleotide-based therapeutics.
Collapse
Affiliation(s)
- Avencia Sanchez-Mejias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
| |
Collapse
|
41
|
Tan JY, Sirey T, Honti F, Graham B, Piovesan A, Merkenschlager M, Webber C, Ponting CP, Marques AC. Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells. Genome Res 2015; 25:655-66. [PMID: 25792609 PMCID: PMC4417114 DOI: 10.1101/gr.181974.114] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 03/17/2015] [Indexed: 12/14/2022]
Abstract
Recently, a handful of intergenic long noncoding RNAs (lncRNAs) have been shown to compete with mRNAs for binding to miRNAs and to contribute to development and disease. Beyond these reports, little is yet known of the extent and functional consequences of miRNA-mediated regulation of mRNA levels by lncRNAs. To gain further insight into lncRNA-mRNA miRNA-mediated crosstalk, we reanalyzed transcriptome-wide changes induced by the targeted knockdown of over 100 lncRNA transcripts in mouse embryonic stem cells (mESCs). We predicted that, on average, almost one-fifth of the transcript level changes induced by lncRNAs are dependent on miRNAs that are highly abundant in mESCs. We validated these findings experimentally by temporally profiling transcriptome-wide changes in gene expression following the loss of miRNA biogenesis in mESCs. Following the depletion of miRNAs, we found that >50% of lncRNAs and their miRNA-dependent mRNA targets were up-regulated coordinately, consistent with their interaction being miRNA-mediated. These lncRNAs are preferentially located in the cytoplasm, and the response elements for miRNAs they share with their targets have been preserved in mammals by purifying selection. Lastly, miRNA-dependent mRNA targets of each lncRNA tended to share common biological functions. Post-transcriptional miRNA-mediated crosstalk between lncRNAs and mRNA, in mESCs, is thus surprisingly prevalent, conserved in mammals, and likely to contribute to critical developmental processes.
Collapse
Affiliation(s)
- Jennifer Y Tan
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, United Kingdom; University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom; Department of Physiology, University of Lausanne, 1005 Lausanne, Switzerland
| | - Tamara Sirey
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, United Kingdom; University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom
| | - Frantisek Honti
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, United Kingdom; University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom; Department of Physiology, University of Lausanne, 1005 Lausanne, Switzerland
| | - Bryony Graham
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom; Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES),Unit of Histology, Embryology and Applied Biology, University of Bologna, 40126 Bologna, BO, Italy
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Caleb Webber
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, United Kingdom; University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom
| | - Chris P Ponting
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, United Kingdom; University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom
| | - Ana C Marques
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, United Kingdom; University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom; Department of Physiology, University of Lausanne, 1005 Lausanne, Switzerland
| |
Collapse
|
42
|
Poliseno L, Pandolfi PP. PTEN ceRNA networks in human cancer. Methods 2015; 77-78:41-50. [PMID: 25644446 DOI: 10.1016/j.ymeth.2015.01.013] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/19/2015] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
In multiple human cancer types, a close link exists between the expression levels of Phosphatase and Tensin Homolog deleted on chromosome 10 (PTEN) and its oncosuppressive activities. Therefore, an in depth understanding of the molecular mechanisms by which PTEN expression is modulated is crucial in order to achieve a comprehensive knowledge of its biological roles. In recent years, the competition between PTEN mRNA and other RNAs for shared microRNA molecules has emerged as one such mechanism and has brought into focus the coding-independent activities of PTEN and other mRNAs. In this review article, we examine the competing endogenous RNA (ceRNA) partners of PTEN that have been identified so far. We also discuss how PTEN-centered ceRNA networks can contribute to a deeper understanding of PTEN function and tumorigenesis.
Collapse
Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori, Pisa, Italy; Institute of Clinical Physiology, CNR, Pisa, Italy.
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
43
|
Abstract
Pseudogenes were once considered genomic fossils, but recent studies indicate that they may function as gene regulators through the generation of endogenous small interfering RNAs (esiRNAs), antisense RNAs, and decoys for microRNAs. In this review, we summarize pseudogene study methods, emphasizing relevant publicly available resources, and we describe a systematic pipeline to identify pseudogene-derived esiRNAs and their targets, which can lead to a deeper understanding of pseudogene function.
Collapse
Affiliation(s)
- Wen-Ling Chan
- Biomedical Informatics, Asia University, Taichung, Taiwan
| | | |
Collapse
|
44
|
Shidhi PR, Suravajhala P, Nayeema A, Nair AS, Singh S, Dhar PK. Making novel proteins from pseudogenes. Bioinformatics 2015; 31:33-9. [PMID: 25236460 DOI: 10.1093/bioinformatics/btu615] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
MOTIVATION Recently, we made synthetic proteins from non-coding DNA of Escherichia coli. Encouraged by this, we asked: can we artificially express pseudogenes into novel and functional proteins? What kind of structures would be generated? Would these proteins be stable? How would the organism respond to the artificial reactivation of pseudogenes? RESULTS To answer these questions, we studied 16 full-length protein equivalents of pseudogenes. The sequence-based predictions indicated interesting molecular and cellular functional roles for pseudogene-derived proteins. Most of the proteins were predicted to be involved in the amino acid biosynthesis, energy metabolism, purines and pyrimidine biosynthesis, central intermediary metabolism, transport and binding. Interestingly, many of the pseudogene-derived proteins were predicted to be enzymes. Furthermore, proteins showed strong evidence of stable tertiary structures. The prediction scores for structure, function and stability were found to be favorable in most of the cases. IMPACT To our best knowledge, this is the first such report that predicts the possibility of making functional and stable proteins from pseudogenes. In future, it would be interesting to experimentally synthesize and validate these predictions.
Collapse
Affiliation(s)
- P R Shidhi
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Prashanth Suravajhala
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Aysha Nayeema
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Shailja Singh
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| | - Pawan K Dhar
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, Bioclues.org, India, Bioclues.org, Denmark, National College, University of Kerala, Trivandrum- 695 009, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India
| |
Collapse
|
45
|
Vitiello M, Tuccoli A, Poliseno L. Long non-coding RNAs in cancer: implications for personalized therapy. Cell Oncol (Dordr) 2014; 38:17-28. [PMID: 25113790 DOI: 10.1007/s13402-014-0180-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2014] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs, pseudogenes and circRNAs) have recently come into light as powerful players in cancer pathogenesis and it is becoming increasingly clear that they have the potential of greatly contributing to the spread and success of personalized cancer medicine. In this concise review, we briefly introduce these three classes of long non-coding RNAs. We then discuss their applications as diagnostic and prognostic biomarkers. Finally, we describe their appeal as targets and as drugs, while pointing out the limitations that still lie ahead of their definitive entry into clinical practice.
Collapse
Affiliation(s)
- Marianna Vitiello
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori c/o IFC-CNR, via Moruzzi 1, 56124, Pisa, Italy
| | | | | |
Collapse
|
46
|
Marques AC, Ponting CP. Intergenic lncRNAs and the evolution of gene expression. Curr Opin Genet Dev 2014; 27:48-53. [PMID: 24852186 DOI: 10.1016/j.gde.2014.03.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/19/2014] [Accepted: 03/19/2014] [Indexed: 11/24/2022]
Abstract
Eukaryote genomes encode a surprisingly large number of noncoding transcripts. Around two-thirds of human transcribed loci do not encode protein, and many are intergenic and produce long (>200 nucleotides) noncoding RNAs (lncRNAs). Extensive analyses using comparative genomics and transcriptomics approaches have established that lncRNA sequence and transcription tend to turn over rapidly during evolution. Our appreciation of the biological roles of lncRNAs, based only on a handful of transcripts with well-characterized functions, is that lncRNAs have diverse roles in regulating gene expression. These proposed roles together with their rapid rates of evolution suggest that lncRNAs could contribute to the divergent expression patterns observed among species and potentially to the origin of new traits.
Collapse
Affiliation(s)
- Ana C Marques
- MRC Functional Genomics Unit, University of Oxford, South Parks Road, OX1 3QX, UK; University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, OX1 3QX, UK.
| | - Chris P Ponting
- MRC Functional Genomics Unit, University of Oxford, South Parks Road, OX1 3QX, UK; University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, OX1 3QX, UK
| |
Collapse
|
47
|
Characterization of human pseudogene-derived non-coding RNAs for functional potential. PLoS One 2014; 9:e93972. [PMID: 24699680 PMCID: PMC3974860 DOI: 10.1371/journal.pone.0093972] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/10/2014] [Indexed: 11/19/2022] Open
Abstract
Thousands of pseudogenes exist in the human genome and many are transcribed, but their functional potential remains elusive and understudied. To explore these issues systematically, we first developed a computational pipeline to identify transcribed pseudogenes from RNA-Seq data. Applying the pipeline to datasets from 16 distinct normal human tissues identified ∼ 3,000 pseudogenes that could produce non-coding RNAs in a manner of low abundance but high tissue specificity under normal physiological conditions. Cross-tissue comparison revealed that the transcriptional profiles of pseudogenes and their parent genes showed mostly positive correlations, suggesting that pseudogene transcription could have a positive effect on the expression of their parent genes, perhaps by functioning as competing endogenous RNAs (ceRNAs), as previously suggested and demonstrated with the PTEN pseudogene, PTENP1. Our analysis of the ENCODE project data also found many transcriptionally active pseudogenes in the GM12878 and K562 cell lines; moreover, it showed that many human pseudogenes produced small RNAs (sRNAs) and some pseudogene-derived sRNAs, especially those from antisense strands, exhibited evidence of interfering with gene expression. Further integrated analysis of transcriptomics and epigenomics data, however, demonstrated that trimethylation of histone 3 at lysine 9 (H3K9me3), a posttranslational modification typically associated with gene repression and heterochromatin, was enriched at many transcribed pseudogenes in a transcription-level dependent manner in the two cell lines. The H3K9me3 enrichment was more prominent in pseudogenes that produced sRNAs at pseudogene loci and their adjacent regions, an observation further supported by the co-enrichment of SETDB1 (a H3K9 methyltransferase), suggesting that pseudogene sRNAs may have a role in regional chromatin repression. Taken together, our comprehensive and systematic characterization of pseudogene transcription uncovers a complex picture of how pseudogene ncRNAs could influence gene and pseudogene expression, at both epigenetic and post-transcriptional levels.
Collapse
|
48
|
Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature 2014; 505:344-52. [PMID: 24429633 DOI: 10.1038/nature12986] [Citation(s) in RCA: 2888] [Impact Index Per Article: 288.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 11/06/2013] [Indexed: 12/11/2022]
Abstract
Recent reports have described an intricate interplay among diverse RNA species, including protein-coding messenger RNAs and non-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs. These RNA transcripts act as competing endogenous RNAs (ceRNAs) or natural microRNA sponges - they communicate with and co-regulate each other by competing for binding to shared microRNAs, a family of small non-coding RNAs that are important post-transcriptional regulators of gene expression. Understanding this novel RNA crosstalk will lead to significant insight into gene regulatory networks and have implications in human development and disease.
Collapse
Affiliation(s)
- Yvonne Tay
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - John Rinn
- 1] Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA. [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. [3] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| |
Collapse
|
49
|
The miRNA-mediated cross-talk between transcripts provides a novel layer of posttranscriptional regulation. ADVANCES IN GENETICS 2014; 85:149-99. [PMID: 24880735 DOI: 10.1016/b978-0-12-800271-1.00003-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Endogenously expressed transcripts that are posttranscriptionally regulated by the same microRNAs (miRNAs) will, in principle, compete for the binding of their shared small noncoding RNA regulators and modulate each other's abundance. Recently, the levels of some coding as well as noncoding transcripts have indeed been found to be regulated in this way. Transcripts that engage in such regulatory interactions are referred to as competitive endogenous RNAs (ceRNAs). This novel layer of posttranscriptional regulation has been shown to contribute to diverse aspects of organismal and cellular biology, despite the number of functionally characterized ceRNAs being as yet relatively low. Importantly, increasing evidence suggests that the dysregulation of some ceRNA interactions is associated with disease etiology, most preeminently with cancer. Here we review how posttranscriptional regulation by miRNAs contributes to the cross-talk between transcripts and review examples of known ceRNAs by highlighting the features underlying their interactions and what might be their biological relevance.
Collapse
|
50
|
Abstract
Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in mammalian genomes and might play widespread roles in gene regulation and other cellular processes. This Review outlines the emerging understanding of lincRNAs in vertebrate animals, with emphases on how they are being identified and current conclusions and questions regarding their genomics, evolution and mechanisms of action.
Collapse
Affiliation(s)
- Igor Ulitsky
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | |
Collapse
|