351
|
Kong H, Zhu M, Cui F, Wang S, Gao X, Lu S, Wu Y, Zhu H. Quantitative assessment of short amplicons in FFPE-derived long-chain RNA. Sci Rep 2014; 4:7246. [PMID: 25430878 PMCID: PMC5384205 DOI: 10.1038/srep07246] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are important resources for molecular medical research. However, long-chain RNA analysis is restricted in FFPE tissues due to high levels of degradation. To explore the possibility of long RNA quantification in FFPE tissues, we selected 14 target RNAs (8 mRNAs and 6 long noncoding RNAs) from literatures, and designed short (~60 bp) and long (~200 bp) amplicons for each of them. Colorectal carcinomas with adjacent normal tissues were subjected to quantitative reverse-transcription PCR (quantitative RT-PCR) in 3 cohorts, including 18 snap-frozen and 83 FFPE tissues. We found that short amplicons were amplified more efficiently than long amplicons both in snap-frozen (P = 0.0006) and FFPE (P = 0.0152) tissues. Nonetheless, comparison of colorectal carcinomas with their adjacent normal tissues demonstrated that the consistency of fold-change trends in a single short amplicon between snap-frozen and FFPE tissues was only 36%. Therefore, we innovatively performed quantitative RT-PCR with 3 non-overlapping short amplicons for 14 target RNAs in FFPE tissues. All target RNAs showed a concordance of 100% of fold-change trends in at least two short amplicons, which offers sufficient information for accurate quantification of target RNAs. Our findings demonstrated the possibility of long-chain RNA analysis with 3 non-overlapping short amplicons in standardized-preserved FFPE tissues.
Collapse
Affiliation(s)
- Hui Kong
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Mengou Zhu
- Harvard College, Harvard University, Cambridge, MA, 02138, USA
| | - Fengyun Cui
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuyang Wang
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xue Gao
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Shaohua Lu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ying Wu
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hongguang Zhu
- 1] Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China [2] Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China [3] Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| |
Collapse
|
352
|
Gopalakrishnan K, Kumarasamy S, Mell B, Joe B. Genome-wide identification of long noncoding RNAs in rat models of cardiovascular and renal disease. Hypertension 2014; 65:200-10. [PMID: 25385761 DOI: 10.1161/hypertensionaha.114.04498] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Long noncoding RNAs (lncRNAs) are an emerging class of genomic regulatory molecules reported in various species. In the rat, which is one of the major mammalian model organisms, discovery of lncRNAs on a genome-wide scale is lagging. Renal lncRNA sequencing and lncRNA transcriptome analysis were conducted in 3 rat strains that are widely used in cardiovascular and renal research: the Dahl salt-sensitive rat, the spontaneously hypertensive rat, and the Dahl salt-resistant rat. Through the RNA sequencing approach, 3273 transcripts were identified as rat lncRNAs. A majority of lncRNAs were without predicted target genes. Differential expression of 273 and 749 lncRNAs was detected between Dahl salt-sensitive versus Dahl salt-resistant and Dahl salt-sensitive versus spontaneously hypertensive rat comparisons, respectively. To couple the observed differential expression of lncRNAs with the status of mRNAs, an mRNA transcriptome analysis was conducted. Several cis mRNA genes were coregulated with lncRNAs. Of these, the protein expression status of 4 target genes, Asb3, Chac2, Pex11b, and Sp5, were differentially expressed between the relevant strain comparisons, thereby suggesting that the differentially expressed lncRNAs associated with these genes are candidate genetic determinants of blood pressure. This study serves as a first-generation catalog of rat lncRNAs and illustrates the prioritization of lncRNAs as candidates for complex polygenic traits.
Collapse
Affiliation(s)
- Kathirvel Gopalakrishnan
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Sivarajan Kumarasamy
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Blair Mell
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Bina Joe
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH.
| |
Collapse
|
353
|
Li J, Chen Z, Tian L, Zhou C, He MY, Gao Y, Wang S, Zhou F, Shi S, Feng X, Sun N, Liu Z, Skogerboe G, Dong J, Yao R, Zhao Y, Sun J, Zhang B, Yu Y, Shi X, Luo M, Shao K, Li N, Qiu B, Tan F, Chen R, He J. LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma. Gut 2014; 63:1700-1710. [PMID: 24522499 PMCID: PMC4215280 DOI: 10.1136/gutjnl-2013-305806] [Citation(s) in RCA: 342] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 01/02/2014] [Accepted: 01/13/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND Oesophageal cancer is one of the most deadly forms of cancer worldwide. Long non-coding RNAs (lncRNAs) are often found to have important regulatory roles. OBJECTIVE To assess the lncRNA expression profile of oesophageal squamous cell carcinoma (OSCC) and identify prognosis-related lncRNAs. METHOD LncRNA expression profiles were studied by microarray in paired tumour and normal tissues from 119 patients with OSCC and validated by qRT-PCR. The 119 patients were divided randomly into training (n=60) and test (n=59) groups. A prognostic signature was developed from the training group using a random Forest supervised classification algorithm and a nearest shrunken centroid algorithm, then validated in a test group and further, in an independent cohort (n=60). The independence of the signature in survival prediction was evaluated by multivariable Cox regression analysis. RESULTS LncRNAs showed significantly altered expression in OSCC tissues. From the training group, we identified a three-lncRNA signature (including the lncRNAs ENST00000435885.1, XLOC_013014 and ENST00000547963.1) which classified the patients into two groups with significantly different overall survival (median survival 19.2 months vs >60 months, p<0.0001). The signature was applied to the test group (median survival 21.5 months vs >60 months, p=0.0030) and independent cohort (median survival 25.8 months vs >48 months, p=0.0187) and showed similar prognostic values in both. Multivariable Cox regression analysis showed that the signature was an independent prognostic factor for patients with OSCC. Stratified analysis suggested that the signature was prognostic within clinical stages. CONCLUSIONS Our results suggest that the three-lncRNA signature is a new biomarker for the prognosis of patients with OSCC, enabling more accurate prediction of survival.
Collapse
Affiliation(s)
- Jiagen Li
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Zhaoli Chen
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Liqing Tian
- Bioinformatics Laboratory and Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, The People's Republic of China
| | - Chengcheng Zhou
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Max Yifan He
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Yibo Gao
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Suya Wang
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Fang Zhou
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Susheng Shi
- Department of Pathology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Xiaoli Feng
- Department of Pathology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Nan Sun
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Ziyuan Liu
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Geir Skogerboe
- Bioinformatics Laboratory and Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, The People's Republic of China
| | - Jingsi Dong
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Ran Yao
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Yuda Zhao
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Jian Sun
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Baihua Zhang
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Yue Yu
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Xuejiao Shi
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Mei Luo
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Kang Shao
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Ning Li
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Bin Qiu
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Fengwei Tan
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| | - Runsheng Chen
- Bioinformatics Laboratory and Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, The People's Republic of China
| | - Jie He
- !
Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
| |
Collapse
|
354
|
Zhao T, Xu J, Liu L, Bai J, Xu C, Xiao Y, Li X, Zhang L. Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features. MOLECULAR BIOSYSTEMS 2014; 11:126-36. [PMID: 25354589 DOI: 10.1039/c4mb00478g] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
LncRNAs have become rising stars in biology and medicine, due to their versatile functions in a wide range of important biological processes and active roles in various human cancers. Here, we developed a computational method based on the naïve Bayesian classifier method to identify cancer-related lncRNAs by integrating genome, regulome and transcriptome data, and identified 707 potential cancer-related lncRNAs. We demonstrated the performance of the method by ten-fold cross-validation, and found that integration of multi-omic data was necessary to identify cancer-related lncRNAs. We identified 707 potential cancer-related lncRNAs and our results showed that these lncRNAs tend to exhibit significant differential expression and differential DNA methylation in multiple cancer types, and prognosis effects in prostate cancer. We also found that these lncRNAs were more likely to be direct targets of TP53 family members than others. Moreover, based on 147 lncRNA knockdown data in mice, we validated that four of six mouse orthologous lncRNAs were significantly involved in many cancer-related processes, such as cell differentiation and the Wnt signaling pathway. Notably, one lncRNA, lnc-SNURF-1, which was found to be associated with TNF-mediated signaling pathways, was up-regulated in prostate cancer and the protein-coding genes affected by knockdown of the lncRNA were also significantly aberrant in prostate cancer patients, suggesting its probable importance in tumorigenesis. Taken together, our method underlines the power of integrating multi-omic data to uncover cancer-related lncRNAs.
Collapse
Affiliation(s)
- Tingting Zhao
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
| | | | | | | | | | | | | | | |
Collapse
|
355
|
Abstract
Long non-coding RNAs (lncRNAs) are series of transcripts with important biological functions. Various diseases have been associated with aberrant expression of lncRNAs and the related dysregulation of mRNAs. In this review, we highlight the mechanisms of dynamic lncRNA expression. The chromatin state contributes to the low and specific expression of lncRNAs. The transcription of non-coding RNA genes is regulated by many core transcription factors applied to protein-coding genes. However, specific DNA sequences may allow their unsynchronized transcription with their location-associated mRNAs. Additionally, there are multiple mechanisms involved in the post-transcriptional regulation of lncRNAs. Among these, microRNAs might have indispensible regulatory effects on lncRNAs, based on recent discoveries.
Collapse
|
356
|
Kapusta A, Feschotte C. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet 2014; 30:439-52. [PMID: 25218058 PMCID: PMC4464757 DOI: 10.1016/j.tig.2014.08.004] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 02/08/2023]
Abstract
Thousands of genes encoding long noncoding RNAs (lncRNAs) have been identified in all vertebrate genomes thus far examined. The list of lncRNAs partaking in arguably important biochemical, cellular, and developmental activities is steadily growing. However, it is increasingly clear that lncRNA repertoires are subject to weak functional constraint and rapid turnover during vertebrate evolution. We discuss here some of the factors that may explain this apparent paradox, including relaxed constraint on sequence to maintain lncRNA structure/function, extensive redundancy in the regulatory circuits in which lncRNAs act, as well as adaptive and non-adaptive forces such as genetic drift. We explore the molecular mechanisms promoting the birth and rapid evolution of lncRNA genes, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes. Together these properties reveal a remarkably dynamic and malleable noncoding transcriptome which may represent an important source of robustness and evolvability.
Collapse
Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| |
Collapse
|
357
|
Cao J. The functional role of long non-coding RNAs and epigenetics. Biol Proced Online 2014; 16:11. [PMID: 25276098 PMCID: PMC4177375 DOI: 10.1186/1480-9222-16-11] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/06/2014] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review will focus on the functional roles of lncRNAs in epigenetics and related research progress will be summarized.
Collapse
Affiliation(s)
- Jinneng Cao
- Department of respiratory medicine, Fuyong People's Hospital, Baoan District, Shenzhen 518103, Guangdong, People's Republic of China
| |
Collapse
|
358
|
Jiang HJ, Wang S, Ding Y. Emerging paradigms of long non-coding RNAs in gastrointestinal cancer. AMERICAN JOURNAL OF STEM CELLS 2014; 3:63-73. [PMID: 25232506 PMCID: PMC4163605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 08/07/2014] [Indexed: 06/03/2023]
Abstract
A large number of long non-coding RNAs (lncRNAs) have been discovered by genome-wide transcriptional analyses. Emerging evidence has indicated that lncRNAs regulate gene expression at epigenetic, transcription, and post-transcription levels, are widely involved in various pathobiology of human diseases, and may play an important role in the biology of cancer stem cells. Alterations of specific lncRNAs have been revealed to interact with the major pathways of cell proliferation, apoptosis, differentiation, invasion and metastasis in many human malignancies, such as gastrointestinal cancer. This review summarizes the current understandings in biological functions and implications of lncRNAs in gastrointestinal cancer.
Collapse
Affiliation(s)
- Hui-Juan Jiang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, China
| | - Shuang Wang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, China
| | - Yanqing Ding
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University Guangzhou 510515, China
| |
Collapse
|
359
|
Minning C, Mokhtar NM, Abdullah N, Muhammad R, Emran NA, Ali SAMD, Harun R, Jamal R. Exploring breast carcinogenesis through integrative genomics and epigenomics analyses. Int J Oncol 2014; 45:1959-68. [PMID: 25175708 DOI: 10.3892/ijo.2014.2625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 07/18/2014] [Indexed: 11/05/2022] Open
Abstract
There have been many DNA methylation studies on breast cancer which showed various methylation patterns involving tumour suppressor genes and oncogenes but only a few of those studies link the methylation data with gene expression. More data are required especially from the Asian region and to analyse how the epigenome data correlate with the transcriptome. DNA methylation profiling was carried out on 76 fresh frozen primary breast tumour tissues and 25 adjacent non-cancerous breast tissues using the Illumina Infinium(®) HumanMethylation27 BeadChip. Validation of methylation results was performed on 7 genes using either MS-MLPA or MS-qPCR. Gene expression profiling was done on 15 breast tumours and 5 adjacent non-cancerous breast tissues using the Affymetrix GeneChip(®) Human Gene 1.0 ST array. The overlapping genes between DNA methylation and gene expression datasets were further mapped to the KEGG database to identify the molecular pathways that linked these genes together. Supervised hierarchical cluster analysis revealed 1,389 hypermethylated CpG sites and 22 hypomethylated CpG sites in cancer compared to the normal samples. Gene expression microarray analysis using a fold-change of at least 1.5 and a false discovery rate (FDR) at p>0.05 identified 404 upregulated and 463 downregulated genes in cancer samples. Integration of both datasets identified 51 genes with hypermethylation with low expression (negative association) and 13 genes with hypermethylation with high expression (positive association). Most of the overlapping genes belong to the focal adhesion and extracellular matrix-receptor interaction that play important roles in breast carcinogenesis. The present study displayed the value of using multiple datasets in the same set of tissues and how the integrative analysis can create a list of well-focused genes as well as to show the correlation between epigenetic changes and gene expression. These gene signatures can help us understand the epigenetic regulation of gene expression and could be potential targets for therapeutic intervention in the future.
Collapse
Affiliation(s)
- Chin Minning
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Norlia Abdullah
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rohaizak Muhammad
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nor Aina Emran
- Department of Surgery, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Siti Aishah M D Ali
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Roslan Harun
- Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| |
Collapse
|
360
|
Ramírez-Castrillón M, Mendes SDC, Inostroza-Ponta M, Valente P. (GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? PLoS One 2014; 9:e105870. [PMID: 25171185 PMCID: PMC4149466 DOI: 10.1371/journal.pone.0105870] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 07/28/2014] [Indexed: 12/11/2022] Open
Abstract
In microbiology, identification of all isolates by sequencing is still unfeasible in small research laboratories. Therefore, many yeast diversity studies follow a screening procedure consisting of clustering the yeast isolates using MSP-PCR fingerprinting, followed by identification of one or a few selected representatives of each cluster by sequencing. Although this procedure has been widely applied in the literature, it has not been properly validated. We evaluated a standardized protocol using MSP-PCR fingerprinting with the primers (GTG)5 and M13 for the discrimination of wine associated yeasts in South Brazil. Two datasets were used: yeasts isolated from bottled wines and vineyard environments. We compared the discriminatory power of both primers in a subset of 16 strains, choosing the primer (GTG)5 for further evaluation. Afterwards, we applied this technique to 245 strains, and compared the results with the identification obtained by partial sequencing of the LSU rRNA gene, considered as the gold standard. An array matrix was constructed for each dataset and used as input for clustering with two methods (hierarchical dendrograms and QAPGrid layout). For both yeast datasets, unrelated species were clustered in the same group. The sensitivity score of (GTG)5 MSP-PCR fingerprinting was high, but specificity was low. As a conclusion, the yeast diversity inferred in several previous studies may have been underestimated and some isolates were probably misidentified due to the compliance to this screening procedure.
Collapse
Affiliation(s)
- Mauricio Ramírez-Castrillón
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, Brazil
- Departamento de Microbiologia, Imunologia e Parasitologia, ICBS, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, Porto Alegre, Brazil
| | - Sandra Denise Camargo Mendes
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, Brazil
- Departamento de Microbiologia, Imunologia e Parasitologia, ICBS, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, Porto Alegre, Brazil
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina, Laboratório de Análises de Vinhos e Derivados, Estação Experimental de Videira, Campo Experimental, Videira, Brazil
| | - Mario Inostroza-Ponta
- Departamento de Ingeniería Informática, Universidad de Santiago de Chile, Santiago de Chile, Chile
| | - Patricia Valente
- Departamento de Microbiologia, Imunologia e Parasitologia, ICBS, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, Porto Alegre, Brazil
- * E-mail:
| |
Collapse
|
361
|
The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol Cell 2014; 55:791-802. [PMID: 25155612 DOI: 10.1016/j.molcel.2014.07.012] [Citation(s) in RCA: 520] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 06/09/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023]
Abstract
Mechanistic roles for many lncRNAs are poorly understood, in part because their direct interactions with genomic loci and proteins are difficult to assess. Using a method to purify endogenous RNAs and their associated factors, we mapped the genomic binding sites for two highly expressed human lncRNAs, NEAT1 and MALAT1. We show that NEAT1 and MALAT1 localize to hundreds of genomic sites in human cells, primarily over active genes. NEAT1 and MALAT1 exhibit colocalization to many of these loci, but display distinct gene body binding patterns at these sites, suggesting independent but complementary functions for these RNAs. We also identified numerous proteins enriched by both lncRNAs, supporting complementary binding and function, in addition to unique associated proteins. Transcriptional inhibition or stimulation alters localization of NEAT1 on active chromatin sites, implying that underlying DNA sequence does not target NEAT1 to chromatin, and that localization responds to cues involved in the transcription process.
Collapse
|
362
|
Griseri P, Pagès G. Regulation of the mRNA half-life in breast cancer. World J Clin Oncol 2014; 5:323-334. [PMID: 25114848 PMCID: PMC4127604 DOI: 10.5306/wjco.v5.i3.323] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/31/2014] [Accepted: 05/14/2014] [Indexed: 02/06/2023] Open
Abstract
The control of the half-life of mRNA plays a central role in normal development and in disease progression. Several pathological conditions, such as breast cancer, correlate with deregulation of the half-life of mRNA encoding growth factors, oncogenes, cell cycle regulators and inflammatory cytokines that participate in cancer. Substantial stability means that a mRNA will be available for translation for a longer time, resulting in high levels of protein gene products, which may lead to prolonged responses that subsequently result in over-production of cellular mediators that participate in cancer. The stability of these mRNA is regulated at the 3’UTR level by different mechanisms involving mRNA binding proteins, micro-RNA, long non-coding RNA and alternative polyadenylation. All these events are tightly inter-connected to each other and lead to steady state levels of target mRNAs. Compelling evidence also suggests that both mRNA binding proteins and regulatory RNAs which participate to mRNA half-life regulation may be useful prognostic markers in breast cancers, pointing to a potential therapeutic approach to treatment of patients with these tumors. In this review, we summarize the main mechanisms involved in the regulation of mRNA decay and discuss the possibility of its implication in breast cancer aggressiveness and the efficacy of targeted therapy.
Collapse
|
363
|
Herriges MJ, Swarr DT, Morley MP, Rathi KS, Peng T, Stewart KM, Morrisey EE. Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. Genes Dev 2014; 28:1363-79. [PMID: 24939938 PMCID: PMC4066405 DOI: 10.1101/gad.238782.114] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Long noncoding RNAs (lncRNAs) are thought to play important roles in regulating gene transcription, yet few have known biological functions. Using a conservative pipeline, Herriges et al. identify lncRNAs with key functions during mammalian development. Loss-of-function analyses show that two lncRNAs play distinct roles in endoderm development by controlling the expression of critical transcription factors and pathways, including retinoic acid signaling. The data demonstrate that lncRNAs regulate multiple aspects of gene transcription during foregut and lung endoderm development. Long noncoding RNAs (lncRNAs) are thought to play important roles in regulating gene transcription, but few have well-defined expression patterns or known biological functions during mammalian development. Using a conservative pipeline to identify lncRNAs that have important biological functions, we identified 363 lncRNAs in the lung and foregut endoderm. Importantly, we show that these lncRNAs are spatially correlated with transcription factors across the genome. In-depth expression analyses of lncRNAs with genomic loci adjacent to the critical transcription factors Nkx2.1, Gata6, Foxa2 (forkhead box a2), and Foxf1 mimic the expression patterns of their protein-coding neighbor. Loss-of-function analysis demonstrates that two lncRNAs, LL18/NANCI (Nkx2.1-associated noncoding intergenic RNA) and LL34, play distinct roles in endoderm development by controlling expression of critical developmental transcription factors and pathways, including retinoic acid signaling. In particular, we show that LL18/NANCI acts upstream of Nkx2.1 and downstream from Wnt signaling to regulate lung endoderm gene expression. These studies reveal that lncRNAs play an important role in foregut and lung endoderm development by regulating multiple aspects of gene transcription, often through regulation of transcription factor expression.
Collapse
Affiliation(s)
- Michael J Herriges
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daniel T Swarr
- Division of Neonatology, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | | - Edward E Morrisey
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Department of Medicine, Institute for Regenerative Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
364
|
Yan B, Wang ZH, Liu JY, Tao ZF, Li XM, Qin J. Long noncoding RNAs: versatile players in biologcial processes and human disorders. Epigenomics 2014; 6:375-9. [PMID: 25333847 DOI: 10.2217/epi.14.29] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Biao Yan
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Zhen-Hua Wang
- The Institute of Digital Ocean, College of InformationTechnology, Shanghai Ocean University, Shanghai, China
| | - Jing-Yu Liu
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Zhi-Fu Tao
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Xiu-Miao Li
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Jiang Qin
- Eye Hospital, Nanjing Medical University, Nanjing, China
| |
Collapse
|
365
|
Turner M, Galloway A, Vigorito E. Noncoding RNA and its associated proteins as regulatory elements of the immune system. Nat Immunol 2014; 15:484-91. [PMID: 24840979 DOI: 10.1038/ni.2887] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/01/2014] [Indexed: 12/11/2022]
Abstract
The rapid changes in gene expression that accompany developmental transitions, stress responses and proliferation are controlled by signal-mediated coordination of transcriptional and post-transcriptional mechanisms. In recent years, understanding of the mechanics of these processes and the contexts in which they are employed during hematopoiesis and immune challenge has increased. An important aspect of this progress is recognition of the importance of RNA-binding proteins and noncoding RNAs. These have roles in the development and function of the immune system and in pathogen life cycles, and they represent an important aspect of intracellular immunity.
Collapse
Affiliation(s)
- Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Alison Galloway
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Elena Vigorito
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| |
Collapse
|
366
|
Marguerat S, Lawler K, Brazma A, Bähler J. Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress. RNA Biol 2014; 11:702-14. [PMID: 25007214 PMCID: PMC4156502 DOI: 10.4161/rna.29196] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The cooperation of transcriptional and post-transcriptional levels of control to shape gene regulation is only partially understood. Here we show that a combination of two simple and non-invasive genomic techniques, coupled with kinetic mathematical modeling, afford insight into the intricate dynamics of RNA regulation in response to oxidative stress in the fission yeast Schizosaccharomyces pombe. This study reveals a dominant role of transcriptional regulation in response to stress, but also points to the first minutes after stress induction as a critical time when the coordinated control of mRNA turnover can support the control of transcription for rapid gene regulation. In addition, we uncover specialized gene expression strategies associated with distinct functional gene groups, such as simultaneous transcriptional repression and mRNA destabilization for genes encoding ribosomal proteins, delayed mRNA destabilization with varying contribution of transcription for ribosome biogenesis genes, dominant roles of mRNA stabilization for genes functioning in protein degradation, and adjustment of both transcription and mRNA turnover during the adaptation to stress. We also show that genes regulated independently of the bZIP transcription factor Atf1p are predominantly controlled by mRNA turnover, and identify putative cis-regulatory sequences that are associated with different gene expression strategies during the stress response. This study highlights the intricate and multi-faceted interplay between transcription and RNA turnover during the dynamic regulatory response to stress.
Collapse
Affiliation(s)
- Samuel Marguerat
- Department of Genetics, Evolution & Environment and UCL Cancer Institute; University College London; London, UK
| | - Katherine Lawler
- European Molecular Biology Laboratory; EMBL-EBI; Wellcome Trust Genome Campus; Hinxton, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory; EMBL-EBI; Wellcome Trust Genome Campus; Hinxton, UK
| | - Jürg Bähler
- Department of Genetics, Evolution & Environment and UCL Cancer Institute; University College London; London, UK
| |
Collapse
|
367
|
Wang L, Zhou D, Tu J, Wang Y, Lu Z. Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets. Biol Direct 2014; 9:15. [PMID: 24996425 PMCID: PMC4094694 DOI: 10.1186/1745-6150-9-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 07/01/2014] [Indexed: 12/15/2022] Open
Abstract
Background The stability of long intergenic non-coding RNAs (lincRNAs) that possess tissue/cell-specific expression, might be closely related to their physiological functions. However, the mechanism associated with stability of lincRNA remains elusive. In this study, we try to study the stability of lincRNA in K562 cells, an important model cell, through comparing two K562 transcriptomes which are obtained from ENCODE Consortium and our sequenced RNA-Seq dataset (PH) respectively. Results By lincRNAs analysis pipeline, 1804 high-confidence lincRNAs involving 1564 annotated lincRNAs and 240 putative novel lincRNAs were identified in PH, and 1587 high-confidence lincRNAs including 1429 annotated lincRNAs and 158 putative novel lincRNAs in ENCODE. There are 1009 unique lincRNAs in PH, 792 unique lincRNAs were in ENCODE, and 795 overlapping lincRNAs in both datasets. The analysis of differences in minimum free energy distribution and lincRNA half-life showed that a large proportion of overlapping lincRNAs were more stable than the unique lincRNAs. Most lincRNAs were more unstable than protein-coding RNAs through comparing their minimum free energy. Conclusions Identification of overlapping and unique lincRNAs can be helpful to classify the stability of lincRNAs. Our results suggest that overlapping lincRNAs (relatively stable linRNAs) and unique lincRNAs (relatively unstable lincRNAs) might be involved in different cellular processes. Reviewers This article has been reviewed by Prof. Oliviero Carugo, Dr. Alistair Forrest and Prof. Manju Bansal.
Collapse
Affiliation(s)
| | | | | | | | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Sipailou #2, Nanjing, Jiangsu Province 210096, China.
| |
Collapse
|
368
|
Johnson R, Guigó R. The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA (NEW YORK, N.Y.) 2014; 20:959-76. [PMID: 24850885 PMCID: PMC4114693 DOI: 10.1261/rna.044560.114] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Our genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which are likely to have genetic regulatory functions. It has been proposed that lncRNA are organized into combinations of discrete functional domains, but the nature of these and their identification remain elusive. One class of sequence elements that is enriched in lncRNA is represented by transposable elements (TEs), repetitive mobile genetic sequences that have contributed widely to genome evolution through a process termed exaptation. Here, we link these two concepts by proposing that exonic TEs act as RNA domains that are essential for lncRNA function. We term such elements Repeat Insertion Domains of LncRNAs (RIDLs). A growing number of RIDLs have been experimentally defined, where TE-derived fragments of lncRNA act as RNA-, DNA-, and protein-binding domains. We propose that these reflect a more general phenomenon of exaptation during lncRNA evolution, where inserted TE sequences are repurposed as recognition sites for both protein and nucleic acids. We discuss a series of genomic screens that may be used in the future to systematically discover RIDLs. The RIDL hypothesis has the potential to explain how functional evolution can keep pace with the rapid gene evolution observed in lncRNA. More practically, TE maps may in the future be used to predict lncRNA function.
Collapse
Affiliation(s)
- Rory Johnson
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
- Corresponding authorE-mail
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| |
Collapse
|
369
|
Zhang B, Gunawardane L, Niazi F, Jahanbani F, Chen X, Valadkhan S. A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA. Mol Cell Biol 2014; 34:2318-29. [PMID: 24732794 PMCID: PMC4054287 DOI: 10.1128/mcb.01673-13] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/06/2014] [Accepted: 04/03/2014] [Indexed: 12/14/2022] Open
Abstract
The ubiquitous presence of long noncoding RNAs (lncRNAs) in eukaryotes points to the importance of understanding how their sequences impact function. As many lncRNAs regulate nuclear events and thus must localize to nuclei, we analyzed the sequence requirements for nuclear localization in an intergenic lncRNA named BORG (BMP2-OP1-responsive gene), which is both spliced and polyadenylated but is strictly localized in nuclei. Subcellular localization of BORG was not dependent on the context or level of its expression or decay but rather depended on the sequence of the mature, spliced transcript. Mutational analyses indicated that nuclear localization of BORG was mediated through a novel RNA motif consisting of the pentamer sequence AGCCC with sequence restrictions at positions -8 (T or A) and -3 (G or C) relative to the first nucleotide of the pentamer. Mutation of the motif to a scrambled sequence resulted in complete loss of nuclear localization, while addition of even a single copy of the motif to a cytoplasmically localized RNA was sufficient to impart nuclear localization. Further, the presence of this motif in other cellular RNAs showed a direct correlation with nuclear localization, suggesting that the motif may act as a general nuclear localization signal for cellular RNAs.
Collapse
Affiliation(s)
- Bing Zhang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Lalith Gunawardane
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Farshad Niazi
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Fereshteh Jahanbani
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Xin Chen
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Saba Valadkhan
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| |
Collapse
|
370
|
Abstract
Discoveries over the past decade portend a paradigm shift in molecular biology. Evidence suggests that RNA is not only functional as a messenger between DNA and protein but also involved in the regulation of genome organization and gene expression, which is increasingly elaborate in complex organisms. Regulatory RNA seems to operate at many levels; in particular, it plays an important part in the epigenetic processes that control differentiation and development. These discoveries suggest a central role for RNA in human evolution and ontogeny. Here, we review the emergence of the previously unsuspected world of regulatory RNA from a historical perspective.
Collapse
Affiliation(s)
- Kevin V Morris
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John S Mattick
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; the School of Biotechnology and Biomedical Sciences, and St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
371
|
The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry 2014; 19:486-94. [PMID: 23628989 DOI: 10.1038/mp.2013.45] [Citation(s) in RCA: 319] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 02/08/2013] [Accepted: 03/18/2013] [Indexed: 02/08/2023]
Abstract
Schizophrenia (SZ) is a complex disease characterized by impaired neuronal functioning. Although defective alternative splicing has been linked to SZ, the molecular mechanisms responsible are unknown. Additionally, there is limited understanding of the early transcriptomic responses to neuronal activation. Here, we profile these transcriptomic responses and show that long non-coding RNAs (lncRNAs) are dynamically regulated by neuronal activation, including acute downregulation of the lncRNA Gomafu, previously implicated in brain and retinal development. Moreover, we demonstrate that Gomafu binds directly to the splicing factors QKI and SRSF1 (serine/arginine-rich splicing factor 1) and dysregulation of Gomafu leads to alternative splicing patterns that resemble those observed in SZ for the archetypal SZ-associated genes DISC1 and ERBB4. Finally, we show that Gomafu is downregulated in post-mortem cortical gray matter from the superior temporal gyrus in SZ. These results functionally link activity-regulated lncRNAs and alternative splicing in neuronal function and suggest that their dysregulation may contribute to neurological disorders.
Collapse
|
372
|
Liu Z, Li X, Sun N, Xu Y, Meng Y, Yang C, Wang Y, Zhang K. Microarray profiling and co-expression network analysis of circulating lncRNAs and mRNAs associated with major depressive disorder. PLoS One 2014; 9:e93388. [PMID: 24676134 PMCID: PMC3968145 DOI: 10.1371/journal.pone.0093388] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 03/04/2014] [Indexed: 12/22/2022] Open
Abstract
LncRNAs, which represent one of the most highly expressed classes of ncRNAs in the brain, are becoming increasingly interesting with regard to brain functions and disorders. However, changes in the expression of regulatory lncRNAs in Major Depressive Disorder (MDD) have not yet been reported. Using microarrays, we profiled the expression of 34834 lncRNAs and 39224 mRNAs in peripheral blood sampled from MDD patients as well as demographically-matched controls. Among these, we found that 2007 lncRNAs and 1667 mRNAs were differentially expressed, 17 of which were documented as depression-related gene in previous studies. Gene Ontology (GO) and pathway analyses indicated that the biological functions of differentially expressed mRNAs were related to fundamental metabolic processes and neurodevelopment diseases. To investigate the potential regulatory roles of the differentially expressed lncRNAs on the mRNAs, we also constructed co-expression networks composed of the lncRNAs and mRNAs, which shows significant correlated patterns of expression. In the MDD-derived network, there were a greater number of nodes and connections than that in the control-derived network. The lncRNAs located at chr10:874695-874794, chr10:75873456-75873642, and chr3:47048304-47048512 may be important factors regulating the expression of mRNAs as they have previously been reported associations with MDD. This study is the first to explore genome-wide lncRNA expression and co-expression with mRNA patterns in MDD using microarray technology. We identified circulating lncRNAs that are aberrantly expressed in MDD and the results suggest that lncRNAs may contribute to the molecular pathogenesis of MDD.
Collapse
Affiliation(s)
- Zhifen Liu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xinrong Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Ning Sun
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Yong Xu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Yaqin Meng
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Chunxia Yang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Yanfang Wang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Kerang Zhang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
- * E-mail:
| |
Collapse
|
373
|
Hall LL, Carone DM, Gomez AV, Kolpa HJ, Byron M, Mehta N, Fackelmayer FO, Lawrence JB. Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes. Cell 2014; 156:907-19. [PMID: 24581492 PMCID: PMC4023122 DOI: 10.1016/j.cell.2014.01.042] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 10/15/2013] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
Abstract
Recent studies recognize a vast diversity of noncoding RNAs with largely unknown functions, but few have examined interspersed repeat sequences, which constitute almost half our genome. RNA hybridization in situ using C0T-1 (highly repeated) DNA probes detects surprisingly abundant euchromatin-associated RNA comprised predominantly of repeat sequences (C0T-1 RNA), including LINE-1. C0T-1-hybridizing RNA strictly localizes to the interphase chromosome territory in cis and remains stably associated with the chromosome territory following prolonged transcriptional inhibition. The C0T-1 RNA territory resists mechanical disruption and fractionates with the nonchromatin scaffold but can be experimentally released. Loss of repeat-rich, stable nuclear RNAs from euchromatin corresponds to aberrant chromatin distribution and condensation. C0T-1 RNA has several properties similar to XIST chromosomal RNA but is excluded from chromatin condensed by XIST. These findings impact two "black boxes" of genome science: the poorly understood diversity of noncoding RNA and the unexplained abundance of repetitive elements.
Collapse
Affiliation(s)
- Lisa L Hall
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Dawn M Carone
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Alvin V Gomez
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Heather J Kolpa
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Nitish Mehta
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Frank O Fackelmayer
- Laboratory of Epigenetics and Chromosome Biology, Department of Biomedical Research, Institute for Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 45110 Ioannina, Greece
| | - Jeanne B Lawrence
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| |
Collapse
|
374
|
Witte S, Muljo SA. Integrating non-coding RNAs in JAK-STAT regulatory networks. JAKSTAT 2014; 3:e28055. [PMID: 24778925 PMCID: PMC3995732 DOI: 10.4161/jkst.28055] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 01/25/2014] [Accepted: 01/30/2014] [Indexed: 02/07/2023] Open
Abstract
Being a well-characterized pathway, JAK-STAT signaling serves as a valuable paradigm for studying the architecture of gene regulatory networks. The discovery of untranslated or non-coding RNAs, namely microRNAs and long non-coding RNAs, provides an opportunity to elucidate their roles in such networks. In principle, these regulatory RNAs can act as downstream effectors of the JAK-STAT pathway and/or affect signaling by regulating the expression of JAK-STAT components. Examples of interactions between signaling pathways and non-coding RNAs have already emerged in basic cell biology and human diseases such as cancer, and can potentially guide the identification of novel biomarkers or drug targets for medicine.
Collapse
Affiliation(s)
- Steven Witte
- Integrative Immunobiology Unit; Laboratory of Immunology; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, MD USA ; Wellcome Trust Sanger Institute; Genome Campus; Hinxton, UK
| | - Stefan A Muljo
- Integrative Immunobiology Unit; Laboratory of Immunology; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, MD USA
| |
Collapse
|
375
|
Bergmann JH, Spector DL. Long non-coding RNAs: modulators of nuclear structure and function. Curr Opin Cell Biol 2014; 26:10-18. [PMID: 24529241 PMCID: PMC3927160 DOI: 10.1016/j.ceb.2013.08.005] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 02/06/2023]
Abstract
Long non-coding (lnc)RNAs are emerging key factors in the regulation of various cellular processes. In the nucleus, these include the organization of nuclear sub-structures, the alteration of chromatin state, and the regulation of gene expression through the interaction with effector proteins and modulation of their activity. Collectively, lncRNAs form the core of attractive models explaining aspects of structural and dynamic regulation in the nucleus across time and space. Here we review recent studies that characterize the molecular function of a subset of these molecules in the regulation and fine-tuning of nuclear state.
Collapse
Affiliation(s)
- Jan H Bergmann
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
376
|
Wang Y, Pang WJ, Wei N, Xiong Y, Wu WJ, Zhao CZ, Shen QW, Yang GS. Identification, stability and expression of Sirt1 antisense long non-coding RNA. Gene 2014; 539:117-24. [PMID: 24480449 DOI: 10.1016/j.gene.2014.01.037] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/31/2013] [Accepted: 01/10/2014] [Indexed: 01/23/2023]
Abstract
Natural antisense transcripts (NATs) exist ubiquitously as pivotal molecules to regulate coding gene expression. Sirtuin 1 (Sirt1) is a NAD-dependent deacetylase which is involved in myogenesis. However, whether Sirt1 transcribes NAT during C2C12 differentiation is still unknown. In this study, we identified a Sirt1 NAT which was designated as Sirt1 antisense long non-coding RNA (AS lncRNA) by sequencing and bioinformatic analysis. The level of Sirt1 AS lncRNA was greater in spleen but less in muscle tissue. The expression of both Sirt1 mRNA and Sirt1 AS lncRNA decreased during C2C12 myogenic differentiation, whereas the levels of miR-34a, which targets Sirt1, increased gradually. We further found that the half-life of Sirt1 AS lncRNA was 10h, but that of Sirt1 mRNA was 6h in C2C12 cells treated with 2 μg/ml Actinomycin D. Therefore, compared with Sirt1 mRNA, Sirt1 AS lncRNA was more stable. Overexpression of Sirt1 AS lncRNA increased the levels of Sirt1 protein, whereas overexpression of Sirt1 AS lncRNA mutant did not affect the level of Sirt1 protein in C2C12 cells. Moreover, downregulation of Sirt1 mRNA caused by miR-34a was counteracted by Sirt1 AS lncRNA in C2C12 cells. Taken together, we identified a novel NAT of Sirt1 which implicated in myogenesis through regulating Sirt1 expression.
Collapse
Affiliation(s)
- Yu Wang
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China.
| | - Wei-Jun Pang
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China.
| | - Ning Wei
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Yan Xiong
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Wen-Jing Wu
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Cun-Zhen Zhao
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Qing-Wu Shen
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| | - Gong-She Yang
- College of Animal Science and Technology, Northwest A&F University, Laboratory of Animal Fat Deposition & Muscle Development, Yangling Shaanxi 712100, China
| |
Collapse
|
377
|
Novikova IV, Hennelly SP, Sanbonmatsu KY. Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure? BIOARCHITECTURE 2014; 2:189-99. [PMID: 23267412 PMCID: PMC3527312 DOI: 10.4161/bioa.22592] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) play a key role in many important areas of epigenetics, stem cell biology, cancer, signaling and brain function. This emerging class of RNAs constitutes a large fraction of the transcriptome, with thousands of new lncRNAs reported each year. The molecular mechanisms of these RNAs are not well understood. Currently, very little structural data exist. We review the available lncRNA sequence and secondary structure data. Since almost no tertiary information is available for lncRNAs, we review crystallographic structures for other RNA systems and discuss the possibilities for lncRNAs in the context of existing constraints.
Collapse
|
378
|
Flavell CR, Lambert EA, Winters BD, Bredy TW. Mechanisms governing the reactivation-dependent destabilization of memories and their role in extinction. Front Behav Neurosci 2013; 7:214. [PMID: 24421762 PMCID: PMC3872723 DOI: 10.3389/fnbeh.2013.00214] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/13/2013] [Indexed: 12/28/2022] Open
Abstract
The extinction of learned associations has traditionally been considered to involve new learning, which competes with the original memory for control over behavior. However, a recent resurgence of interest in reactivation-dependent amnesia has revealed that the retrieval of fear-related memory (with what is essentially a brief extinction session) can result in its destabilization. This review discusses some of the cellular and molecular mechanisms that are involved in the destabilization of a memory following its reactivation and/or extinction, and investigates the evidence that extinction may involve both new learning as well as a partial destabilization-induced erasure of the original memory trace.
Collapse
Affiliation(s)
- Charlotte R Flavell
- Queensland Brain Institute, The University of Queensland Brisbane, QLD, Australia
| | - Elliot A Lambert
- Queensland Brain Institute, The University of Queensland Brisbane, QLD, Australia
| | - Boyer D Winters
- Department of Psychology, University of Guelph Guelph, ON, Canada
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland Brisbane, QLD, Australia
| |
Collapse
|
379
|
Emerging epigenetic mechanisms of long non-coding RNAs. Neuroscience 2013; 264:25-38. [PMID: 24342564 DOI: 10.1016/j.neuroscience.2013.12.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 01/15/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been increasingly appreciated as an integral component of gene regulatory networks. Genome-wide features of their origin and expression patterns ascribed a prominent role for lncRNAs to the regulation of protein-coding genes, and also suggest a potential link to many human diseases. Recent studies have begun to unravel the intricate regulatory mechanism of lncRNAs occurring at multiple levels. The brain is one of the richest sources of lncRNAs, many of which have already shown a close relationship with genes or genetic loci implicated in a wide range of neurological disorders. This review describes recently emerging mechanistic principles of lncRNA functions to provide neuroscientists with molecular insights that will help future research on lncRNAs in the brain.
Collapse
|
380
|
Popadin K, Gutierrez-Arcelus M, Dermitzakis ET, Antonarakis SE. Genetic and epigenetic regulation of human lincRNA gene expression. Am J Hum Genet 2013; 93:1015-26. [PMID: 24268656 DOI: 10.1016/j.ajhg.2013.10.022] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/11/2013] [Accepted: 10/21/2013] [Indexed: 02/06/2023] Open
Abstract
Large intergenic noncoding RNAs (lincRNAs) are still poorly functionally characterized. We analyzed the genetic and epigenetic regulation of human lincRNA expression in the GenCord collection by using three cell types from 195 unrelated European individuals. We detected a considerable number of cis expression quantitative trait loci (cis-eQTLs) and demonstrated that the genetic regulation of lincRNA expression is independent of the regulation of neighboring protein-coding genes. lincRNAs have relatively more cis-eQTLs than do equally expressed protein-coding genes with the same exon number. lincRNA cis-eQTLs are located closer to transcription start sites (TSSs) and their effect sizes are higher than cis-eQTLs found for protein-coding genes, suggesting that lincRNA expression levels are less constrained than that of protein-coding genes. Additionally, lincRNA cis-eQTLs can influence the expression level of nearby protein-coding genes and thus could be considered as QTLs for enhancer activity. Enrichment of expressed lincRNA promoters in enhancer marks provides an additional argument for the involvement of lincRNAs in the regulation of transcription in cis. By investigating the epigenetic regulation of lincRNAs, we observed both positive and negative correlations between DNA methylation and gene expression (expression quantitative trait methylation [eQTMs]), as expected, and found that the landscapes of passive and active roles of DNA methylation in gene regulation are similar to protein-coding genes. However, lincRNA eQTMs are located closer to TSSs than are protein-coding gene eQTMs. These similarities and differences in genetic and epigenetic regulation between lincRNAs and protein-coding genes contribute to the elucidation of potential functions of lincRNAs.
Collapse
Affiliation(s)
- Konstantin Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva (iGE3), 1211 Geneva, Switzerland; Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow 127994, Russia
| | | | | | | |
Collapse
|
381
|
Huang JL, Zheng L, Hu YW, Wang Q. Characteristics of long non-coding RNA and its relation to hepatocellular carcinoma. Carcinogenesis 2013; 35:507-14. [PMID: 24296588 DOI: 10.1093/carcin/bgt405] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide with high prevalence and lethality. However, the underlying mechanism for HCC has not been entirely elucidated. Recent studies have highlighted the roles of long non-coding RNAs (lncRNAs) in carcinogenesis, and it is suggested that they might play critical roles in HCC progression. Here, we will briefly introduce the biology of lncRNAs, emphasizing the mechanisms and emerging roles of HCC-related lncRNAs. To date, HCC-related lncRNAs are demonstrated to influence the life cycle of genes by various means including epigenetic silencing, splicing regulation, lncRNA-miRNA interaction, lncRNA-protein interaction and genetic variation. Moreover, they can participate in diverse biological processes involved in HCC progression through impacts upon cell proliferation, apoptosis, invasion and metastasis and angiogenesis. Since lncRNA can present in body fluid and have good specificity and accessibility, some HCC-related lncRNAs are suggested to be useful as novel potential biomarkers for HCC diagnosis, prognosis and prediction of response to therapy. Those HCC-related lncRNAs may provide potential novel therapeutic targets for HCC and other diseases.
Collapse
Affiliation(s)
- Jin-Lan Huang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, 1838 Guangzhou Road, Guangzhou, Guangdong 510515, China
| | | | | | | |
Collapse
|
382
|
Schwarz TM, Volpe LAM, Abraham CG, Kulesza CA. Molecular investigation of the 7.2 kb RNA of murine cytomegalovirus. Virol J 2013; 10:348. [PMID: 24295514 PMCID: PMC4220806 DOI: 10.1186/1743-422x-10-348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/22/2013] [Indexed: 11/10/2022] Open
Abstract
Background HCMV encodes a stable 5 kb RNA of unknown function that is conserved across cytomegalovirus species. In vivo studies of the MCMV orthologue, a 7.2 kb RNA, demonstrated that viruses that do not express the RNA fail to establish efficient persistent replication in the salivary glands of mice. To gain further insight into the function and properties of this conserved locus, we characterized the MCMV intron in finer detail. Methods We performed multiple analyses to evaluate transcript expression kinetics, identify transcript termini and promoter elements. The half-lives of intron locus RNAs were quantified by measuring RNA levels following actinomycin D treatment in a qRT-PCR-based assay. We also constructed a series of recombinant viruses to evaluate protein coding potential in the locus and test the role of putative promoter elements. These recombinant viruses were tested in both in vitro and in vivo assays. Results We show that the 7.2 kb RNA is expressed with late kinetics during productive infection of mouse fibroblasts. The termini of the precursor RNA that is processed to produce the intron were identified and we demonstrate that the m106 open reading frame, which resides on the spliced mRNA derived from precursor processing, can be translated during infection. Mapping the 5′ end of the primary transcript revealed minimal promoter elements located upstream that contribute to transcript expression. Analysis of recombinant viruses with deletions in the putative promoter elements, however, revealed these elements exert only minor effects on intron expression and viral persistence in vivo. Low transcriptional output by the putative promoter element(s) is compensated by the long half-life of the 7.2 kb RNA of approximately 28.8 hours. Detailed analysis of viral spread prior to the establishment of persistence also showed that the intron is not likely required for efficient spread to the salivary gland, but rather enhances persistent replication in this tissue site. Conclusions This data provides a comprehensive transcriptional analysis of the MCMV 7.2 kb intron locus. Our studies indicate that the 7.2 kb RNA is an extremely long-lived RNA, a feature which is likely to be important in its role promoting viral persistence in the salivary gland.
Collapse
Affiliation(s)
| | | | | | - Caroline A Kulesza
- Department of Microbiology, University of Colorado School of Medicine, MS8333, 12800 E, 19th Ave, Aurora, Colorado 80045, USA.
| |
Collapse
|
383
|
Nguyen TT, Seoighe C. Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts. PLoS One 2013; 8:e79627. [PMID: 24260269 PMCID: PMC3832542 DOI: 10.1371/journal.pone.0079627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/03/2013] [Indexed: 11/19/2022] Open
Abstract
Genetic variation in gene expression makes an important contribution to phenotypic variation and susceptibility to disease. Recently, a subset of cis-acting expression quantitative loci (eQTLs) has been found to result from polymorphisms that affect RNA stability. Here we carried out a search for trans-acting variants that influence RNA stability. We first demonstrate that differences in the activity of trans-acting factors that stabilize RNA can be detected by comparing the expression levels of long-lived (stable) and short-lived (unstable) transcripts in high-throughput gene expression experiments. Using gene expression microarray data generated from eight HapMap3 populations, we calculated the relative expression ranks of long-lived transcripts versus short-lived transcripts in each sample. Treating this as a quantitative trait, we applied genome-wide association and identified a single nucleotide polymorphism (SNP), rs6137010, on chromosome 20p13 with which it is strongly associated in two Asian populations (p = 4×10−10 in CHB – Han Chinese from Beijing; p = 1×10−4 in JPT – Japanese from Tokyo). This SNP is a cis-eQTL for SNRPB in CHB and JPT but not in the other six HapMap3 populations. SNRPB is a core component of the spliceosome, and has previously been shown to affect the expression of many RNA processing factors. We propose that a cis-eQTL of SNRPB may be directly responsible for inter-individual variation in relative expression of long-lived versus short-lived transcript in Asian populations. In support of this hypothesis, knockdown of SNRPB results in a significant reduction in the relative expression of long-lived versus short-lived transcripts. Samples with higher relative expression of long-lived transcripts also had higher relative expression of coding compared to non-coding RNA and of RNA from housekeeping compared to non-housekeeping genes, due to the lower decay rates of coding RNAs, particularly those that perform housekeeping functions, compared to non-coding RNAs.
Collapse
Affiliation(s)
- Thong T. Nguyen
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Cathal Seoighe
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, Ireland
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
- * E-mail:
| |
Collapse
|
384
|
The Editors. Recent Developments in Cardiovascular Genetics. Circ Res 2013; 113:e88-91. [DOI: 10.1161/circresaha.113.302634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
385
|
Mathiyalagan P, Keating ST, Du XJ, El-Osta A. Interplay of chromatin modifications and non-coding RNAs in the heart. Epigenetics 2013; 9:101-12. [PMID: 24247090 DOI: 10.4161/epi.26405] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Precisely regulated patterns of gene expression are dependent on the binding of transcription factors and chromatin-associated determinants referred to as co-activators and co-repressors. These regulatory components function with the core transcriptional machinery to serve in critical activities to alter chromatin modification and regulate gene expression. While we are beginning to understand that cell-type specific patterns of gene expression are necessary to achieve selective cardiovascular developmental programs, we still do not know the molecular machineries that localize these determinants in the heart. With clear implications for the epigenetic control of gene expression signatures, the ENCODE (Encyclopedia of DNA Elements) Project Consortium determined that about 90% of the human genome is transcribed while only 1-2% of transcripts encode proteins. Emerging evidence suggests that non-coding RNA (ncRNA) serves as a signal for decoding chromatin modifications and provides a potential molecular basis for cell type-specific and promoter-specific patterns of gene expression. The discovery of the histone methyltransferase enzyme EZH2 in the regulation of gene expression patterns implicated in cardiac hypertrophy suggests a novel role for chromatin-associated ncRNAs and is the focus of this article.
Collapse
Affiliation(s)
- Prabhu Mathiyalagan
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia
| | - Samuel T Keating
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia
| | - Xiao-Jun Du
- Experimental Cardiology Laboratory; Baker IDI Heart and Diabetes Institute; Melbourne, VIC Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia; Epigenomics Profiling Facility; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia; Department of Pathology; The University of Melbourne; Melbourne, VIC Australia; Faculty of Medicine; Monash University; Melbourne, VIC Australia
| |
Collapse
|
386
|
Genome-wide analysis of human microRNA stability. BIOMED RESEARCH INTERNATIONAL 2013; 2013:368975. [PMID: 24187663 PMCID: PMC3804285 DOI: 10.1155/2013/368975] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/26/2013] [Indexed: 11/18/2022]
Abstract
Increasing studies have shown that microRNA (miRNA) stability plays important roles in physiology. However, the global picture of miRNA stability remains largely unknown. Here, we had analyzed genome-wide miRNA stability across 10 diverse cell types using miRNA arrays. We found that miRNA stability shows high dynamics and diversity both within individual cells and across cell types. Strikingly, we observed a negative correlation between miRNA stability and miRNA expression level, which is different from current findings on other biological molecules such as proteins and mRNAs that show positive and not negative correlations between stability and expression level. This finding indicates that miRNA has a distinct action mode, which we called "rapid production, rapid turnover; slow production, slow turnover." This mode further suggests that high expression miRNAs normally degrade fast and may endow the cell with special properties that facilitate cellular status-transition. Moreover, we revealed that the stability of miRNAs is affected by cohorts of factors that include miRNA targets, transcription factors, nucleotide content, evolution, associated disease, and environmental factors. Together, our results provided an extensive description of the global landscape, dynamics, and distinct mode of human miRNA stability, which provide help in investigating their functions in physiology and pathophysiology.
Collapse
|
387
|
Spies N, Burge CB, Bartel DP. 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res 2013; 23:2078-90. [PMID: 24072873 PMCID: PMC3847777 DOI: 10.1101/gr.156919.113] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Variation in protein output across the genome is controlled at several levels, but the relative contributions of different regulatory mechanisms remain poorly understood. Here, we obtained global measurements of decay and translation rates for mRNAs with alternative 3′ untranslated regions (3′ UTRs) in murine 3T3 cells. Distal tandem isoforms had slightly but significantly lower mRNA stability and greater translational efficiency than proximal isoforms on average. The diversity of alternative 3′ UTRs also enabled inference and evaluation of both positively and negatively acting cis-regulatory elements. The 3′ UTR elements with the greatest implied influence were microRNA complementary sites, which were associated with repression of 32% and 4% at the stability and translational levels, respectively. Nonetheless, both the decay and translation rates were highly correlated for proximal and distal 3′ UTR isoforms from the same genes, implying that in 3T3 cells, alternative 3′ UTR sequences play a surprisingly small regulatory role compared to other mRNA regions.
Collapse
Affiliation(s)
- Noah Spies
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | | | | |
Collapse
|
388
|
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
|
389
|
Tani H, Torimura M. Identification of short-lived long non-coding RNAs as surrogate indicators for chemical stress response. Biochem Biophys Res Commun 2013; 439:547-51. [PMID: 24036268 DOI: 10.1016/j.bbrc.2013.09.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/02/2013] [Indexed: 11/30/2022]
Abstract
Abiotic and biotic stressors in human cells are often a result of sudden and/or frequent changes in environmental factors. The molecular response to stress involves elaborate modulation of gene expression and is of homeostatic, ecological, and evolutionary importance. Although attention has primarily focused on signaling pathways and protein networks, long non-coding RNAs (ncRNAs) are increasingly involved in the molecular mechanisms associated with responses to cellular stresses. We identified six novel short-lived long ncRNAs (MIR22HG, GABPB-AS1, LINC00152, IDI2-AS1, SNHG15, and FLJ33630) that responded to chemical stressors (cisplatin, cycloheximide, and mercury (II) oxide) in HeLa Tet-off cells. Our results indicate that short-lived long ncRNAs respond to general and specific chemical stressors. The expression levels of the short-lived long ncRNAs were elevated because of prolonged decay rates in response to chemical stressors and interruption of RNA degradation pathways. We propose that these long ncRNAs have the potential to be surrogate indicators of cellular stress responses.
Collapse
Affiliation(s)
- Hidenori Tani
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1, Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
| | | |
Collapse
|
390
|
Smith MA, Gesell T, Stadler PF, Mattick JS. Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res 2013; 41:8220-36. [PMID: 23847102 PMCID: PMC3783177 DOI: 10.1093/nar/gkt596] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/29/2013] [Accepted: 06/16/2013] [Indexed: 12/14/2022] Open
Abstract
Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies >4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5-22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1. This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes.
Collapse
Affiliation(s)
- Martin A. Smith
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology; and Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany, Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent’s Clinical School, University of New South Wales, Level 5, de Lacy, Victoria St, St Vincent's Hospital, Sydney, NSW 2010 Australia
| | - Tanja Gesell
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology; and Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany, Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent’s Clinical School, University of New South Wales, Level 5, de Lacy, Victoria St, St Vincent's Hospital, Sydney, NSW 2010 Australia
| | - Peter F. Stadler
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology; and Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany, Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent’s Clinical School, University of New South Wales, Level 5, de Lacy, Victoria St, St Vincent's Hospital, Sydney, NSW 2010 Australia
| | - John S. Mattick
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology; and Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany, Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent’s Clinical School, University of New South Wales, Level 5, de Lacy, Victoria St, St Vincent's Hospital, Sydney, NSW 2010 Australia
| |
Collapse
|
391
|
Ilott NE, Ponting CP. Predicting long non-coding RNAs using RNA sequencing. Methods 2013; 63:50-9. [PMID: 23541739 DOI: 10.1016/j.ymeth.2013.03.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/12/2013] [Accepted: 03/19/2013] [Indexed: 02/01/2023] Open
Abstract
The advent of next-generation sequencing, and in particular RNA-sequencing (RNA-seq), technologies has expanded our knowledge of the transcriptional capacity of human and other animal, genomes. In particular, recent RNA-seq studies have revealed that transcription is widespread across the mammalian genome, resulting in a large increase in the number of putative transcripts from both within, and intervening between, known protein-coding genes. Long transcripts that appear to lack protein-coding potential (long non-coding RNAs, lncRNAs) have been the focus of much recent research, in part owing to observations of their cell-type and developmental time-point restricted expression patterns. A variety of sequencing protocols are currently available for identifying lncRNAs including RNA polymerase II occupancy, chromatin state maps and - the focus of this review - deep RNA sequencing. In addition, there are numerous analytical methods available for mapping reads and assembling transcript models that predict the presence and structure of lncRNAs from RNA-seq data. Here we review current methods for identifying lncRNAs using large-scale sequencing data from RNA-seq experiments and highlight analytical considerations that are required when undertaking such projects.
Collapse
Affiliation(s)
- Nicholas E Ilott
- CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, UK.
| | | |
Collapse
|
392
|
Spicuglia S, Maqbool MA, Puthier D, Andrau JC. An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function. Methods 2013; 63:3-17. [DOI: 10.1016/j.ymeth.2013.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/02/2013] [Accepted: 04/04/2013] [Indexed: 12/17/2022] Open
|
393
|
Dynamic nature of noncoding RNA regulation of adaptive immune response. Int J Mol Sci 2013; 14:17347-77. [PMID: 23975170 PMCID: PMC3794731 DOI: 10.3390/ijms140917347] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/30/2013] [Accepted: 08/12/2013] [Indexed: 02/06/2023] Open
Abstract
Immune response plays a fundamental role in protecting the organism from infections; however, dysregulation often occurs and can be detrimental for the organism, leading to a variety of immune-mediated diseases. Recently our understanding of the molecular and cellular networks regulating the immune response, and, in particular, adaptive immunity, has improved dramatically. For many years, much of the focus has been on the study of protein regulators; nevertheless, recent evidence points to a fundamental role for specific classes of noncoding RNAs (ncRNAs) in regulating development, activation and homeostasis of the immune system. Although microRNAs (miRNAs) are the most comprehensive and well-studied, a number of reports suggest the exciting possibility that long ncRNAs (lncRNAs) could mediate host response and immune function. Finally, evidence is also accumulating that suggests a role for miRNAs and other small ncRNAs in autocrine, paracrine and exocrine signaling events, thus highlighting an elaborate network of regulatory interactions mediated by different classes of ncRNAs during immune response. This review will explore the multifaceted roles of ncRNAs in the adaptive immune response. In particular, we will focus on the well-established role of miRNAs and on the emerging role of lncRNAs and circulating ncRNAs, which all make indispensable contributions to the understanding of the multilayered modulation of the adaptive immune response.
Collapse
|
394
|
Van Roosbroeck K, Pollet J, Calin GA. miRNAs and long noncoding RNAs as biomarkers in human diseases. Expert Rev Mol Diagn 2013; 13:183-204. [PMID: 23477558 DOI: 10.1586/erm.12.134] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) are transcripts that have no apparent protein-coding capacity; however, many ncRNAs have been found to play a major biological role in human physiology. Their deregulation is implicated in many human diseases, but their exact roles are only beginning to be elucidated. Nevertheless, ncRNAs are extensively studied as a novel source of biomarkers, and the fact that they can be detected in body fluids makes them extremely suitable for this purpose. The authors mainly focus on ncRNAs as biomarkers in cancer, but also touch on other human diseases such as cardiovascular diseases, autoimmune diseases, neurological disorders and infectious diseases. The authors discuss the established methods and provide a selection of emerging new techniques that can be used to detect and quantify ncRNAs. Finally, the authors discuss ncRNAs as a new strategy for therapeutic interventions.
Collapse
Affiliation(s)
- Katrien Van Roosbroeck
- Department of Experimental Therapeutics, Unit 1950, The University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, TX 77054, USA
| | | | | |
Collapse
|
395
|
Abstract
Understanding of the roles of noncoding RNAs (ncRNAs) within complex organisms has fundamentally changed. It is increasingly possible to use ncRNAs as diagnostic and therapeutic tools in medicine. Regarding disease pathogenesis, it has become evident that confinement to the analysis of protein-coding regions of the human genome is insufficient because ncRNA variants have been associated with important human diseases. Thus, inclusion of noncoding genomic elements in pathogenetic studies and their consideration as therapeutic targets is warranted. We consider aspects of the evolutionary and discovery history of ncRNAs, as far as they are relevant for the identification and selection of ncRNAs with likely therapeutic potential. Novel therapeutic strategies are based on ncRNAs, and we discuss here RNA interference as a highly versatile tool for gene silencing. RNA interference-mediating RNAs are small, but only parts of a far larger spectrum encompassing ncRNAs up to many kilobasepairs in size. We discuss therapeutic options in cardiovascular medicine offered by ncRNAs and key issues to be solved before clinical translation. Convergence of multiple technical advances is highlighted as a prerequisite for the translational progress achieved in recent years. Regarding safety, we review properties of RNA therapeutics, which may immunologically distinguish them from their endogenous counterparts, all of which underwent sophisticated evolutionary adaptation to specific biological contexts. Although our understanding of the noncoding human genome is only fragmentary to date, it is already feasible to develop RNA interference against a rapidly broadening spectrum of therapeutic targets and to translate this to the clinical setting under certain restrictions.
Collapse
Affiliation(s)
- Wolfgang Poller
- From the Department of Cardiology and Pneumology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Juliane Tank
- From the Department of Cardiology and Pneumology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Skurk
- From the Department of Cardiology and Pneumology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Martina Gast
- From the Department of Cardiology and Pneumology, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
396
|
Lv J, Cui W, Liu H, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y, Zhang Y, Wu Q. Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PLoS One 2013; 8:e71152. [PMID: 23967161 PMCID: PMC3743905 DOI: 10.1371/journal.pone.0071152] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.
Collapse
Affiliation(s)
- Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Wei Cui
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hongbo Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hongjuan He
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Youcheng Xiu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Jing Guo
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hui Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Qi Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Tiebo Zeng
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yan Chen
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
- * E-mail:
| |
Collapse
|
397
|
|
398
|
Tirosh Y, Ofer D, Eliyahu T, Linial M. Short toxin-like proteins attack the defense line of innate immunity. Toxins (Basel) 2013; 5:1314-31. [PMID: 23881252 PMCID: PMC3737499 DOI: 10.3390/toxins5071314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 01/30/2023] Open
Abstract
ClanTox (classifier of animal toxins) was developed for identifying toxin-like candidates from complete proteomes. Searching mammalian proteomes for short toxin-like proteins (coined TOLIPs) revealed a number of overlooked secreted short proteins with an abundance of cysteines throughout their sequences. We applied bioinformatics and data-mining methods to infer the function of several top predicted candidates. We focused on cysteine-rich peptides that adopt the fold of the three-finger proteins (TFPs). We identified a cluster of duplicated genes that share a structural similarity with elapid neurotoxins, such as α-bungarotoxin. In the murine proteome, there are about 60 such proteins that belong to the Ly6/uPAR family. These proteins are secreted or anchored to the cell membrane. Ly6/uPAR proteins are associated with a rich repertoire of functions, including binding to receptors and adhesion. Ly6/uPAR proteins modulate cell signaling in the context of brain functions and cells of the innate immune system. We postulate that TOLIPs, as modulators of cell signaling, may be associated with pathologies and cellular imbalance. We show that proteins of the Ly6/uPAR family are associated with cancer diagnosis and malfunction of the immune system.
Collapse
Affiliation(s)
- Yitshak Tirosh
- Department of Biological Chemistry, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | | | | | | |
Collapse
|
399
|
Long and short non-coding RNAs as regulators of hematopoietic differentiation. Int J Mol Sci 2013; 14:14744-70. [PMID: 23860209 PMCID: PMC3742271 DOI: 10.3390/ijms140714744] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/05/2013] [Accepted: 07/09/2013] [Indexed: 02/06/2023] Open
Abstract
Genomic analyses estimated that the proportion of the genome encoding proteins corresponds to approximately 1.5%, while at least 66% are transcribed, suggesting that many non-coding DNA-regions generate non-coding RNAs (ncRNAs). The relevance of these ncRNAs in biological, physiological as well as in pathological processes increased over the last two decades with the understanding of their implication in complex regulatory networks. This review particularly focuses on the involvement of two large families of ncRNAs, namely microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the regulation of hematopoiesis. To date, miRNAs have been widely studied, leading to a wealth of data about processing, regulation and mechanisms of action and more specifically, their involvement in hematopoietic differentiation. Notably, the interaction of miRNAs with the regulatory network of transcription factors is well documented whereas roles, regulation and mechanisms of lncRNAs remain largely unexplored in hematopoiesis; this review gathers current data about lncRNAs as well as both potential and confirmed roles in normal and pathological hematopoiesis.
Collapse
|
400
|
Perez P, Jang SI, Alevizos I. Emerging landscape of non-coding RNAs in oral health and disease. Oral Dis 2013; 20:226-35. [PMID: 23781896 DOI: 10.1111/odi.12142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022]
Abstract
The world of non-coding RNAs has only recently started being discovered. For the past 40 years, coding genes, mRNA, and proteins have been the center of cellular and molecular biology, and pathologic alterations were attributed to either the aberration of gene sequence or altered promoter activity. It was only after the completion of the human genome sequence that the scientific community started seriously wondering why only a very small portion of the genome corresponded to protein-coding genes. New technologies such as the whole-genome and whole-transcriptome sequencing demonstrated that at least 90% of the genome is actively transcribed. The identification and cataloguing of multiple kinds of non-coding RNA (ncRNA) have exponentially increased, and it is now widely accepted that ncRNAs play major biological roles in cellular physiology, development, metabolism, and are also implicated in a variety of diseases. The aim of this review is to describe the two major classes (long and short forms) of non-coding RNAs and describe their subclasses in terms of function and their relevance and potential in oral diseases.
Collapse
Affiliation(s)
- P Perez
- Sjögren's Clinic, Molecular Physiology & Therapeutics, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | | | | |
Collapse
|