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Seal RL, Tweedie S, Bruford EA. A standardised nomenclature for long non-coding RNAs. IUBMB Life 2023; 75:380-389. [PMID: 35880706 PMCID: PMC9877250 DOI: 10.1002/iub.2663] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/08/2022] [Indexed: 01/29/2023]
Abstract
The HUGO Gene Nomenclature Committee (HGNC) is the sole group with the authority to approve symbols for human genes, including long non-coding RNA (lncRNA) genes. Use of approved symbols ensures that publications and biomedical databases are easily searchable and reduces the risks of confusion that can be caused by using the same symbol to refer to different genes or using many different symbols for the same gene. Here, we describe how the HGNC names lncRNA genes and review the nomenclature of the seven lncRNA genes most mentioned in the scientific literature.
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Affiliation(s)
- Ruth L. Seal
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
- Department of HaematologyUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Susan Tweedie
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
| | - Elspeth A. Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
- Department of HaematologyUniversity of Cambridge School of Clinical MedicineCambridgeUK
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2
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Rashid S, Shah S, Bar-Joseph Z, Pandya R. Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data. Bioinformatics 2021; 37:1535-1543. [PMID: 30768159 PMCID: PMC11025345 DOI: 10.1093/bioinformatics/btz095] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 01/18/2019] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION Intra-tumor heterogeneity is one of the key confounding factors in deciphering tumor evolution. Malignant cells exhibit variations in their gene expression, copy numbers and mutation even when originating from a single progenitor cell. Single cell sequencing of tumor cells has recently emerged as a viable option for unmasking the underlying tumor heterogeneity. However, extracting features from single cell genomic data in order to infer their evolutionary trajectory remains computationally challenging due to the extremely noisy and sparse nature of the data. RESULTS Here we describe 'Dhaka', a variational autoencoder method which transforms single cell genomic data to a reduced dimension feature space that is more efficient in differentiating between (hidden) tumor subpopulations. Our method is general and can be applied to several different types of genomic data including copy number variation from scDNA-Seq and gene expression from scRNA-Seq experiments. We tested the method on synthetic and six single cell cancer datasets where the number of cells ranges from 250 to 6000 for each sample. Analysis of the resulting feature space revealed subpopulations of cells and their marker genes. The features are also able to infer the lineage and/or differentiation trajectory between cells greatly improving upon prior methods suggested for feature extraction and dimensionality reduction of such data. AVAILABILITY AND IMPLEMENTATION All the datasets used in the paper are publicly available and developed software package and supporting info is available on Github https://github.com/MicrosoftGenomics/Dhaka. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sabrina Rashid
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15232, USA
| | - Sohrab Shah
- Department of Computer Science
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada
| | - Ziv Bar-Joseph
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15232, USA
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15232, USA
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Jia Y, Shi L, Yun F, Liu X, Chen Y, Wang M, Chen C, Ren Y, Bao Y, Wang L. Transcriptome sequencing profiles reveal lncRNAs may involve in breast cancer (ER/PR positive type) by interaction with RAS associated genes. Pathol Res Pract 2019; 215:152405. [PMID: 30981459 DOI: 10.1016/j.prp.2019.03.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/18/2019] [Accepted: 03/31/2019] [Indexed: 01/22/2023]
Abstract
To reveal novel lncRNAs and explore how could lncRNA affect the ER/PR positive type breast cancer, 16 different lncRNA transcriptomes (8 breast cancer tissues and 8 normal breast tissues) were successfully sequenced. In total, 8,954 high quality lncRNAs, including 5,516 lncRNAs reported in the previous studies and 3,438 novel lncRNAs, were annotated. The highest expressed lncRNAs were MALAT1, SCARNA10, RP11-206M11.7 and NEAT1, and the highest expressing mRNAs were RPL19, SCGB2A2, FTL and TMSB4 × . Of the 615 differentially expressed lncRNAs, 323 showed up regulated (P < 0.05) expression patterns in breast cancer, and 292 showed down regulated expression patterns. Of the 8,954 genes, 5,516 genes were upregulated in breast cancer, and 3,438 were downregulated. In total, the targets of 238 lncRNAs were confirmed by two lncRNA target prediction programs. Within these genes, Ras responsive element binding protein 1, Ras association domain family member 6, Ras association domain family member 8, Ras protein specific guanine nucleotide releasing factor 1and other 10 different Ras associated different expressed genes were predicted as targets of lncRNAs. These different expressed lncRNAs which could regulate the Ras gene families and ECM pathway may be another mechanism why the expression pattern of Ras genes changed in breast cancer. All these cancer-related genes (Ras genes) were annotated as targets of lncRNAs in the breast cancer transcriptome may provide us with a new way to understand the occurrence and development of breast cancer.
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Affiliation(s)
- Yongfeng Jia
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China; Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Lin Shi
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Fen Yun
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Xia Liu
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yongxia Chen
- Tumor Molecular Diagnostic Laboratory, The Inner Mongolia Cancer Hospital, Hohhot, Inner Mongolia, China
| | - Minjie Wang
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Chen Chen
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yanni Ren
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yulong Bao
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China.
| | - Li Wang
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China.
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Nakagawa S. Lessons from reverse-genetic studies of lncRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:177-83. [PMID: 26117798 DOI: 10.1016/j.bbagrm.2015.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 11/18/2022]
Abstract
The functions of long noncoding RNAs (lncRNAs) have mainly been studied using cultured cell lines, and this approach has revealed the involvement of lncRNAs in a variety of biological processes, including the epigenetic control of gene expression, post-transcriptional regulation of mRNA, and cellular proliferation and differentiation. Recently, increasing numbers of studies have investigated the functions of lncRNAs using gene-targeted model mice, largely confirming the physiological importance of lncRNA-mediated regulation in individual animals. In some cases, however, the results obtained by studies using knockout mice have been somewhat inconsistent with those of the preceding cell-based analyses. In this review, I will summarize the lessons that we are learning from the reverse-genetic studies of lncRNAs, namely the importance of noncoding DNA elements, the weak correlation between expression level and phenotypic prominence, the existence of tissue- and condition-specific phenotypes and incomplete penetrance, and the function of lncRNAs as precursor molecules. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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5
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Vikram R, Ramachandran R, Abdul KSM. Functional significance of long non-coding RNAs in breast cancer. Breast Cancer 2014; 21:515-21. [PMID: 25038622 DOI: 10.1007/s12282-014-0554-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 06/30/2014] [Indexed: 01/26/2023]
Abstract
Most of the genome is transcribed to transcripts of no protein-coding potential. However, these transcripts do not represent transcriptional 'noise', rather they play an important role in cellular metabolism and development. Non-coding transcripts of 200 bases to 100 kb length are termed as long non-coding RNAs, majority of which are yet to be characterised thoroughly. Long non-coding RNAs (lncRNAs) play a significant role in cellular process ranging from transcriptional to post-transcriptional regulation. In this review, we highlight the recent efforts to characterise the major functions of lncRNAs in breast cancer. lncRNA expression is altered in several cancer types. Further, the aberrant regulation of lncRNAs promotes tumour development as they are involved in several cancer-associated pathways.
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Affiliation(s)
- Rajeev Vikram
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, UK,
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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.
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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
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Ghorpade DS, Holla S, Sinha AY, Alagesan SK, Balaji KN. Nitric oxide and KLF4 protein epigenetically modify class II transactivator to repress major histocompatibility complex II expression during Mycobacterium bovis bacillus Calmette-Guerin infection. J Biol Chem 2013; 288:20592-606. [PMID: 23733190 DOI: 10.1074/jbc.m113.472183] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Pathogenic mycobacteria employ several immune evasion strategies such as inhibition of class II transactivator (CIITA) and MHC-II expression, to survive and persist in host macrophages. However, precise roles for specific signaling components executing down-regulation of CIITA/MHC-II have not been adequately addressed. Here, we demonstrate that Mycobacterium bovis bacillus Calmette-Guérin (BCG)-mediated TLR2 signaling-induced iNOS/NO expression is obligatory for the suppression of IFN-γ-induced CIITA/MHC-II functions. Significantly, NOTCH/PKC/MAPK-triggered signaling cross-talk was found critical for iNOS/NO production. NO responsive recruitment of a bifunctional transcription factor, KLF4, to the promoter of CIITA during M. bovis BCG infection of macrophages was essential to orchestrate the epigenetic modifications mediated by histone methyltransferase EZH2 or miR-150 and thus calibrate CIITA/MHC-II expression. NO-dependent KLF4 regulated the processing and presentation of ovalbumin by infected macrophages to reactive T cells. Altogether, our study delineates a novel role for iNOS/NO/KLF4 in dictating the mycobacterial capacity to inhibit CIITA/MHC-II-mediated antigen presentation by infected macrophages and thereby elude immune surveillance.
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Affiliation(s)
- Devram Sampat Ghorpade
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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Berretta R, Moscato P. Cancer biomarker discovery: the entropic hallmark. PLoS One 2010; 5:e12262. [PMID: 20805891 PMCID: PMC2923618 DOI: 10.1371/journal.pone.0012262] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 06/26/2010] [Indexed: 12/29/2022] Open
Abstract
Background It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-througput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases.
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Affiliation(s)
- Regina Berretta
- Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
- Information Based Medicine Program, Hunter Medical Research Institute, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Pablo Moscato
- Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
- Information Based Medicine Program, Hunter Medical Research Institute, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
- Australian Research Council Centre of Excellence in Bioinformatics, Callaghan, New South Wales, Australia
- * E-mail:
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Kim YH, Jyoti MA, Youn MH, Youn HS, Seo HS, Lee BT, Song HY. In vitro and in vivo evaluation of a macro porous β-TCP granule-shaped bone substitute fabricated by the fibrous monolithic process. Biomed Mater 2010; 5:35007. [PMID: 20460686 DOI: 10.1088/1748-6041/5/3/035007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this study, a new porous beta-tricalcium phosphate (β-TCP) granule was fabricated using the fibrous monolithic (FM) process and its in vitro biocompatibility and in vivo bone formation were evaluated. SEM micrograph images showed that MG-63 cells attached to the surfaces of the implant and were well proliferated. Cellular viability was as high as 75% in a50% extract dilution solution. cDNA micro array analysis was also carried out. In this analysis, we found a total of 12 up-regulated and 25 down-regulated genes. Four rabbits were used in the in vivo experiments. 3D micro-CT images showed that the formation of new bone was almost three times greater than that of normal trabecular bone (BV/TV). The histomorphometric results correlated with the micro-CT findings; a greater amount of new bone formation and osteoblast lineage along with osteocytes were observed in the implanted animals. Also x-ray radiographic and 2D micro-CT images were taken to demonstrate the superior biodegradability of the porous granule. As biodegradation occurred along with bone formation, 6 months after implantation, the porous granule structure was not distinguishable separately from that of the trabecular bone.
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Affiliation(s)
- Young-Hee Kim
- Department of Immunology, School of Medicine, Soonchunhyang University, Cheonan, Chungnum 330-090, Korea
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10
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Functional genomic analysis of peripheral blood during early acute renal allograft rejection. Transplantation 2010; 88:942-51. [PMID: 19935467 DOI: 10.1097/tp.0b013e3181b7ccc6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Acute graft rejection is an important clinical problem in renal transplantation and an adverse predictor for long-term graft survival. Peripheral blood biomarkers that provide evidence of early graft rejection may offer an important option for posttransplant monitoring, optimize the utility of graft biopsy, and permit timely and effective therapeutic intervention to minimize the graft damage. METHODS In this feasibility study (n=58), we have used gene expression profiling in a case-control design to compare whole blood samples between normal subjects (n=20) and patients with (n=11) or without (n=22) biopsy-confirmed acute rejection (BCAR) or borderline changes (n=5). RESULTS A total of 183 probe sets representing 160 genes were differentially expressed (false discovery rate [FDR] <0.01) between subjects with or without BCAR, from which linear discriminant analysis and cross-validation identified an initial gene signature of 24 probe sets, and a more refined set of 11 probe sets found to classify subject samples correctly. Cross-validation suggested an out-of-sample sensitivity of 73% and specificity of 91% for identification of samples with or without BCAR. An increase in classifier gene expression correlated closely with acute rejection during the first 3 months posttransplant. Biological evaluation indicated that the differentially expressed genes encompassed processes related to immune response, signal transduction, and cytoskeletal reorganization. CONCLUSION Preliminary evidence indicates that gene expression in the peripheral blood may yield a relevant measure for the occurrence of BCAR and offer a potential tool for immunologic monitoring. These results now require confirmation in a larger cohort.
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Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε. ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2010. [DOI: 10.1007/978-3-642-15060-9_1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A 2009; 106:2525-30. [PMID: 19188602 DOI: 10.1073/pnas.0807899106] [Citation(s) in RCA: 479] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent transcriptome analyses have shown that thousands of noncoding RNAs (ncRNAs) are transcribed from mammalian genomes. Although the number of functionally annotated ncRNAs is still limited, they are known to be frequently retained in the nucleus, where they coordinate regulatory networks of gene expression. Some subnuclear organelles or nuclear bodies include RNA species whose identity and structural roles are largely unknown. We identified 2 abundant overlapping ncRNAs, MENepsilon and MENbeta (MENepsilon/beta), which are transcribed from the corresponding site in the multiple endocrine neoplasia (MEN) I locus and which localize to nuclear paraspeckles. This finding raises the intriguing possibility that MENepsilon/beta are involved in paraspeckle organization, because paraspeckles are, reportedly, RNase-sensitive structures. Successful removal of MENepsilon/beta by a refined knockdown method resulted in paraspeckle disintegration. Furthermore, the reassembly of paraspeckles disassembled by transcriptional arrest appeared to be unsuccessful in the absence of MENepsilon/beta. RNA interference and immunoprecipitation further revealed that the paraspeckle proteins p54/nrb and PSF selectively associate with and stabilize the longer MENbeta, thereby contributing to the organization of the paraspeckle structure. The paraspeckle protein PSP1 is not directly involved in either MENepsilon/beta stabilization or paraspeckle organization. We postulate a model for nuclear paraspeckle body organization where specific ncRNAs and RNA-binding proteins cooperate to maintain and, presumably, establish the structure.
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MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 2008; 19:347-59. [PMID: 19106332 DOI: 10.1101/gr.087775.108] [Citation(s) in RCA: 517] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Studies of the transcriptional output of the human and mouse genomes have revealed that there are many more transcripts produced than can be accounted for by predicted protein-coding genes. Using a custom microarray, we have identified 184 non-coding RNAs that exhibit more than twofold up- or down-regulation upon differentiation of C2C12 myoblasts into myotubes. Here, we focus on the Men epsilon/beta locus, which is up-regulated 3.3-fold during differentiation. Two non-coding RNA isoforms are produced from a single RNA polymerase II promoter, differing in the location of their 3' ends. Men epsilon is a 3.2-kb polyadenylated RNA, whereas Men beta is an approximately 20-kb transcript containing a genomically encoded poly(A)-rich tract at its 3'-end. The 3'-end of Men beta is generated by RNase P cleavage. The Men epsilon/beta transcripts are localized to nuclear paraspeckles and directly interact with NONO. Knockdown of MEN epsilon/beta expression results in the disruption of nuclear paraspeckles. Furthermore, the formation of paraspeckles, after release from transcriptional inhibition by DRB treatment, was suppressed in MEN epsilon/beta-depleted cells. Our findings indicate that the MEN epsilon/beta non-coding RNAs are essential structural/organizational components of paraspeckles.
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Abstract
Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.
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Tang Z, Li Y, Wan P, Li X, Zhao S, Liu B, Fan B, Zhu M, Yu M, Li K. LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs. Genome Biol 2008; 8:R115. [PMID: 17573972 PMCID: PMC2394763 DOI: 10.1186/gb-2007-8-6-r115] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 01/30/2007] [Accepted: 06/16/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Obese and lean pig breeds show obvious differences in muscle growth; however, the molecular mechanism underlying phenotype variation remains unknown. Prenatal muscle development programs postnatal performance. Here, we describe a genome-wide analysis of differences in prenatal skeletal muscle between Tongcheng (a typical indigenous Chinese breed) and Landrace (a leaner Western breed) pigs. RESULTS We generated transcriptome profiles of skeletal muscle from Tongcheng and Landrace pigs at 33, 65 and 90 days post coitus (dpc), using long serial analysis of gene expression (LongSAGE). We sequenced 317,115 LongSAGE tags and identified 1,400 and 1,201 differentially expressed transcripts during myogenesis in Tongcheng and Landrace pigs, respectively. From these, the Gene Ontology processes and expression patterns of these differentially expressed genes were constructed. Most of the genes showed different expression patterns in the two breeds. We also identified 532, 653 and 459 transcripts at 33, 65 and 90 dpc, respectively, that were differentially expressed between the two breeds. Growth factors, anti-apoptotic factors and genes involved in the regulation of protein synthesis were up-regulated in Landrace pigs. Finally, 12 differentially expressed genes were validated by quantitative PCR. CONCLUSION Our data show that gene expression phenotypes differ significantly between the two breeds. In particular, a slower muscle growth rate and more complicated molecular changes were found in Tongcheng pigs, while genes responsible for increased cellular growth and myoblast survival were up-regulated in Landrace pigs. Our analyses will assist in the identification of candidate genes for meat production traits and elucidation of the development of prenatal skeletal muscle in mammals.
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Affiliation(s)
- Zhonglin Tang
- Department of Gene and Cell Engineering, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100094, PR China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yong Li
- Department of Gene and Cell Engineering, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100094, PR China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ping Wan
- Shanghai Huaguan Biochip Co. Ltd, Shanghai, 201203, PR China
- Life and Environment Science College, Shanghai Normal University, Shanghai, 200234, PR China
| | - Xiaoping Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shuhong Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Bang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Bin Fan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mengjin Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mei Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Kui Li
- Department of Gene and Cell Engineering, State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100094, PR China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education of China, Huazhong Agricultural University, Wuhan 430070, PR China
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Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 2007; 8:39. [PMID: 17270048 PMCID: PMC1800850 DOI: 10.1186/1471-2164-8-39] [Citation(s) in RCA: 761] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Accepted: 02/01/2007] [Indexed: 01/03/2023] Open
Abstract
Background Noncoding RNA species play a diverse set of roles in the eukaryotic cell. While much recent attention has focused on smaller RNA species, larger noncoding transcripts are also thought to be highly abundant in mammalian cells. To search for large noncoding RNAs that might control gene expression or mRNA metabolism, we used Affymetrix expression arrays to identify polyadenylated RNA transcripts displaying nuclear enrichment. Results This screen identified no more than three transcripts; XIST, and two unique noncoding nuclear enriched abundant transcripts (NEAT) RNAs strikingly located less than 70 kb apart on human chromosome 11: NEAT1, a noncoding RNA from the locus encoding for TncRNA, and NEAT2 (also known as MALAT-1). While the two NEAT transcripts share no significant homology with each other, each is conserved within the mammalian lineage, suggesting significant function for these noncoding RNAs. NEAT2 is extraordinarily well conserved for a noncoding RNA, more so than even XIST. Bioinformatic analyses of publicly available mouse transcriptome data support our findings from human cells as they confirm that the murine homologs of these noncoding RNAs are also nuclear enriched. RNA FISH analyses suggest that these noncoding RNAs function in mRNA metabolism as they demonstrate an intimate association of these RNA species with SC35 nuclear speckles in both human and mouse cells. These studies show that one of these transcripts, NEAT1 localizes to the periphery of such domains, whereas the neighboring transcript, NEAT2, is part of the long-sought polyadenylated component of nuclear speckles. Conclusion Our genome-wide screens in two mammalian species reveal no more than three abundant large non-coding polyadenylated RNAs in the nucleus; the canonical large noncoding RNA XIST and NEAT1 and NEAT2. The function of these noncoding RNAs in mRNA metabolism is suggested by their high levels of conservation and their intimate association with SC35 splicing domains in multiple mammalian species.
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Affiliation(s)
- John N Hutchinson
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge St., Boston, MA-02114, USA
| | - Alexander W Ensminger
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge St., Boston, MA-02114, USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA-02139, USA
| | - Christine M Clemson
- Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Christopher R Lynch
- Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Andrew Chess
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge St., Boston, MA-02114, USA
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17
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Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 2007; 8:39. [PMID: 17270048 DOI: 10.1186/1471-1-2164-8-39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Accepted: 02/01/2007] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Noncoding RNA species play a diverse set of roles in the eukaryotic cell. While much recent attention has focused on smaller RNA species, larger noncoding transcripts are also thought to be highly abundant in mammalian cells. To search for large noncoding RNAs that might control gene expression or mRNA metabolism, we used Affymetrix expression arrays to identify polyadenylated RNA transcripts displaying nuclear enrichment. RESULTS This screen identified no more than three transcripts; XIST, and two unique noncoding nuclear enriched abundant transcripts (NEAT) RNAs strikingly located less than 70 kb apart on human chromosome 11: NEAT1, a noncoding RNA from the locus encoding for TncRNA, and NEAT2 (also known as MALAT-1). While the two NEAT transcripts share no significant homology with each other, each is conserved within the mammalian lineage, suggesting significant function for these noncoding RNAs. NEAT2 is extraordinarily well conserved for a noncoding RNA, more so than even XIST. Bioinformatic analyses of publicly available mouse transcriptome data support our findings from human cells as they confirm that the murine homologs of these noncoding RNAs are also nuclear enriched. RNA FISH analyses suggest that these noncoding RNAs function in mRNA metabolism as they demonstrate an intimate association of these RNA species with SC35 nuclear speckles in both human and mouse cells. These studies show that one of these transcripts, NEAT1 localizes to the periphery of such domains, whereas the neighboring transcript, NEAT2, is part of the long-sought polyadenylated component of nuclear speckles. CONCLUSION Our genome-wide screens in two mammalian species reveal no more than three abundant large non-coding polyadenylated RNAs in the nucleus; the canonical large noncoding RNA XIST and NEAT1 and NEAT2. The function of these noncoding RNAs in mRNA metabolism is suggested by their high levels of conservation and their intimate association with SC35 splicing domains in multiple mammalian species.
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Affiliation(s)
- John N Hutchinson
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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18
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Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA, Moreira YB, El-Jundi TA, da Silva AM, Reis EM, Verjovski-Almeida S. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol 2007; 8:R43. [PMID: 17386095 PMCID: PMC1868932 DOI: 10.1186/gb-2007-8-3-r43] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 01/17/2007] [Accepted: 03/26/2007] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND RNAs transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression. However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known. RESULTS A survey of mRNA and EST public databases revealed more than 55,000 totally intronic noncoding (TIN) RNAs transcribed from the introns of 74% of all unique RefSeq genes. Guided by this information, we designed an oligoarray platform containing sense and antisense probes for each of 7,135 randomly selected TIN transcripts plus the corresponding protein-coding genes. We identified exonic and intronic tissue-specific expression signatures for human liver, prostate and kidney. The most highly expressed antisense TIN RNAs were transcribed from introns of protein-coding genes significantly enriched (p = 0.002 to 0.022) in the 'Regulation of transcription' Gene Ontology category. RNA polymerase II inhibition resulted in increased expression of a fraction of intronic RNAs in cell cultures, suggesting that other RNA polymerases may be involved in their biosynthesis. Members of a subset of intronic and protein-coding signatures transcribed from the same genomic loci have correlated expression patterns, suggesting that intronic RNAs regulate the abundance or the pattern of exon usage in protein-coding messages. CONCLUSION We have identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles. This gene-oriented approach, using a combined intron-exon oligoarray, should permit further comparative analysis of intronic transcription under various physiological and pathological conditions, thus advancing current knowledge about the biological functions of these noncoding RNAs.
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Affiliation(s)
- Helder I Nakaya
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Paulo P Amaral
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Rodrigo Louro
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - André Lopes
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Angela A Fachel
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Yuri B Moreira
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Tarik A El-Jundi
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Aline M da Silva
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Eduardo M Reis
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Sergio Verjovski-Almeida
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
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Wright KL, Ting JPY. Epigenetic regulation of MHC-II and CIITA genes. Trends Immunol 2006; 27:405-12. [PMID: 16870508 DOI: 10.1016/j.it.2006.07.007] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 06/23/2006] [Accepted: 07/12/2006] [Indexed: 02/02/2023]
Abstract
This review describes recent advances in understanding how epigenetic events control MHC-class-II-family (MHC-II) gene expression. To address this issue, two phases of gene transcription have to be considered. First, the control of MHC-II by chromatin-modifying events such as histone acetylation, methylation, deacetylation, ubiquitination and the interplay between these different epigenetic events will be examined. The interactions of chromatin-modifying enzymes with class II transactivator (CIITA) and relevant DNA-binding proteins for activating and silencing MHC-II gene transcription will be reviewed. Second, the transcriptional control of the promoter of CIITA, the master regulator of MHC-II, by DNA methylation and chromatin modification will be discussed, and the novel role of noncoding RNA will be explored. Finally, the relevance of these findings to infection, transplantation and cancer will be reviewed.
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Affiliation(s)
- Kenneth L Wright
- H. Lee Moffitt Cancer Center and Research Institute, and the Department of Interdisciplinary Oncology, University of South Florida, Tampa, FL 33612, USA.
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20
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Timmons JA, Larsson O, Jansson E, Fischer H, Gustafsson T, Greenhaff PL, Ridden J, Rachman J, Peyrard-Janvid M, Wahlestedt C, Sundberg CJ. Human muscle gene expression responses to endurance training provide a novel perspective on Duchenne muscular dystrophy. FASEB J 2005; 19:750-60. [PMID: 15857889 DOI: 10.1096/fj.04-1980com] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Global gene expression profiling is used to generate novel insight into a variety of disease states. Such studies yield a bewildering number of data points, making it a challenge to validate which genes specifically contribute to a disease phenotype. Aerobic exercise training represents a plausible model for identification of molecular mechanisms that cause metabolic-related changes in human skeletal muscle. We carried out the first transcriptome-wide characterization of human skeletal muscle responses to 6 wk of supervised aerobic exercise training in 8 sedentary volunteers. Biopsy samples before and after training allowed us to identify approximately 470 differentially regulated genes using the Affymetrix U95 platform (80 individual hybridization steps). Gene ontology analysis indicated that extracellular matrix and calcium binding gene families were most up-regulated after training. An electronic reanalysis of a Duchenne muscular dystrophy (DMD) transcript expression dataset allowed us to identify approximately 90 genes modulated in a nearly identical fashion to that observed in the endurance exercise dataset. Trophoblast noncoding RNA, an interfering RNA species, was the singular exception-being up-regulated by exercise and down-regulated in DMD. The common overlap between gene expression datasets may be explained by enhanced alpha7beta1 integrin signaling, and specific genes in this signaling pathway were up-regulated in both datasets. In contrast to these common features, OXPHOS gene expression is subdued in DMD yet elevated by exercise, indicating that more than one major mechanism must exist in human skeletal muscle to sense activity and therefore regulate gene expression. Exercise training modulated diabetes-related genes, suggesting our dataset may contain additional and novel gene expression changes relevant for the anti-diabetic properties of exercise. In conclusion, gene expression profiling after endurance exercise training identified a range of processes responsible for the physiological remodeling of human skeletal muscle tissue, many of which were similarly regulated in DMD. Furthermore, our analysis demonstrates that numerous genes previously suggested as being important for the DMD disease phenotype may principally reflect compensatory integrin signaling.
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Affiliation(s)
- James A Timmons
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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Ranella A, Vassiliadis S, Mastora C, Valentina M, Dionyssopoulou E, Athanassakis I. Constitutive intracellular expression of human leukocyte antigen (HLA)-DO and HLA-DR but not HLA-DM in trophoblast cells. Hum Immunol 2005; 66:43-55. [PMID: 15620461 DOI: 10.1016/j.humimm.2004.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 10/05/2004] [Accepted: 10/07/2004] [Indexed: 11/19/2022]
Abstract
The nonclassic human leukocyte antigen (HLA)-DM molecules have been proved to positively regulate antigen presentation in classic antigen-presenting cells, whereas in B lymphocytes HLA-DO have been identified as negative regulators of the process. The present report examines whether the negative expression of classic class II molecules in trophoblasts implies negative regulation by HLA-DO. It was revealed by immunofluorescence, confocal microscopy, and subcellular fractionation techniques that human trophoblasts, although not expressing any surface HLA-DR antigens, constitutively express intracellular HLA-DR, HLA-DO, and CD74, but not HLA-DM. Administration of interferon-gamma to the cell culture increased HLA-DR and CD74, induced HLA-DM, but did not alter the expression of HLA-DO and induced HLA-DR release from the cells. These results were confirmed by reverse transcriptase-polymerase chain reaction analysis except that HLA-DM mRNA was detected in control cells, indicating a posttranscriptional regulation. Under the same experimental conditions, human monocytes/macrophages were not expressing intracellular HLA-DO while exhibiting significant levels of HLA-DR, HLA-DM, and CD74. The results presented here reveal for the first time expression of HLA-DO in trophoblasts, which can be of great importance in maintaining the class II-negative state in these cells and consequently protecting the fetus from maternal immune attack.
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Affiliation(s)
- Anthi Ranella
- Department of Biology, Laboratory of Immunology, University of Crete, Heraklion, Crete, Greece
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22
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Geirsson A, Bothwell ALM, Hammond GL. Inhibition of alloresponse by a human trophoblast non-coding RNA suppressing class II transactivator promoter III and major histocompatibility class II expression in murine B-lymphocytes. J Heart Lung Transplant 2004; 23:1077-81. [PMID: 15454174 DOI: 10.1016/j.healun.2004.07.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 06/28/2004] [Accepted: 07/04/2004] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Trophoblasts are a model of natural allograft tolerance. A unique characteristic is the complete lack of expression of all classic major histocompatibility (MHC) antigens. We cloned a human trophoblast non-coding RNA (TncRNA) that suppresses MHC class II expression through inhibition of the class II transactivator (CIITA) promoter. We assessed the functional affects of TncRNA on an alloresponse and dissected the functional domain on CIITA promoter III. METHODS Murine B-cell line A20 was transfected with TncRNA. Class II suppressed clones were selected and characterized by flow cytometry and Northern analysis. The clones were then subjected to lymphocyte proliferation assay to assess the stimulation of T-lymphocytes. CIITA promoter III-luciferase reporter plasmids were used with TncRNA plasmids in co-transfection assays; 5'-end deletion plasmids were used to dissect the promoter. RESULTS Significant suppression of I-Ad expression was seen. Northern blot scans demonstrated 84% to 93% suppression of class II transcripts. Lymphocyte proliferation assay demonstrated a 50% and 64% inhibition of lymphocyte stimulation in the 2 clones, compared to A20 wild type. Dissection of promoter III indicated that an area between bp -152 to -107 contains the functional site of TncRNA. CONCLUSION Human TncRNA is active across species lines and significantly inhibits allogenic response to B-cells. There is concurrent suppression of constitutive class II expression in TncRNA clones mediated through a defined region of CIITA promoter III.
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Affiliation(s)
- Arnar Geirsson
- Department of Surgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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23
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Murphy SP, Choi JC, Holtz R. Regulation of major histocompatibility complex class II gene expression in trophoblast cells. Reprod Biol Endocrinol 2004; 2:52. [PMID: 15236650 PMCID: PMC479700 DOI: 10.1186/1477-7827-2-52] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2004] [Accepted: 07/05/2004] [Indexed: 11/18/2022] Open
Abstract
Trophoblast cells are unique because they are one of the few mammalian cell types that do not express major histocompatibility complex (MHC) class II antigens, either constitutively or after exposure to IFN-gamma. The absence of MHC class II antigen expression on trophoblast cells has been postulated to be one of the essential mechanisms by which the semi-allogeneic fetus evades immune rejection reactions by the maternal immune system. Consistent with this hypothesis, trophoblast cells from the placentas of women suffering from chronic inflammation of unknown etiology and spontaneous recurrent miscarriages have been reported to aberrantly express MHC class II antigens. The lack of MHC class II antigen expression on trophoblast cells is due to silencing of expression of the class II transactivator (CIITA), a transacting factor that is essential for constitutive and IFN-gamma-inducible MHC class II gene transcription. Transfection of trophoblast cells with CIITA expression vectors activates both MHC class II and class Ia antigen expression, which confers on trophoblast cells both the ability to activate helper T cells, and sensitivity to lysis by cytotoxic T lymphocytes. Collectively, these studies strongly suggest that stringent silencing of CIITA (and therefore MHC class II) gene expression in trophoblast cells is critical for the prevention of immune rejection responses against the fetus by the maternal immune system. The focus of this review is to summarize studies examining the novel mechanisms by which CIITA is silenced in trophoblast cells. The elucidation of the silencing of CIITA in trophoblast cells may shed light on how the semi-allogeneic fetus evades immune rejection by the maternal immune system during pregnancy.
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Affiliation(s)
- Shawn P Murphy
- Department of Immunology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Jason C Choi
- Department of Immunology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Renae Holtz
- Department of Immunology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
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