1
|
[Letter to the Editor] Accelerated RNA-RNA hybridization by concentrated guanidinium thiocyanate solution in single-step RNA isolation. Biotechniques 2016; 61:61-5. [PMID: 27528070 DOI: 10.2144/000114441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/09/2016] [Indexed: 11/23/2022] Open
Abstract
Address correspondence to Mart Speek, Department of Gene Technology, Akadeemia tee 15, Room 129, Tallinn University of Technology, Tallinn 19086, Estonia. E-mail: mart.speek@ttu.ee.
Collapse
|
2
|
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: 28] [Impact Index Per Article: 2.5] [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
|
3
|
Castillo AF, Fan J, Papadopoulos V, Podestá EJ. Hormone-dependent expression of a steroidogenic acute regulatory protein natural antisense transcript in MA-10 mouse tumor Leydig cells. PLoS One 2011; 6:e22822. [PMID: 21829656 PMCID: PMC3148237 DOI: 10.1371/journal.pone.0022822] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/03/2011] [Indexed: 01/17/2023] Open
Abstract
Cholesterol transport is essential for many physiological processes, including steroidogenesis. In steroidogenic cells hormone-induced cholesterol transport is controlled by a protein complex that includes steroidogenic acute regulatory protein (StAR). Star is expressed as 3.5-, 2.8-, and 1.6-kb transcripts that differ only in their 3′-untranslated regions. Because these transcripts share the same promoter, mRNA stability may be involved in their differential regulation and expression. Recently, the identification of natural antisense transcripts (NATs) has added another level of regulation to eukaryotic gene expression. Here we identified a new NAT that is complementary to the spliced Star mRNA sequence. Using 5′ and 3′ RACE, strand-specific RT-PCR, and ribonuclease protection assays, we demonstrated that Star NAT is expressed in MA-10 Leydig cells and steroidogenic murine tissues. Furthermore, we established that human chorionic gonadotropin stimulates Star NAT expression via cAMP. Our results show that sense-antisense Star RNAs may be coordinately regulated since they are co-expressed in MA-10 cells. Overexpression of Star NAT had a differential effect on the expression of the different Star sense transcripts following cAMP stimulation. Meanwhile, the levels of StAR protein and progesterone production were downregulated in the presence of Star NAT. Our data identify antisense transcription as an additional mechanism involved in the regulation of steroid biosynthesis.
Collapse
Affiliation(s)
- Ana Fernanda Castillo
- Department of Human Biochemistry, School of Medicine, Instituto de Investigaciones Moleculares de Enfermedades Hormonales Neurodegenerativas y Oncológicas (IIMHNO), University of Buenos Aires, Buenos Aires, Argentina
| | - Jinjiang Fan
- Department of Medicine and The Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Vassilios Papadopoulos
- Department of Medicine and The Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Ernesto J. Podestá
- Department of Human Biochemistry, School of Medicine, Instituto de Investigaciones Moleculares de Enfermedades Hormonales Neurodegenerativas y Oncológicas (IIMHNO), University of Buenos Aires, Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
4
|
Lai J, Lehman ML, Dinger ME, Hendy SC, Mercer TR, Seim I, Lawrence MG, Mattick JS, Clements JA, Nelson CC. A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells. RNA (NEW YORK, N.Y.) 2010; 16:1156-1166. [PMID: 20406994 PMCID: PMC2874168 DOI: 10.1261/rna.2019810] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Accepted: 02/18/2010] [Indexed: 05/29/2023]
Abstract
In humans, more than 30,000 chimeric transcripts originating from 23,686 genes have been identified. The mechanisms and association of chimeric transcripts arising from chromosomal rearrangements with cancer are well established, but much remains unknown regarding the biogenesis and importance of other chimeric transcripts that arise from nongenomic alterations. Recently, a SLC45A3-ELK4 chimera has been shown to be androgen-regulated, and is overexpressed in metastatic or high-grade prostate tumors relative to local prostate cancers. Here, we characterize the expression of a KLK4 cis sense-antisense chimeric transcript, and show other examples in prostate cancer. Using non-protein-coding microarray analyses, we initially identified an androgen-regulated antisense transcript within the 3' untranslated region of the KLK4 gene in LNCaP cells. The KLK4 cis-NAT was validated by strand-specific linker-mediated RT-PCR and Northern blotting. Characterization of the KLK4 cis-NAT by 5' and 3' rapid amplification of cDNA ends (RACE) revealed that this transcript forms multiple fusions with the KLK4 sense transcript. Lack of KLK4 antisense promoter activity using reporter assays suggests that these transcripts are unlikely to arise from a trans-splicing mechanism. 5' RACE and analyses of deep sequencing data from LNCaP cells treated +/-androgens revealed six high-confidence sense-antisense chimeras of which three were supported by the cDNA databases. In this study, we have shown complex gene expression at the KLK4 locus that might be a hallmark of cis sense-antisense chimeric transcription.
Collapse
Affiliation(s)
- John Lai
- Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology and Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Lee TL, Pang ALY, Rennert OM, Chan WY. Genomic landscape of developing male germ cells. BIRTH DEFECTS RESEARCH. PART C, EMBRYO TODAY : REVIEWS 2009; 87:43-63. [PMID: 19306351 PMCID: PMC2939912 DOI: 10.1002/bdrc.20147] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Spermatogenesis is a highly orchestrated developmental process by which spermatogonia develop into mature spermatozoa. This process involves many testis- or male germ cell-specific gene products whose expressions are strictly regulated. In the past decade the advent of high-throughput gene expression analytical techniques has made functional genomic studies of this process, particularly in model animals such as mice and rats, feasible and practical. These studies have just begun to reveal the complexity of the genomic landscape of the developing male germ cells. Over 50% of the mouse and rat genome are expressed during testicular development. Among transcripts present in germ cells, 40% - 60% are uncharacterized. A number of genes, and consequently their associated biological pathways, are differentially expressed at different stages of spermatogenesis. Developing male germ cells present a rich repertoire of genetic processes. Tissue-specific as well as spermatogenesis stage-specific alternative splicing of genes exemplifies the complexity of genome expression. In addition to this layer of control, discoveries of abundant presence of antisense transcripts, expressed psuedogenes, non-coding RNAs (ncRNA) including long ncRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and retrogenes all point to the presence of multiple layers of expression and functional regulation in male germ cells. It is anticipated that application of systems biology approaches will further our understanding of the regulatory mechanism of spermatogenesis.
Collapse
Affiliation(s)
- Tin-Lap Lee
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alan Lap-Yin Pang
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Owen M. Rennert
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Wai-Yee Chan
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Department of Pediatrics, Georgetown University College of Medicine, Washington, DC
| |
Collapse
|
6
|
Voigtsberger S, Bartsch H, Baumann G, Luther HP. Cell type-specific expression of endogenous cardiac Troponin I antisense RNA in the neonatal rat heart. Mol Cell Biochem 2009; 324:1-11. [PMID: 19184367 DOI: 10.1007/s11010-008-9974-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 11/28/2008] [Indexed: 01/14/2023]
Abstract
Since the number of detected natural antisense RNA is growing, investigations upon the expression pattern of the antisense RNA become more important. As we focused our work on natural occurring antisense transcripts in human and rat heart tissues, we were interested in the question, whether the expression pattern of antisense and sense RNA can vary in different cell types of the same tissue. In our previous analysis of total neonatal rat heart tissue, we demonstrated the co-expression of both cTnI RNA species in this tissue. Now we investigated the expression of antisense and sense RNA quantitatively in neonatal cardiomyocytes (NCMs) and neonatal cardiac fibroblasts (NCFs). Performing northern blot as well as RT-PCR, we could detect natural antisense and sense RNA transcripts of cTnI in NCM and NCF implying that these transcripts are co-expressed in both cell types. The absolute amounts of the RNA transcripts were higher in NCM. Both RNA species showed identical sizes in the northern blot. Quantification by real-time PCR revealed a higher relative level of natural antisense RNA in NCF compared to NCM which points out to a cell type-specific expression of sense and antisense RNA. Our observations suggest that antisense RNA transcription may contribute to a cell type-specific regulation of the cTnI gene.
Collapse
Affiliation(s)
- Stefanie Voigtsberger
- Medizinische Klinik mit Schwerpunkt Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany
| | | | | | | |
Collapse
|
7
|
Chan WY, Wu SM, Ruszczyk L, Law E, Lee TL, Baxendale V, Lap-Yin Pang A, Rennert OM. The complexity of antisense transcription revealed by the study of developing male germ cells. Genomics 2006; 87:681-92. [PMID: 16458478 DOI: 10.1016/j.ygeno.2005.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2005] [Revised: 11/24/2005] [Accepted: 12/13/2005] [Indexed: 11/29/2022]
Abstract
Computational analyses have identified the widespread occurrence of antisense transcripts in the human and the mouse genome. However, the structure and the origin of the majority of the antisense transcripts are unknown. The presence of antisense transcripts for 19 of 64 differentially expressed genes during mouse spermatogenesis was demonstrated with orientation-specific RT-PCR. These antisense transcripts were derived from a wide variety of origins, including processed sense transcripts, intronic and exonic sequences of a single gene or multiple genes, intergenic sequences, and pseudogenes. They underwent normal and alternative splicing, 5' capping, and 3' polyadenylation, similar to the sense transcripts. There were also antisense transcripts that were not capped and/or polyadenylated. The testicular levels of the sense transcripts were higher than those of the antisense transcripts in all cases, while the relative expression in nontesticular tissues was variable. Thus antisense transcripts have complex origins and structures and the sense and antisense transcripts can be regulated independently.
Collapse
Affiliation(s)
- Wai-Yee Chan
- Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Building 49, Room 2A08, 49 Convent Drive, MSC 4429, Bethesda, MD 20892-4429, USA.
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Richards M, Tan SP, Chan WK, Bongso A. Reverse Serial Analysis of Gene Expression (SAGE) Characterization of Orphan SAGE Tags from Human Embryonic Stem Cells Identifies the Presence of Novel Transcripts and Antisense Transcription of Key Pluripotency Genes. Stem Cells 2006; 24:1162-73. [PMID: 16456128 DOI: 10.1634/stemcells.2005-0304] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Serial analysis of gene expression (SAGE) is a powerful technique for the analysis of gene expression. A significant portion of SAGE tags, designated as orphan tags, however, cannot be reliably assigned to known transcripts. We used an improved reverse SAGE (rSAGE) strategy to convert human embryonic stem cell (hESC)-specific orphan SAGE tags into longer 3' cDNAs. We show that the systematic analysis of these 3' cDNAs permitted the discovery of hESC-specific novel transcripts and cis-natural antisense transcripts (cis-NATs) and improved the assignment of SAGE tags that resulted from splice variants, insertion/deletion, and single-nucleotide polymorphisms. More importantly, this is the first description of cis-NATs for several key pluripotency markers in hESCs and mouse embryonic stem cells, suggesting that the formation of short interfering RNA could be an important regulatory mechanism. A systematic large-scale analysis of the remaining orphan SAGE tags in the hESC SAGE libraries by rSAGE or other 3' cDNA extension strategies should unravel additional novel transcripts and cis-NATs that are specifically expressed in hESCs. Besides contributing to the complete catalog of human transcripts, many of them should prove to be a valuable resource for the elucidation of the molecular pathways involved in the self-renewal and lineage commitment of hESCs.
Collapse
Affiliation(s)
- Mark Richards
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | | | | | | |
Collapse
|
9
|
Yan MD, Hong CC, Lai GM, Cheng AL, Lin YW, Chuang SE. Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Hum Mol Genet 2005; 14:1465-74. [PMID: 15829500 DOI: 10.1093/hmg/ddi156] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Apoptosis is a morphologically distinct form of cell death involved in many physiological and pathological processes. The regulation of Fas/Apo-1 involved in membrane-mediated apoptosis has also been known to play crucial roles in many systems. More and more naturally occurring antisense RNAs are now known to regulate, at least in part, a growing number of eukaryotic genes. In this report, we describe the findings of a novel RNA transcribed from the opposite strand of the intron 1 of the human Fas gene. Using orientation-specific RT-PCR and northern blot analysis, we show that this transcript is 1.5 kb in length and was expressed in several human tissues and cell lines. This transcript was cloned by 5'- and 3'-RACE (rapid amplification of cDNA ends) and the transcription start site was determined by primer extension. This novel gene was named Saf. To assess the functions of Saf, Jurkat cells transfected with human Saf or control vector was prepared. The stable Saf-transfectant was highly resistant to Fas-mediated but not to TNF-alpha-mediated apoptosis. Although the overall mRNA expression level of Fas was not affected, expression of some novel forms of Fas transcripts was increased in Saf-transfectant, especially the inhibitory soluble forms. These findings collectively suggest that Saf might protect T lymphocytes from Fas-mediated apoptosis by blocking the binding of FasL or its agonistic Fas antibody. Saf might regulate the expression of Fas alternative splice forms through pre-mRNA processing.
Collapse
Affiliation(s)
- Ming-De Yan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
| | | | | | | | | | | |
Collapse
|
10
|
Gräf S, Borisova BE, Nellen W, Steger G, Hammann C. A database search for double-strand containing RNAs in Dictyostelium discoideum. Biol Chem 2005; 385:961-5. [PMID: 15551871 DOI: 10.1515/bc.2004.125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In eukaryotic cells, double-stranded RNA is degraded to 21mers and triggers RNA interference. Using a pattern description language, we have searched the EMBL database for sequences with the potential to form double strands in cis in Dictyostelium discoideum. No extended inverted repeats were found in mRNAs. However, the antisense direction of some mRNAs encoding regulatory or developmentally regulated proteins showed the ability to form double-stranded regions. In EST archives, we found potential double strands derived from a few genes, but these transcripts are not continuously encoded in the genome. Most likely, they represent hybrid molecules of sense and antisense RNAs.
Collapse
Affiliation(s)
- Stefan Gräf
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | | | | | | | | |
Collapse
|
11
|
Luther HP. Role of endogenous antisense RNA in cardiac gene regulation. J Mol Med (Berl) 2004; 83:26-32. [PMID: 15592803 DOI: 10.1007/s00109-004-0613-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Accepted: 10/21/2004] [Indexed: 11/24/2022]
Abstract
Endogenous antisense RNA has been detected for a range of eukaryotic genes and now appears to be a common phenomenon in mammalian cells. Its abundance compared to levels of its complementary sense mRNA indicates that antisense RNA may be involved in posttrancriptional regulation of a gene. In general a downregulating effect on gene expression has been demonstrated or suggested. Due to the heterogeneity in origin and character of different antisense transcripts alternative functions such as stabilizing the corresponding sense transcript and being part of gene recombination must be considered. Regulation by endogenous antisense RNA has been shown for a plethora of genes, including cardiac genes, such as myosin heavy chainMHC, atrial light chain, and troponin I. There is now growing evidence that antisense transcription is involved in human disease, and it is reasonable to consider antisense as a target for intervention procedures. Here we review the progress in our understanding of as well as the controversies arising from investigating the regulatory mechanisms of antisense RNA, with special focus on cardiac genes. Finally, links between antisense transcription and heart disease and the possible use of antisense as a target of cardiac intervention procedures are discussed.
Collapse
Affiliation(s)
- Hans Peter Luther
- Medical Clinic I, Department of Cardiology, Humboldt University, Charité Hospital, Ziegelstrasse 5-9, 10117 Berlin, Germany.
| |
Collapse
|