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Analysis of Reverse Transcribed mRNA Using PCR and Polyacrylamide Gel Electrophoresis. Methods Mol Biol 2018. [PMID: 29423848 DOI: 10.1007/978-1-4939-7546-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The patterns of gene expression in the fission yeast Schizosaccharomyces pombe under various experimental conditions form the basis of any transcriptomic study. We describe a method involving reverse transcription of the mRNA, Polymerase Chain Reaction (PCR), and the subsequent separation of the products onto Urea-Polyacrylamide gel that can be used to study the gene expression patterns in the fission yeast. The method described is cost effective and reproducible with satisfactory resolution of expressed transcripts in the gel. The method has the following essential steps: total RNA isolation and purification, cDNA synthesis from mRNAs, PCR amplification of cDNAs, visualization of PCR products, re-amplification and cloning of the differentially expressed PCR products, sequencing the confirmed clones, and finally cDNA library screening to isolate the genes of interest. The technique is also popularly known as Differential Display Reverse Transcription (DDRT-PCR). After its invention in 1992, a number of modifications have been introduced to optimize the technique and specifically to reduce the major problem of "false positives." Since understanding of specific gene expression patterns that regulate developmental and stress responses is a major concern of biology, DDRT-PCR has become a very popular molecular technique during the past two decades.
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Gene expression profiling in zebrafish embryos exposed to diclofenac, an environmental toxicant. Mol Biol Rep 2011; 39:2119-28. [DOI: 10.1007/s11033-011-0959-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
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Samra HS, Gao F, He F, Hoang E, Chen Z, Gegenheimer PA, Berrie CL, Richter ML. Structural Analysis of the Regulatory Dithiol-containing Domain of the Chloroplast ATP Synthase γ Subunit. J Biol Chem 2006; 281:31041-9. [PMID: 16895914 DOI: 10.1074/jbc.m603315200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gamma subunit of the F1 portion of the chloroplast ATP synthase contains a critically placed dithiol that provides a redox switch converting the enzyme from a latent to an active ATPase. The switch prevents depletion of intracellular ATP pools in the dark when photophosphorylation is inactive. The dithiol is located in a special regulatory segment of about 40 amino acids that is absent from the gamma subunits of the eubacterial and mitochondrial enzymes. Site-directed mutagenesis was used to probe the relationship between the structure of the gamma regulatory segment and its function in ATPase regulation via its interaction with the inhibitory epsilon subunit. Mutations were designed using a homology model of the chloroplast gamma subunit based on the analogous structures of the bacterial and mitochondrial homologues. The mutations included (a) substituting both of the disulfide-forming cysteines (Cys199 and Cys205) for alanines, (b) deleting nine residues containing the dithiol, (c) deleting the region distal to the dithiol (residues 224-240), and (d) deleting the entire segment between residues 196 and 241 with the exception of a small spacer element, and (e) deleting pieces from a small loop segment predicted by the model to interact with the dithiol domain. Deletions within the dithiol domain and within parts of the loop segment resulted in loss of redox control of the ATPase activity of the F1 enzyme. Deleting the distal segment, the whole regulatory domain, or parts of the loop segment had the additional effect of reducing the maximum extent of inhibition obtained upon adding the epsilon subunit but did not abolish epsilon binding. The results suggest a mechanism by which the gamma and epsilon subunits interact with each other to induce the latent state of the enzyme.
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Affiliation(s)
- Hardeep S Samra
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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Chambers D, Mason I. A high throughput messenger RNA differential display screen identifies discrete domains of gene expression and novel patterning processes along the developing neural tube. BMC DEVELOPMENTAL BIOLOGY 2006; 6:9. [PMID: 16504111 PMCID: PMC1397802 DOI: 10.1186/1471-213x-6-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 02/24/2006] [Indexed: 11/15/2022]
Abstract
BACKGROUND During early development the vertebrate neural tube is broadly organized into the forebrain, midbrain, hindbrain and spinal cord regions. Each of these embryonic zones is patterned by a combination of genetic pathways and the influences of local signaling centres. However, it is clear that much remains to be learned about the complete set of molecular cues that are employed to establish the identity and intrinsic neuronal diversity of these territories. In order to address this, we performed a high-resolution messenger RNA differential display screen to identify molecules whose expression is regionally restricted along the anteroposterior (AP) neuraxis during early chick development, with particular focus on the midbrain and hindbrain vesicles. RESULTS This approach identified 44 different genes, with both known and unknown functions, whose transcription is differentially regulated along the AP axis. The identity and ontological classification of these genes is presented. The wide variety of functional classes of transcripts isolated in this screen reflects the diverse spectrum of known influences operating across these embryonic regions. Of these 44 genes, several have been selected for detailed in situ hybridization analysis to validate the screen and accurately define the expression domains. Many of the identified cDNAs showed no identity to the current databases of known or predicted genes or ESTs. Others represent genes whose embryonic expression has not been previously reported. Expression studies confirmed the predictions of the primary differential display data. Moreover, the nature of identified genes, not previously associated with regionalisation of the brain, identifies novel potential mechanisms in that process. CONCLUSION This study provides an insight into some of the varied and novel molecular networks that operate during the regionalization of embryonic neural tissue and expands our knowledge of molecular repertoire used during development.
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Affiliation(s)
- David Chambers
- MRC Centre for Developmental Neurobiology, 4Floor New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL, UK
- Wellcome Trust Functional Genomics Development Initiative, MRC Centre for Developmental Neurobiology, 4Floor New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Ivor Mason
- MRC Centre for Developmental Neurobiology, 4Floor New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL, UK
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Chen Y, Wang B, Weining S, Daggard G. Anchor primer associated problems in differential display reverse transcription polymerase chain reaction. Anal Biochem 2005; 329:145-7. [PMID: 15136178 DOI: 10.1016/j.ab.2004.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Indexed: 10/26/2022]
Affiliation(s)
- Yihua Chen
- Centre for Rural and Environmental Biotechnology, Faculty of Sciences, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia
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Bhogal RK, Mitchell AL, Coen CW. Identification of putative rat ribonuclease III by differential display: a novel rat mRNA expressed in a circadian manner in the rat suprachiasmatic nucleus. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 2004; 131:51-7. [PMID: 15530651 DOI: 10.1016/j.molbrainres.2004.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/27/2004] [Indexed: 05/01/2023]
Abstract
The suprachiasmatic nucleus (SCN) of the hypothalamus constitutes the principal site responsible for the generation and entrainment of circadian rhythms in mammals. The mechanisms of the circadian clock involve periodic gene expression. Here we report the use of differential display reverse transcriptase polymerase chain reaction to identify a novel rat mRNA sequence which is highly homologous to human ribonuclease III. Analysis of its expression in the rat brain by in situ hybridization histochemistry showed this transcript to be expressed at differing intensities at various sites. Temporal variation in expression was observed in the SCN, with a peak at circadian time (CT) 2 and a nadir at CT14. No significant changes in its expression were detected across the cycle within the supraoptic nucleus, cingulate cortex or caudate putamen.
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Affiliation(s)
- Ranjit K Bhogal
- School of Biomedical Sciences, King's College London, London SE1 1UL, UK
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Lorkowski S, Ellinghaus P, Galinski EA, Assmann G, Cullen P. Use of longer extension phases to improve yield of high molecular weight products in differential display PCR. Clin Chim Acta 2000; 299:199-204. [PMID: 10900305 DOI: 10.1016/s0009-8981(00)00292-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- S Lorkowski
- Institute of Arteriosclerosis Research, University of Münster, D-48149, Münster, Germany
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Newton RA, Bingham S, Davey PD, Medhurst AD, Piercy V, Raval P, Parsons AA, Sanger GJ, Case CP, Lawson SN. Identification of differentially expressed genes in dorsal root ganglia following partial sciatic nerve injury. Neuroscience 2000; 95:1111-20. [PMID: 10682718 DOI: 10.1016/s0306-4522(99)00515-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Partial sciatic nerve injury, a model of neuropathic pain, elicits a variety of neurochemical, electrophysiological and neuroanatomical changes in primary sensory neurons. We have used the technique of messenger RNA differential display to identify genes with altered expression in these neurons which may contribute to the development of aberrant sensation following such peripheral nerve damage. This approach identified 14 distinct complementary DNA clones, representing transcripts with increased ipsilateral expression in L4/5 dorsal root ganglia, two weeks after unilateral partial ligation of the rat sciatic nerve. Both Zucker diabetic fatty rats and their lean counterparts were used in this study but none of the transcripts identified showed an induction that was confined to one of the two groups. The majority of the clones did not show significant sequence similarity to previously reported genes and therefore may represent novel messenger RNA sequences or, alternatively, unknown regions of partially characterised messenger RNAs. Two of the clones represented transcripts for the known proteins muscle LIM protein and acidic epididymal glycoprotein, neither of which had previously been associated with expression in the nervous system. Reverse transcriptase-polymerase chain reaction analysis and in situ hybridization confirmed that the messenger RNA expression of both muscle LIM protein and acidic epididymal glycoprotein was induced in an ipsilateral-specific manner. Their localisations, examined with in situ hybridization in L5 dorsal root ganglia, were limited in each case to a sub-population of neuronal profiles. Those neuronal profiles that demonstrated muscle LIM protein hybridization were distributed across the profile size range, whereas the distribution of acidic epididymal glycoprotein-positive profiles appeared to be skewed towards smaller profiles. The induction of muscle LIM protein and acidic epididymal glycoprotein in dorsal root ganglia may play an important functional role in the adaptive response of primary sensory neurons following partial sciatic nerve injury.
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Affiliation(s)
- R A Newton
- Department of Physiology, The School of Medical Sciences, Bristol, UK
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Tucker WC, Du Z, Hein R, Richter ML, Gromet-Elhanan Z. Hybrid Rhodospirillum rubrum F(0)F(1) ATP synthases containing spinach chloroplast F(1) beta or alpha and beta subunits reveal the essential role of the alpha subunit in ATP synthesis and tentoxin sensitivity. J Biol Chem 2000; 275:906-12. [PMID: 10625626 DOI: 10.1074/jbc.275.2.906] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trace amounts ( approximately 5%) of the chloroplast alpha subunit were found to be absolutely required for effective restoration of catalytic function to LiCl-treated chromatophores of Rhodospirillum rubrum with the chloroplast beta subunit (Avital, S., and Gromet-Elhanan, Z. (1991) J. Biol. Chem. 266, 7067-7072). To clarify the role of the alpha subunit in the rebinding of beta, restoration of catalytic function, and conferral of sensitivity to the chloroplast-specific inhibitor tentoxin, LiCl-treated chromatophores were analyzed by immunoblotting before and after reconstitution with mixtures of R. rubrum and chloroplast alpha and beta subunits. The treated chromatophores were found to have lost, in addition to most of their beta subunits, approximately a third of the alpha subunits, and restoration of catalytic activity required rebinding of both subunits. The hybrid reconstituted with the R. rubrum alpha and chloroplast beta subunits was active in ATP synthesis as well as hydrolysis, and both activities were completely resistant to tentoxin. In contrast, a hybrid reconstituted with both chloroplast alpha and beta subunits restored only a MgATPase activity, which was fully inhibited by tentoxin. These results indicate that all three copies of the R. rubrum alpha subunit are required for proton-coupled ATP synthesis, whereas for conferral of tentoxin sensitivity at least one copy of the chloroplast alpha subunit is required together with the chloroplast beta subunit. The hybrid system was further used to examine the effects of amino acid substitution at position 83 of the beta subunit on sensitivity to tentoxin.
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Affiliation(s)
- W C Tucker
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Affiliation(s)
- K J Martin
- Dana-Farber Cancer Institute, Boston, Massachusetts 02113, USA
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von der Kammer H, Albrecht C, Mayhaus M, Hoffmann B, Stanke G, Nitsch RM. Identification of genes regulated by muscarinic acetylcholine receptors: application of an improved and statistically comprehensive mRNA differential display technique. Nucleic Acids Res 1999; 27:2211-8. [PMID: 10219095 PMCID: PMC148442 DOI: 10.1093/nar/27.10.2211] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In order to identify genes that are regulated by muscarinic acetylcholine receptors, we developed an mRNA differential display technique (DD) approach. By increasing redundancy and by evaluating optimised reagents and conditions for reverse transcription of total RNA, PCR and separation of PCR products, we generated a DD protocol that yields highly consistent results. A set of 64 distinct random primers was specifically designed in order to approach a statistically comprehensive analysis of all mRNA species in a defined cell population. This modified DD protocol was applied to total RNA of HEK293 cells stably expressing muscarinic m1 acetylcholine receptors and cells stimulated with the receptor agonist carbachol were compared to identical but non-stimulated cells. In 81 of 192 possible PCR experiments, 38 differential bands were identified. Sequence analysis followed by northern blot analyses confirmed differentially expressed genes in 19 of 23 bands analysed. These represented 10 distinct immediate-early genes that were up-regulated by m1AChR activation: Egr-1, Egr-2, Egr-3, NGFi-B, ETR101, c- jun, jun -D, Gos-3 and hcyr61, as well as the unknown gene Gig-2. These data show that this improved DD protocol can be readily applied to reliably identify differentially expressed genes.
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Affiliation(s)
- H von der Kammer
- Center for Molecular Neurobiology Hamburg, University of Hamburg, Martinistrasse 52, D-20246 Hamburg, Germany.
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Sokolov M, Lu L, Tucker W, Gao F, Gegenheimer PA, Richter ML. The 20 C-terminal amino acid residues of the chloroplast ATP synthase gamma subunit are not essential for activity. J Biol Chem 1999; 274:13824-9. [PMID: 10318787 DOI: 10.1074/jbc.274.20.13824] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It has been suggested that the last seven to nine amino acid residues at the C terminus of the gamma subunit of the ATP synthase act as a spindle for rotation of the gamma subunit with respect to the alpha beta subunits during catalysis (Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628). To test this hypothesis we selectively deleted C-terminal residues from the chloroplast gamma subunit, two at a time starting at the sixth residue from the end and finishing at the 20th residue from the end. The mutant gamma genes were overexpressed in Escherichia coli and assembled with a native alpha3beta3 complex. All the mutant forms of gamma assembled as effectively as the wild-type gamma. Deletion of the terminal 6 residues of gamma resulted in a significant increase (>50%) in the Ca-dependent ATPase activity when compared with the wild-type assembly. The increased activity persisted even after deletion of the C-terminal 14 residues, well beyond the seven residues proposed to form the spindle. Further deletions resulted in a decreased activity to approximately 19% of that of the wild-type enzyme after deleting all 20 C-terminal residues. The results indicate that the tip of the gammaC terminus is not essential for catalysis and raise questions about the role of the C terminus as a spindle for rotation.
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Affiliation(s)
- M Sokolov
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66045, USA
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Regazzoni C, Winterhalter KH, Rohrer L. Modified differential display technique to generate long cDNA fragments within the coding region. Anal Biochem 1999; 269:192-4. [PMID: 10094793 DOI: 10.1006/abio.1998.3066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- C Regazzoni
- Laboratory of Biochemistry, Swiss Federal Institute of Technology (ETH), Zurich, CH-8092, Switzerland
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Kang DC, LaFrance R, Su ZZ, Fisher PB. Reciprocal subtraction differential RNA display: an efficient and rapid procedure for isolating differentially expressed gene sequences. Proc Natl Acad Sci U S A 1998; 95:13788-93. [PMID: 9811879 PMCID: PMC24898 DOI: 10.1073/pnas.95.23.13788] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/1998] [Accepted: 09/22/1998] [Indexed: 11/18/2022] Open
Abstract
A reciprocal subtraction differential RNA display (RSDD) approach has been developed that permits the rapid and efficient identification and cloning of both abundant and rare differentially expressed genes. RSDD comprises reciprocal subtraction of cDNA libraries followed by differential RNA display. The RSDD strategy was applied to analyze the gene expression alterations resulting during cancer progression as adenovirus-transformed rodent cells developed an aggressive transformed state, as documented by elevated anchorage-independence and enhanced in vivo oncogenesis in nude mice. This approach resulted in the identification and cloning of both known and a high proportion (>65%) of unknown sequences, including cDNAs displaying elevated expression as a function of progression (progression-elevated gene) and cDNAs displaying suppressed expression as a function of progression (progression-suppressed gene). Sixteen differentially expressed genes, including five unknown progression-elevated genes and six unknown progression-suppressed genes, have been characterized. The RSDD scheme should find wide application for the effective detection and isolation of differentially expressed genes.
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Affiliation(s)
- D C Kang
- Departments of Neurosurgery, Pathology and Urology, Herbert Irving Comprehensive Cancer Center, Columbia University, College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA
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White MW, Radke JR. Methods to prepare RNA and to isolate developmentally regulated genes from Eimeria. Methods 1997; 13:158-70. [PMID: 9405199 DOI: 10.1006/meth.1997.0508] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Coccidians represent a large class of important intracellular parasites that traverse multiple developmental stages that are distinct and required to complete the life cycle. The biochemical details underlying the regulation of transformation from one developmental form to the next are limited and the study of such details presents unique obstacles. However, the genetic program is critical and may provide a basis for understanding the biology of these organisms in addition to the opportunity to suppress development and infection. We provide a basic overview of several strategies, including previously unpublished results, used by this laboratory to isolate stage-specific genes from Eimeria bovis. Additionally, we have included detailed discussions that summarize the associated advantages and disadvantages of each as applied to coccidia and potentially to other parasites in the phylum Apicomplexa. Given that the purification of sufficient quantities of high-quality RNA is vital, we have included detailed protocols for the isolation of RNA from various parasite stages. Also included is a detailed protocol to apply mRNA differential display to investigate stage-specific developmental regulation.
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Affiliation(s)
- M W White
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, 59717-0360, USA.
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