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Yadav RK, Barbi F, Ziller A, Luis P, Marmeisse R, Reddy MS, Fraissinet-Tachet L. Construction of sized eukaryotic cDNA libraries using low input of total environmental metatranscriptomic RNA. BMC Biotechnol 2014; 14:80. [PMID: 25183040 PMCID: PMC4170940 DOI: 10.1186/1472-6750-14-80] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/21/2014] [Indexed: 11/25/2022] Open
Abstract
Background Construction of high quality cDNA libraries from the usually low amounts of eukaryotic mRNA extracted from environmental samples is essential in functional metatranscriptomics for the selection of functional, full-length genes encoding proteins of interest. Many of the inserts in libraries constructed by standard methods are represented by truncated cDNAs due to premature stoppage of reverse transcriptase activity and preferential cloning of short cDNAs. Results We report here a simple and cost effective technique for preparation of sized eukaryotic cDNA libraries from as low as three microgram of total soil RNA dominated by ribosomal and bacterial RNA. cDNAs synthesized by a template switching approach were size-fractionated by two dimensional agarose gel electrophoresis prior to PCR amplification and cloning. Effective size selection was demonstrated by PCR amplification of conserved gene families specific of each size class. Libraries of more than one million independent inserts whose sizes ranged between one and four kb were thus produced. Up to 80% of the insert sequences were homologous to eukaryotic gene sequences present in public databases. Conclusions A simple and cost effective technique has been developed to construct sized eukaryotic cDNA libraries from environmental samples. This technique will facilitate expression cloning of environmental eukaryotic genes and contribute to a better understanding of basic biological and/or ecological processes carried out by eukaryotic microbial communities.
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Affiliation(s)
- Rajiv Kumar Yadav
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Lyon 1, Université de Lyon, Villeurbanne, France.
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KE T, DONG CH, MAO H, ZHAO YZ, LIU HY, LIU SY. Construction of a Normalized Full-Length cDNA Library of Sesame Developing Seed by DSN and SMART™. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/s1671-2927(11)60087-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Construction and characterization of a cDNA library from wheat infected with Fusarium graminearum Fg 2. Int J Mol Sci 2011; 12:613-26. [PMID: 21340003 PMCID: PMC3039969 DOI: 10.3390/ijms12010613] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/14/2011] [Accepted: 01/17/2011] [Indexed: 11/16/2022] Open
Abstract
Total RNA from wheat spikes infected with F. graminearum Fg2 was extracted and the mRNA was purified. Switching Mechanism at 5′ end of the RNA Transcript (SMART) technique and CDS Ill/3′ primer were used for first-strand cDNA synthesis using reverse transcriptase by RT-PCR. Primer extension polymerase chain reaction was used to construct the double-strand cDNA that was digested by proteinase K, then by Sfi I and fractionated. cDNAs longer than 0.5 kb were collected and ligated to λTriplEx2 vector followed λ phage packaging reaction and library amplification. The qualities of both unamplified and amplified cDNA libraries were strictly checked by conventional titer determination. One hundred and sixty five plaques were randomly picked and tested using PCR with universal primers derived from the sequence flanking the vector. A high quality cDNA library from wheat spikes that have been infected by F. graminearum was successfully constructed.
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Abstract
Eukaryotes using trans-splicing for transcript processing incorporate a taxon-specific sequence tag (the spliced leader, SL) to a proportion (either all or a fraction) of their mRNAs. This feature may be exploited for the preparation of full-length-enriched cDNA libraries from these organisms (a diverse group including euglenozoa and dinoflagellates, as well as members from five metazoan phyla: Cnidaria, Rotifera, Nematoda, Platyhelminths and Chordata). The strategy has indeed been widely used to construct cDNA libraries for the generation of ESTs, mainly from parasitic euglenozoa and helminths.We describe a set of optimised protocols to prepare directional SL-cDNA libraries; the method involves PCR-amplification of SL-cDNA and its subsequent cloning in a plasmid vector under a specific orientation. It uses small amounts of total RNA as starting material and may be applied to a variety of samples. The approach permits the selective cloning of mRNAs tagged with a particular SL from mixtures including large amounts of non-trans-spliced mRNAs. Thus, it allows exclusion of host contamination when isolating SL-cDNAs from parasitic organisms, and has other potential applications, such as the characterisation of the trans-spliced transcriptome from organisms in mixed pools of species.
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Affiliation(s)
- Cecilia Fernández
- Facultad de Química, Universidad de la República, Montevideo, Uruguay
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Gao PF, Cao GQ, Zhao HT, Zhang GX, Jiang YS, Wang QD. Molecular cloning and characterization of pigeon (Columba liva) ubiquitin and ubiquitin-conjugating enzyme genes from pituitary gland library. Int J Biol Sci 2008; 5:34-43. [PMID: 19158944 PMCID: PMC2605574 DOI: 10.7150/ijbs.5.34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 12/14/2008] [Indexed: 11/10/2022] Open
Abstract
In the study of the regulation of incubation, broodiness and laying performance in pigeons (Columba liva), a cDNA library, which was enriched with full-length brooding-related genes, was constructed by SMART LD-PCR techniques using the pituitary glands of incubating White King pigeons. The titers of optimal primary libraries were 1.54×106 pfu/mL and 1.80×106 pfu/mL and the titers of amplified libraries were 1.89×108 pfu/mL and 2.32×109 pfu/mL. The percentages of recombinant clones of primary libraries and amplified libraries were all over 90%. A positive clone was sequenced and named ubiquitin based on the highly similar from other species. The fragment has the four initial codons of ATG, a termination codon of TAA and a signal sequence of AATAAA for adding the poly-A tail. The open reading frame of 918bp encodes 305 amino acids (NCBI accession number is EU981283). Recombinant pigeon ubiquitin protein was efficiently expressed with the form of insoluble inclusion bodies in E. coli BL21 transformed with a pET28a+ expression vector containing the DNA sequence encoding mature pigeon ubiquitin. The molecular weight of expressed protein is the same as predicted size of approximately 35kD. To improve the efficiency of cloning full-length cDNA, strategies of RACE combined with cDNA library were used. The length of pigeons ubiquitin-conjugating enzyme gene obtained was 1263 bp containing a complete open reading frame of 435 bp that encodes 144 aa (NCBI accession number is EU914824). The results of this study not only provide a starting point for further study of ubiquitin function in pigeon species, but also provide a starting point for investigating the brooding mechanisms of pigeons.
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Affiliation(s)
- Peng-fei Gao
- The Key Laboratory of Animal Breeding and Genetics & Reproduction, Shanxi Agriculture University, Taigu, 030801, Shanxi, China
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Reed J, Mishra B, Pittenger B, Magonov S, Troke J, Teitell MA, Gimzewski JK. Single molecule transcription profiling with AFM. NANOTECHNOLOGY 2007; 18:44032. [PMID: 20721301 PMCID: PMC2922717 DOI: 10.1088/0957-4484/18/4/044032] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.
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Affiliation(s)
- Jason Reed
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Bud Mishra
- Department of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | | | | | - Joshua Troke
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
| | - Michael A Teitell
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
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Mrácek J, Greiner S, Cho WK, Rauwolf U, Braun M, Umate P, Altstätter J, Stoppel R, Mlcochová L, Silber MV, Volz SM, White S, Selmeier R, Rudd S, Herrmann RG, Meurer J. Construction, database integration, and application of an Oenothera EST library. Genomics 2006; 88:372-80. [PMID: 16829020 DOI: 10.1016/j.ygeno.2006.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 04/20/2006] [Accepted: 05/30/2006] [Indexed: 11/18/2022]
Abstract
Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.
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Affiliation(s)
- Jaroslav Mrácek
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, 80638 München, Germany
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Carralot JP, Weide B, Schoor O, Probst J, Scheel B, Teufel R, Hoerr I, Garbe C, Rammensee HG, Pascolo S. Production and characterization of amplified tumor-derived cRNA libraries to be used as vaccines against metastatic melanomas. GENETIC VACCINES AND THERAPY 2005; 3:6. [PMID: 16115316 PMCID: PMC1215502 DOI: 10.1186/1479-0556-3-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 08/22/2005] [Indexed: 01/11/2023]
Abstract
Background Anti-tumor vaccines targeting the entire tumor antigen repertoire represent an attractive immunotherapeutic approach. In the context of a phase I/II clinical trial, we vaccinated metastatic melanoma patients with autologous amplified tumor mRNA. In order to provide the large quantities of mRNA needed for each patient, the Stratagene Creator™ SMART™ cDNA library construction method was modified and applied to produce libraries derived from the tumors of 15 patients. The quality of those mRNA library vaccines was evaluated through sequencing and microarray analysis. Results Random analysis of bacterial clones of the library showed a rate of 95% of recombinant plasmids among which a minimum of 51% of the clones contained a full-Open Reading Frame. In addition, despite a biased amplification toward small abundant transcripts compared to large rare fragments, we could document a relatively conserved gene expression profile between the total RNA of the tumor of origin and the corresponding in vitro transcribed complementary RNA (cRNA). Finally, listing the 30 most abundant transcripts of patient MEL02's library, a large number of tumor associated antigens (TAAs) either patient specific or shared by several melanomas were found. Conclusion Our results show that unlimited amounts of cRNA representing tumor's transcriptome could be obtained and that this cRNA was a reliable source of a large variety of tumor antigens.
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Affiliation(s)
- Jean-Philippe Carralot
- CureVac, Paul Ehrlich Strasse 15, 72076 Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology; Auf der Morgenstelle 15; 72076 Tübingen, Germany
| | - Benjamin Weide
- Section for Dermatological Oncology, Tübingen University Hospital, Liebermeisterstraße 25, 72076 Tübingen, Germany
| | - Oliver Schoor
- University of Tübingen, Institute for Cell Biology, Department of Immunology; Auf der Morgenstelle 15; 72076 Tübingen, Germany
| | - Jochen Probst
- CureVac, Paul Ehrlich Strasse 15, 72076 Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology; Auf der Morgenstelle 15; 72076 Tübingen, Germany
| | - Birgit Scheel
- CureVac, Paul Ehrlich Strasse 15, 72076 Tübingen, Germany
| | - Regina Teufel
- CureVac, Paul Ehrlich Strasse 15, 72076 Tübingen, Germany
| | - Ingmar Hoerr
- CureVac, Paul Ehrlich Strasse 15, 72076 Tübingen, Germany
| | - Claus Garbe
- Section for Dermatological Oncology, Tübingen University Hospital, Liebermeisterstraße 25, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- University of Tübingen, Institute for Cell Biology, Department of Immunology; Auf der Morgenstelle 15; 72076 Tübingen, Germany
| | - Steve Pascolo
- CureVac, Paul Ehrlich Strasse 15, 72076 Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology; Auf der Morgenstelle 15; 72076 Tübingen, Germany
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Wellenreuther R, Schupp I, Poustka A, Wiemann S. SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones. BMC Genomics 2004; 5:36. [PMID: 15198809 PMCID: PMC436056 DOI: 10.1186/1471-2164-5-36] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Accepted: 06/15/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND cDNA libraries are widely used to identify genes and splice variants, and as a physical resource for full-length clones. Conventionally-generated cDNA libraries contain a high percentage of 5'-truncated clones. Current library construction methods that enrich for full-length mRNA are laborious, and involve several enzymatic steps performed on mRNA, which renders them sensitive to RNA degradation. The SMART technique for full-length enrichment is robust but results in limited cDNA insert size of the library. RESULTS We describe a method to construct SMART full-length enriched cDNA libraries with large insert sizes. Sub-libraries were generated from size-fractionated cDNA with an average insert size of up to seven kb. The percentage of full-length clones was calculated for different size ranges from BLAST results of over 12,000 5'ESTs. CONCLUSIONS The presented technique is suitable to generate full-length enriched cDNA libraries with large average insert sizes in a straightforward and robust way. The representation of full-coding clones is high also for large cDNAs (70%, 4-10 kb), when high-quality starting mRNA is used.
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MESH Headings
- Cell Line, Tumor
- Cloning, Molecular/methods
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Electrophoresis, Agar Gel/methods
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/pathology
- Female
- Gene Library
- Humans
- Nucleic Acid Amplification Techniques/methods
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Reverse Transcriptase Polymerase Chain Reaction/methods
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Affiliation(s)
- Ruth Wellenreuther
- Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ingo Schupp
- Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Annemarie Poustka
- Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Wiemann
- Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Jackson A, Jiao PE, Ni I, Fu GK. Agarose gel size fractionation of RNA for the cloning of full-length cDNAs. Anal Biochem 2003; 323:252-5. [PMID: 14656534 DOI: 10.1016/j.ab.2003.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Alan Jackson
- Incyte Corp, 3160 Porter Dr, Palo Alto, CA 94304, USA
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