Rapid Amplification Of cDNA Ends Procedure Research Articles

Molecular Characterization of a Saposin-Like Protein Family Member Isolated from Bovine Lymphocytes

Human and porcine T lymphocytes and natural killer (NK) cells produce antibacterial proteins that belong to the saposin-like family of proteins (SAPLIP). The objective of this study was to determine if a bovine homolog of SAPLIP exists in lymphocytes that exhibit antibacterial activity. Following stimulation with IL-2, bactericidal activity against Staphylococcus aureus was detected to some extent in most major subpopulations of T lymphocytes including CD4+, CD8+, CD3+, and WC1+ γδ T lymphocytes. However, the majority of antibacterial activity was observed in the CD2+CD3− lymphocytes, which are similar phenotypically to NK cells. A partial sequence of a bovine SAPLIP was generated using low specificity primers designed from regions of homology between other SAPLIP including porcine NK-lysin and human granulysin. Enhanced expression of the bovine lysin gene was detected in mRNA isolated from IL-2–stimulated CD2+CD3− lymphocytes. The partial cDNA sequence was then used to make gene specific primers for a rapid amplification of cDNA ends (RACE) procedure that provided repeatable 5′ and 3′ cDNA ends. By examining overlapping regions from the RACE procedure, full-length sequence information was obtained for the bovine lysin homologue. Conceptual translation of the cDNA demonstrated conserved similarities to known SAPLIP members. Further characterization of the bovine lysin may facilitate its use in protecting dairy cattle against bacterial infections.

Circular rapid amplification of cDNA ends for high-throughput extension cloning of partial genes

The rapid amplification of cDNA ends (RACE) procedure is a widely used PCR-based method to clone the cDNA ends of mRNA transcripts. Current RACE methods often produce a high background of nonspecific PCR products, which can exclude the identification of the target cDNA of interest. We describe here an improved RACE procedure using circular cDNA templates and demonstrate the successful extension cloning of 4406 cDNAs.

Determination of the cDNA sequence and mRNA expression of interleukin-1 receptor antagonist in horses

To determine the complementary DNA (cDNA) sequence of interleukin-1 receptor antagonist (IL-1ra) in horses and compare messenger RNA (mRNA) expression of IL-1ra among horses of various breeds. Blood samples from neonatal and adult horses examined for a variety of diseases. A polymerase chain reaction procedure was used to amplify a 220 base pair (bp) portion of the genomic DNA. The upstream and downstream regions of the cDNA sequence were determined by means of 5' and 3' rapid amplification of cDNA ends (RACE) procedures. Northern blot hybridization was used to examine steady-state mRNA expression of IL-1ra. The consensus sequence of the cDNA obtained with the 5'-RACE procedure and the sequence for the 220 bp portion of the genomic DNA represented the putative sequence for secreted IL-1ra. The predicted secreted IL-1ra amino acid sequence contained 176 residues with an in-frame stop codon; the N-terminal 25 amino acid residues resembled the signal peptide reported for human secreted IL-1ra. An approximately 1.3 kilobase pair (kb) band that represented a portion of the 3' end of the coding region and the 3' untranslated region was obtained by use of the 3' -RACE procedure. Northern blot hybridization detected a 1.6 kb transcript in blood RNA from adult Arabian, Belgian, Thoroughbred, and Standardbred horses. Results suggest that the DNA for equine secreted IL-1ra has a short (29 bp) 5' untranslated region, a 534 bp coding region, and a long (approximately 1,080 bp) untranslated region.

Functional Identification of the Transcription Start Site and the Core Promoter of the Juvenile Hormone Esterase Gene in Trichoplusia ni

The juvenile hormone (JH) esterase gene in T. ni encodes a protein that is responsible for the degradation of JH. The 5′ structural characterization of this JH-sensitive gene was accomplished using reverse transcription PCR (RT-PCR) and northern analysis. The transcriptional start site of the JHE gene was biochemically determined by two methods: a 5′ rapid amplification of cDNA ends (RACE) procedure which produced independent products with a sequence identical to the sequence of an exon encoded 5′ to the putative first intron and by northern analysis with intronic and exonic probes. Both the transcription start site and the region containing the core promoter were also functionally identified by use of an in vitro transcription assay. The product of the in vitro transcription reaction, under the control of the putative core promoter region, initiated at the same base as identified by the RACE procedure, whether the reaction was driven by lepidopteran or by dipteran nuclear extracts. This result is the first functional identification of the core promoter region and transcription start site of any JH-sensitive gene.

Structure, expression and chromosomal localization of human p80-coilin gene.

Coiled bodies (CBs) are non-capsular nuclear bodies with a diameter of 0.3-1 micron and appear to be composed of coiled fibrils. Human autoantibodies to CBs recognize an 80-kD nuclear protein highly enriched in CBs, and this protein has been named p80-coilin. CBs are known to assemble and disassemble during the cell cycle, with the highest number of CBs occurring at mid to late G1 where p80-coilin is assembled into several small nuclear body-like structures. In S and G2 phases, CBs become larger and their number decreases and often they are undetectable during mitosis. Using a human autoantibody as a probe for expression cloning, we initially isolated a partial cDNA encoding p80-coilin. In this report, the 5' end of the complete cDNA for p80-coilin was obtained using the 5'-RACE (rapid amplification of cDNA ends) methodology. The size of the reconstructed full-length cDNA corresponds to the 2.7-kb mRNA detected in Northern blot analysis. The complete p80-coilin protein consists of 576 amino acids with a predicted molecular mass of 62,608. A putative p80-coilin pseudogene was also detected during the rescreening of p80-coilin cDNA. To confirm the validity of the cDNA sequence, three overlapping genomic DNA clones representing the human p80-coilin gene were selected for further analysis. The complete gene for p80-coilin contains 7 exons spanning approximately 25kb. Sequence analysis of exons 1 and 2 in genomic DNA clones confirmed the accuracy of the 5' cDNA sequence derived from the 5'-RACE procedure. Furthermore, the human p80-coilin gene was localized to chromosome 17q22-23 by fluorescence in situ hybridization.

Exon-specific northern analysis and rapid amplification of cDNA ends (RACE) reveal that the proximal promoter II (PII) is responsible for aromatase cytochrome P450 ( CYP19) expression in human ovary

Estrogens are synthesized from C 19 steroids by a unique form of cytochrome P 450, aromatase cytochrome P- 450 ( P-450 AROM; the product of the CYP19 gene). We have shown that tissue-specific expression of human P-450 AROM is determined, in part, by the use of alternative promoters. Previous methods of analysis for determining the specific 5'-termini of the different transcripts included S1 nuclease protection, primer extension, and Northern analysis. In the present study we have used the RACE procedure (rapid amplification of cDNA ends) to amplify and clone the 5' termini of P-450 AROM transcripts expressed in human corpus luteum (CL). Sequencing of the resulting clones supports the results of the previously performed studies. Specifically, the proximal promoter, PII, is the predominant promoter utilized in CL, such that the start of transcription occurs 26 bp downstream of the putative TATA sequence. A minority of the clones possess an alternative 5'-end, namely I.3. Exon-specific Northern analysis confirms that the majority of the P-450 AROM transcripts in CL tissue contain sequence specific for promoter II. Similarly, exon-specific Northern analysis indicates that transcripts in human follicles, as well as granulosa cells in culture, contain primarily sequence specific for promoter II.

Characterization of cDNA clones for the 2-methyl branched-chain enoyl-CoA reductase. An enzyme involved in branched-chain fatty acid synthesis in anaerobic mitochondria of the parasitic nematode Ascaris suum.

The 2-methyl branched-chain enoyl-CoA reductase plays a pivotal role in the reversal of beta-oxidation operating in anaerobic mitochondria of the parasitic nematode Ascaris suum. An affinity-purified polyclonal anti-serum against the reductase was used to screen a cDNA library constructed in lambda gt11 with poly(A)+ RNA from adult A. suum muscle. A 1.2-kilobase partial cDNA clone was isolated, subcloned, and sequenced in both directions. Additional sequence at the 5' end of the mRNA was determined by the RACE (rapid amplification of cDNA ends) procedure. Nucleotide sequence analysis of the cDNAs revealed the 22-nucleotide trans-spliced leader sequence characteristic of many nematode mRNAs, an open reading frame of 1236 nucleotides and a 3'-untranslated sequence of 109 nucleotides including a short poly(A) tail 14 nucleotides from a polyadenylation signal (AATAAA). The open reading frame encoded a 396-amino acid sequence (M(r) 43,046) including a 16-amino acid leader peptide. Two-dimensional gel electrophoresis of the purified reductase yielded multiple spots with two distinct but overlapping amino-terminal amino acid sequences. Both sequences overlapped with the sequence predicted from the mRNA, and one of the sequences was identical to the predicted sequence. Comparison of the ascarid sequence with that of mammalian acyl-CoA dehydrogenases revealed a high degree of sequence identity, suggesting that these enzymes may have evolved from a common ancestral gene even though the ascarid enzyme functions as a reductase, not as a dehydrogenase. Immunoblotting of A. suum larval stages and adult tissues with antisera that cross-reacted with each of the spots separated on two-dimensional gels suggested that the reductase was only found in adult muscle. Northern blotting using the partial cDNA revealed a hybridization band of about 1.5 kilobases and also suggested that the enzyme was tissue-specific and developmentally regulated in agreement with the results of the immunoblotting.

Tissue-specific and hormonally controlled alternative promoters regulate aromatase cytochrome P450 gene expression in human adipose tissue.

Estrogen biosynthesis is catalyzed by a microsomal enzyme, aromatase cytochrome P450 (P450arom; the product of the CYP19 gene). The human CYP19 gene comprises nine coding exons, II-X. Additionally, tissue-specific expression is determined by the use of tissue-specific promoters, which give rise to P450arom transcripts with unique 5'-noncoding sequences. In placenta, P450arom transcripts contain one of two 5'-untranslated exons, I.1 or I.2, while ovarian transcripts instead contain sequence consistent with the use of a promoter, PII, which is proximal to the start of translation. To characterize transcripts present in adipose tissue and adipose stromal cells (ASC) in culture, cDNA libraries were constructed by the RACE (rapid amplification of cDNA ends) procedure. Four P450arom transcripts with unique 5' termini were identified, leading to the characterization of two unique 5'-untranslated exons of the CYP19 gene, I.3 and I.4. Whereas I.3-specific sequence is expressed in adipose tissue as well as in ACS maintained under all culture conditions, I.4-specific sequence is apparently present only in breast adipose tissue, and ACS stimulated with glucocorticoids. On the other hand, PII-specific sequence is present only in cells stimulated with cAMP analogues and is absent from cells stimulated with glucocorticoids. We conclude that CYP19 gene expression in human adipose tissue likely utilizes two novel promoters and, furthermore, that alternative promoter usage in cultured ASC is a function of the hormonal environment in which the cells are maintained.

Cloning and characterization of a naturally occurring antisense RNA to human thymidylate synthase mRNA.

Based upon reverse transcription and polymerase chain reaction results with human KB cell RNA, a cDNA (i.e., 3'rTS1, 1557 nt) with complementarity to thymidylate synthase mRNA was cloned and sequenced. Northern blot analysis showed that 3'rTS1 corresponded to a cytoplasmic 1.8 kb RNA found in several tumor cell lines. The remaining 5'region of this antisense RNA was cloned by a RACE (Rapid Amplification of cDNA Ends) procedure. A full length cDNA (i.e., rTS, 1811 nt) was generated by splicing 3'rTS1 with RACE-generated cDNA. rTS RNA is likely a mRNA that contains four open reading frames. Based upon sequence analysis of the RACE cDNAs and the rTS cDNA, rTS RNA is likely processed from a gene containing at least six introns. Northern blot analysis indicates rTS RNA is expressed in a variety of human tumor cell lines and an aberrant from is expressed in a methotrexate-cell line.