The isolation of cloned cDNA sequences which are differentially expressed in human lymphocytes and fibroblasts.

Poly(A)+ RNA populations derived from normal lymphocytes and fibroblasts have been compared by hybridising each RNA to cDNA derived from the other RNA population. This indicated that approximately 75% of the sequences were common to both, and that these were present at different concentrations in the two cell types. The two RNA populations were further compared by hybridising them to a cDNA recombinant library derived from lymphocyte poly(A)+ RNA. This allowed the identification of clones containing sequences which are abundant in lymphocyte poly(A)+ RNA but absent or rare in fibroblast poly(A)+ RNA. A direct estimation of the abundance of five of these sequences in lymphocyte cDNA demonstrated that clones can be detected by such a procedure if they represent 0.2% or greater of the original cDNA population.     

Cloning and nucleotide sequence analysis of complementary deoxyribonucleic acid for bovine preproinsulin

A cDNA library was prepared from poly(A+) RNA isolated from fetal bovine pancreas. Bacterial colonies were screened for sequences homologous to a rat preproinsulin I cDNA probe. Ten positive clones were selected at random and further studied. Northern blot analyses revealed that seven of these clones hybridized to a single RNA species, of approximately 400 nucleotides. Sequence analysis of one of these clones (pbI2885) revealed the entire structural region of bovine preproinsulin mRNA including a 72 nucleotide region encoding a signal peptide enriched in hydrophobic residues. The overall nucleotide homology between bovine and human preproinsulin mRNA was 76% for the preregion, 89% for the A chain, 83% for the B chain, and 68% for the C peptide (including a 15 nucleotide deletion).     

The isolation of cDNA clones for human apolipoprotein E and the detection of apoE RNA in hepatic and extra-hepatic tissues.

We have isolated cDNA clones coding for apolipoprotein E (apoE) from a cDNA library prepared from adult human liver mRNA. Mixtures of 128 different oligonucleotides, 17 residues long were synthesised to be complementary to regions of the mRNA corresponding to amino acids 1-6 and 151-156. Five independent apoE clones were selected by direct screening of 5000 recombinants with the two oligonucleotide mixtures. Two overlapping clones contain the 3'-untranslated sequence, the entire coding sequence and an additional 30 bases 5' to the amino terminus of the mature protein. The DNA sequence has been determined spanning the known sites of amino acid substitutions which account for the observed protein polymorphism of apoE. Using the clones as probes in Northern blot analysis of total human liver and kidney RNAs and leucocyte poly(A)+ RNA we have detected a single species of mRNA in liver and kidney of 1.2 kb and two larger species in leucocyte RNA. The level of expression of the mRNA in kidney is approximately 10% of that in liver while the level of apoE RNA sequences in the leucocytes is less than 1% of that in the liver.     

Identification of a set of genes expressed during the G0/G1 transition of cultured mouse cells.

To identify previously undetected genes that may be involved in the transition from a resting state (G0) to a proliferative state (G1) of mammalian cells, we set out to isolate cDNA clones derived from mRNAs that appear in serum-stimulated cells in the absence of protein synthesis. A lambda cDNA library was prepared using poly(A)+ RNA from BALB/c 3T3 cells that had been brought to quiescence and subsequently stimulated with serum in the presence of cycloheximide. Approximately 50 000 recombinant phage plaques were screened, and 357 clones were isolated that hybridized to probes derived from stimulated-cell RNA but not to probes from resting-cell RNA. Cross hybridization analysis showed that four RNA sequence families account for approximately 90% of these clones. One of the clones hybridized to an actin probe; none hybridized to any of 13 oncogene probes tested. Five different RNAs that appear to be previously uncharacterized have been further analyzed. These RNAs accumulate and decay rapidly following stimulation by serum or purified growth factors, or by a tumor promoter, and they are superinduced by serum in the presence of cycloheximide. Three of the RNAs could be enriched by hybridization to cDNAs and translated in vitro, yielding proteins of approximately 43, 40 and 35 kd, respectively.     

The structure and expression of a distantly related member of the beta-gamma crystallin super gene family from Xenopus.

In an attempt to understand amphibian crystallin gene regulation, we have isolated and partially characterized several genomic clones which hybridized to the gamma 1 cDNA probe from Rana temporaria. A complete sequence of one of these clones showed slight homology to the mammalian beta and gamma crystallins. The deduced amino acid sequence of the coding region and its alignment as a folding unit indicated that all the topologically equivalent residues involved in maintaining the protein folding pattern are highly conserved. Northern blot analysis of total RNAs derived from several adult tissues, including eye lens, suggested that an RNA of approximately 700 nucleotides long is present in lens, heart, spleen and embryos of later stages of development but not in retina, oocytes and embryos of early developmental stages.     

Human serum amyloid A (SAA): biosynthesis and postsynthetic processing of preSAA and structural variants defined by complementary DNA

To study structural variants of human serum amyloid A (SAA), an apoprotein of high-density lipoprotein, complementary DNA clones were isolated from a human liver library with the use of two synthetic oligonucleotide mixtures containing sequences that could code for residues 33-38 and 90-95 of the protein sequence. The SAA-specific cDNA clone (pA1) contains the nucleotide sequence coding for the mature SAA and 10 amino acids of the 18-residue signal peptide. It also includes a 70 nucleotide long 3'-untranslated region and approximately 120 bases of the poly(A) tail. The derived amino acid sequence of pA1 is identical with the alpha form of apoSAA1. A fragment of pA1 containing the conserved (residues 33-38) region of SAA also hybridized with RNA from human acute phase liver and acute phase stimulated, but not unstimulated, mouse and rabbit liver. In contrast, a fragment corresponding to the variable region hybridized to a much greater extent with human than with rabbit or murine RNA. Human acute phase liver SAA mRNA (approximately 600 nucleotides in length) directs synthesis of preSAA (Mr 14 000) in a cell-free translating system. In a Xenopus oocyte translation system preSAA is synthesized and processed to the mature Mr 12 000 product. The complete 18 amino acid signal peptide sequence of preSAA was derived from sequencing cDNA synthesized by "primer extension" from the region of SAA mRNA corresponding to the amino terminus of the mature product. Two other SAA-specific cDNA clones (pA6 and pA10) differed from pA1 in that they lack the internal PstI restriction enzyme site spanning residues 54-56 of pA1.(ABSTRACT TRUNCATED AT 250 WORDS)     

The occurrence of families of repetitive sequences in a library of cloned cDNA from human lymphocytes

A library of cloned cDNAs representative of lymphocyte total poly(A)+ RNA was screened with total DNA probes at high clone density. 10% of the recombinants showed the presence of sequences which are repeated in the genome. Further analysis of six such isolated cDNA clones indicated that they contain different families of repetitive sequences with reiteration frequencies of between 150 and 45,000 copies per haploid genomes. Five of the six clones were found to contain single copy sequences as well as a repetitive sequence. cDNA clones containing repetitive sequences have been found to be derived from high, intermediate and low abundance classes of lymphocyte poly(A)+ RNA.     

Cloning of Salt Tolerance-Related cDNAs from the Mangrove Plant Sesuvium portulacastrum L.

In an attempt to isolate and identify the target genes relevant to salt tolerance in a mangrove plant （Sesuvium portulacastrum L.）, a subtracted cDNA library was constructed via suppressive subtractive hybridization （SSH）, in which the poly（A）＋RNA isolated from salt-tolerant S. portulacastrum leaves was used as a tester, whereas the driver was poly（A）＋RNA, derived from salt-sensitive S. portulacastrum leaves. Screening of this subtracted cDNA library revealed five clones, of which the expression levels in the salt-tolerant plant were markedly higher than those observed in the salt-sensitive plant, indicating that these candidate clones may be involved in salt-tolerance pathways. Among the clones isolated, P66, P175, and P233 are novel because no significant similarity was obtained upon alignment with the GenBank database. Clone P89 demonstrated high homology with NADPH of Arabidopsis thaliana, whereas clone P152 was highly homologous with the gene encoding late embryogenesis abundant （LEA） protein of A. thaliana. The full-length gene of clone P152, with a predicated 344 amino acid residues, was shown to bear LEA-2 domains, a signature motif for proteins that have been enriched under salty and drought conditions. It is thus implied that clone P152 would be a salt-tolerance gene of S. portulacastrum. In addition, we have also developed a strategy for the extraction of total RNA from mangrove plants.     

Structural complexity of defective-interfering RNAs of Semliki Forest virus as revealed by analysis of complementary DNA.

The 18S defective interfering RNA of Semliki Forest virus has been reverse transcribed to cDNA, which was shown to be heterogeneous by restriction enzyme analysis. After transformation to E.coli, using pBR322 as a vector, two clones, pKTH301 and pKTH309 with inserts of 1.7 kb and 2 kb, were characterized, respectively. The restriction maps of the two clones were different but suggested that both contained repeating units. At the 3' terminus, pKTH301 had preserved 106 nucleotides and pKTH309 102 nucleotides from the 3' end of the viral 42S genome. The conserved 3' terminal sequence was joined to a different sequence in the two clones, and these sequences were not derived from the region coding for the viral structural proteins. The DI RNAs represented by the two clones are generated from the viral 42S RNA by several noncontinuous internal deletions, since the largest colinear regions with 42S RNA are 320 nucleotides in pKTH301, and 430 and 340 nucleotides in pKTH309. All these fragments had unique RNase T1 oligonucleotide fingerprints, suggesting that they were derived from different regions of 42S RNA.     

Gene expression and cDNA cloning identified a major basic protein constituent of bovine seminal plasma as bovine monocyte-chemoattractant protein-1 (MCP-1).

P6 is one of the major basic proteins of bovine seminal plasma. Using cell-free translation of poly(A)+RNA from bovine seminal vesicle tissue and monospecific anti-P6-IgGs, we show that P6 is a secretory product of the seminal vesicles. Immunohistochemical experiments supported this finding. Immunoscreening of a lambda gt11 cDNA library derived from seminal vesicle poly(A)+RNA furnished a number of positive cDNA clones, from which clone pH42 was characterized by sequencing. The partial amino acid sequence of a CNBr-fragment of P6 permitted identification of the reading frame of clone pH42 encoding the precursor protein of P6. The P6 precursor contains a signal peptide of 23 amino acids followed by the mature P6 sequence of 76 amino acid residues. The cDNA sequence of pH42 was 80% homologous with that of the human monocyte-chemoattractant protein-1 (hMCP-1). The respective amino acid sequences for the precursor molecules are 72% identical. Northern analysis of seminal vesicle poly(A)+RNA using pH42 as probe probe identified a 0.9-kb P6 mRNA. Stimulation of P6 mRNA expression by phytohemagglutinin in bovine peripheral mononuclear leukocytes suggests that P6 is identical to bovine MCP-1.     

A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community

Clones from the same marine bacterioplankton community were sequenced, 100 clones based on DNA (16S rRNA genes) and 100 clones based on RNA (16S rRNA). This bacterioplankton community was dominated by alpha-Proteobacteria in terms of repetitive DNA clones (52%), but gamma-Proteobacteria dominated in terms of repetitive RNA clones (44%). The combined analysis led to a characterization of phylotypes otherwise uncharacterized if only the DNA or RNA libraries would have been analyzed alone. Of the DNA clones, 25.5% were found only in this library and no close relatives were detected in the RNA library. For clones from the RNA library, 21.5% of RNA clones did not indicate close relatives in the DNA library. Based on the comparisons between DNA and RNA libraries, our data indicate that the characterization of the bacterial community based on RNA has the potential to characterize distinct phylotypes from the marine environment, which remain undetected on the DNA level.     

In vitro selection of a ligase ribozyme carrying alkylamino groups in the side chains

A novel ligase ribozyme was in vitro selected from a random-sequence RNA library including N(6)-aminohexyl-modified adenine residues in place of natural adenine residues. This ribozyme mediated the formation of a phosphodiester bond with a DNA oligonucleotide through condensation with a 5'-triphosphate moiety on the ribozyme. Among the clones isolated from this selection, one was shown to accelerate ligation about 250-fold compared to the original random-sequence RNA library. Almost no rate acceleration was observed when the N(6)-aminohexyl-groups on adenine residues were omitted. Furthermore, ligation was dependent on the presence of a template DNA oligonucleotide that bridged the two strands.     

Isolation of multiple genomic sequences coding for chicken myosin heavy chain protein

A genomic bank has been constructed using DNA isolated from a dystrophic strain of chickens. The library was screened for myosin heavy chain (MHC) sequences using a cDNA probe and 11 positive recombinants isolated. Identity of the clones was confirmed by positive RNA selection via hybridization of the clones with muscle RNA and subsequent translation of the hybridizable RNA in vitro. Restriction maps indicate that the clones can be divided into 7 distinct groups; some of these groups do, however, share similar or homologous sequences. Hydridization of the clones to RNA derived from leg, breast, heart, and brain reveals that all of the clones code for the muscle-specific MHC isoforms. These experiments also show that there are at least 3 size classes of MHC mRNA sequences, whose relative amounts appear to be modulated in a tissue- and developmental stage-specific manner.     

Characterization by cDNA cloning of the mRNA for seminalplasmin, the major basic protein of bull semen

A cDNA library derived from poly(A)+RNA of bull seminal vesicle tissue was screened with synthetic DNA probes specific for seminalplasmin (SAP), the major basic protein of bull semen. From a number of positive clones, pBSV12, containing a 577-bp insert, was identified and sequenced. The derived amino acid sequence comprises the known amino acid sequence of SAP with an amino terminal representing a putative signal sequence; at the carboxyl terminus the sequence contains an additional lysine residue. Present experimental data do not distinguish between two potential SAP precursor molecules, each starting with a methionine residue and differing by 10 amino acid residues in the leader peptide. Comparative Northern analysis reveals a SAP-specific mRNA of 700 bp, which lacks RNA from bovine testis as well as from seminal vesicle tissue of a bull calf; hence, expression of the SAP gene appears to be under androgen and/or developmental control. Southern analysis indicates that one gene appears to specify SAP. SAP-like DNA sequences were detected in ovine and porcine genomic DNA.