Kilobases Of DNA Research Articles

Molecular Cloning, Characterization, and Promoter Analysis of the Mouse Crp2/SmLim Gene: PREFERENTIAL EXPRESSION OF ITS PROMOTER IN THE VASCULAR SMOOTH MUSCLE CELLS OF TRANSGENIC MICE

Several members of the LIM protein family have important roles in development and differentiation. We recently isolated a rat cDNA encoding a new member of this family, CRP2/SmLIM, that contains two LIM domains and is expressed preferentially in vascular smooth muscle cells (VSMC). To study the molecular mechanisms that regulate VSMC-specific transcription of the Crp2/SmLim gene, we cloned the cDNA and gene of mouse Crp2/SmLim. Mouse Crp2/SmLim is a single copy gene of six exons and five introns spanning approximately 20 kilobases of genomic DNA. By 5'-rapid amplification of cDNA ends and S1 nuclease protection assay, we determined that the transcription start site is an A residue 80 base pairs 5' of the translation initiation codon. A TATA-like sequence is located 27 base pairs 5' of the transcription start site, and there are potential cis-acting elements (GATA, Sp1, AP-2, E box, CCAC box, and GArC motif) in the 5'-flanking sequence. In transient transfection assays in rat aortic smooth muscle cells in primary culture, 5 kilobases of the Crp2/SmLim 5'-flanking sequence generated a high level of luciferase reporter gene activity. By deletion analysis and gel mobility shift assay, we found that the region between bases -74 and -39 of this 5 kilobase DNA fragment binds Sp1 and confers basal promoter activity in the Crp2/SmLim gene. In vitro, the 5-kilobase fragment was active in multiple cell types. In vivo, however, the 5-kilobase fragment directed high level expression of the lacZ reporter gene preferentially in the VSMC of transgenic mice, indicating the presence of VSMC-specific element(s) in this fragment.

Structure and mechanism in transcriptional antitermination by the bacteriophage lambda N protein.

Each of the two early operons and the late operon ofbacteriophage λ contain transcriptional terminators (Fig.1a). As a consequence, the pattern of transcription duringa lytic infection by λ can be viewed as a cascade of transcriptional antitermination mechanisms (for review, seeDas 1993; Greenblatt et al. 1993; Friedman and Court1995; Richardson and Greenblatt 1996). These antitermination mechanisms are "processive" in the sense that theycan influence termination through multiple terminatorsover many kilobases of DNA and many minutes of transcription time. The N gene is the first gene to be transcribed in the leftward early pL operon and encodes an antitermination factor. Once N protein is made, it modifiesEscherichia coli RNA polymerase transcribing the earlypL and pR operons so that the RNA polymerase transcribes efficiently through all the intrinsic and Rho-dependent terminators of both operons. This leads to the e...

Functional characterization of a chicken major histocompatibility complex class II B gene promoter.

A 0.7 kilobase (kb) DNA fragment from the 5' flanking region of a chicken major histocompatibility complex (MHC) class II B gene was cloned into chloramphenicol acetyltransferase (CAT) reporter vectors and was transfected into a chicken macrophage cell line that expresses a low level of MHC class II antigens. Positive orientation-dependent promoter activity of the chicken DNA was evident in a reporter construct containing an SV40 enhancer. Deletion analysis of this 0.7 kb DNA fragment revealed a short fragment in the 3' end that was crucial for the promoter function and negative regulatory elements (NRE) located further upstream. The conserved MHC class II X and Y boxes did not have a significant effect on promoter activity. Sequence analysis of the 0.7 kb class II B gene upstream region suggests possible involvement of interferon (IFN), E twenty-six specific (ETS)-related proteins, and other factors in regulating this promoter. A chicken T-cell line culture supernatant increased surface expression of MHC class II antigens, as well as class II promoter activity, in this macrophage cell line. This first functional characterization of a chicken MHC class II B gene promoter will aid in understanding the regulatory mechanisms that control the expression of these genes.

Cloning, characterization, and expression of the transforming growth factor-β type I receptor promoter in fetal rat bone cells

Transforming growth factor (TGF-β) binds several discrete membrane proteins. Of these, a type I receptor appears indispensable for signal transduction. Previous examination of TGF-β receptor expression has been limited to changes in cell surface protein, and more recently, mRNA abundance. In order to learn more about TGF-β function and receptor expression during osteogenesis, we have now cloned a 4 kilobase (kb) DNA fragment 5' proximal to the coding region of the rat TGF-β type I receptor gene. Sequence analysis revealed multiple elements compatible with transcription initiation, including a properly positioned and oriented CCAAT box, six Sp1 binding sites (three defining GC boxes), and two strong AP2 binding sites within a 0.7 kb span directly upstream of the coding region. The 3' terminal 0.3 kb span comprises a GC-enriched (77%) so-called CpG island that, like other similarly organized promoters, lacks a TATA box. Primer extension and RNase protection studies with cRNAs from this area show multiple initiation sites within 220 bp 5' proximal to the initial methionine codon. Transient transfections using nested, deleted, and inverted promoter sequences demonstrated maximal reporter expression by a 1 kb fragment encompassing all of these elements. Truncation of the 1 kb fragment from the 5' and 3' ends indicated the need for several elements for peak promoter activity. These results, and transfections in fetal rat bone and dermal cells, suggest that this promoter contains elements that specify basal and conditional expression of the TGF-β type I receptor in bone. © 1996 Wiley-Liss, Inc.

Genomic Organization of the Mouse and Human Genes for Vascular Endothelial Growth Factor B (VEGF-B) and Characterization of a Second Splice Isoform

A second isoform and the genomic structures of mouse and human vascular endothelial growth factor B are described. Both genes consist of seven coding exons and span about 4 kilobases of DNA. The two identified isoforms of vascular endothelial growth factor B are generated by alternative splicing where different splice acceptor sites in exon 6 introduce a frameshift and a partial use of different but overlapping reading frames. Consequently, the COOH-terminal domains in the two isoforms show no resemblance. Mouse and human cDNA clones for the novel isoform of vascular endothelial growth factor B encoded a secreted protein of 186 amino acid residues. Expression in transfected cells generated a protein of 25 kDa which upon secretion was modified by O-linked glycosylation and displayed a molecular mass of 32 kDa under reducing conditions. The protein was expressed as a disulfide-linked homodimer, and heterodimers were generated when coexpressed with vascular endothelial growth factor. The entirely different COOH-terminal domains in the two isoforms of vascular endothelial growth factor B imply that some functional properties of the two proteins are distinct.

Clusters of DNA Damage Induced by Ionizing Radiation: Formation of Short DNA Fragments. II. Experimental Detection

The basic 30-nm chromatin fiber in the mammalian cell consists of an unknown (possibly helical) arrangement of nucleosomes, with about 1.2 kb of DNA per 10-nm length of fiber. Track-structure considerations suggest that interactions of single delta rays or high-LET particles with the chromatin fiber might result in the formation of multiple lesions spread over a few kilobases of DNA (see the accompanying paper: W.R. Holley and A. Chatterjee, Radiat. Res. 145, 188-199, 1996). In particular, multiple DNA double-strand breaks and single-strand breaks may form. To test this experimentally, primary human fibroblasts were labeled with [3H]thymidine and exposed at 0 degrees C to X rays or accelerated nitrogen or iron ions in the LET range of 97-440 keV/microns. DNA was isolated inside agarose plugs and subjected to agarose gel electrophoresis under conditions that allowed good separation of 0.1-2 kb size DNA. The bulk of DNA remained in the well or migrated only a small distance into the gel. It was found that DNA fragments in the expected size range were formed linearly with dose with an efficiency that increased with LET. A comparison of the yield of such fragments with the yield of total DNA double-strand breaks suggests that for the high-LET ions a substantial proportion (20-90%) of DNA double-strand breaks are accompanied within 0.1-2 kb by at least one additional DNA double-strand break. It is shown that these results are in good agreement with theoretical calculations based on treating the 30-nm chromatin fiber as the target for ionizing particles. Theoretical considerations also predict that the clusters will contain numerous single-strand breaks and base damages. It is proposed that such clusters be designated "regionally multiply damaged sites." Postirradiation incubation at 37 degrees C resulted in a decline in the number of short DNA fragments, suggesting a repair activity. The biological significance of regionally multiply damaged sites is presently unknown.

The centromere: hub of chromosomal activities.

Centromeres are the structures that direct eukaryotic chromosome segregation in mitosis and meiosis. There are two major classes of centromeres. Point centromeres, found in the budding yeasts, are compact loci whose constituent proteins are now beginning to yield to biochemical analysis. Regional centromeres, best described in the fission yeast Schizosaccharomyces pombe, encompass many kilobases of DNA and are packaged into heterochromatin. Their associated proteins are as yet poorly understood. In addition to providing the site for microtubule attachment, centromeres also have an important role in checkpoint regulation during mitosis.

An unequal cross‐over event within the CYP2D gene cluster generates a chimeric CYP2D7/CYP2D6 gene which is associated with the poor metabolizer phenotype.

1. The study of the CYP2D genotype and phenotype of a Caucasian family revealed that a XbaI-9 kb allele was associated with the poor metabolizer phenotype. 2. A Polymerase Chain Reaction (PCR)-based assay showed that the previously described mutations D6A and D6B are not associated with the XbaI-9 kb allele. 3. To explore the molecular basis of the poor metabolizer phenotype associated with the XbaI-9 kb allele, complete sequencing of the nine exons and intron-exon boundaries of the CYP2D6 gene was undertaken after amplification by PCR. 4. All the exons were successfully amplified using CYP2D6 gene-specific primers except exon 1 which required a combination of CYP2D7 gene-specific 5' primer and a CYP2D6 gene-specific 3' primer. 5. Sequence data derived from this amplified product revealed that the XbaI-9 kb allele corresponds to a novel rearrangement of the locus. This involved a deletion of an approximately 20 kilobase (kb) DNA segment generating a hybrid 5' CYP2D7/CYP2D6 3' gene. 6. The chimeric gene is non-functional presumably due to an insertion in exon 1 (characteristic of the exon 1 of the CYP2D7 gene) which causes a shift in the reading frame with premature termination of translation.

Pituitary-type transcription of the human prolactin gene in the absence of Pit-1.

We describe a human (h) PRL-producing cell line, SKUT-1B-20, which we isolated as a subclone of a uterine sarcoma cell line. Although this cell line is of uterine origin, it does not use the decidual-specific upstream promoter of the hPRL gene, but transcribes the hPRL gene from the downstream pituitary-type transcription start site, as determined by Northern blot, reverse transcriptase-polymerase chain reaction and primer extension analyses. This is particularly intriguing because SKUT-1B-20 cells lack the transcription factor Pit-1. No Pit-1 messenger RNA was detectable by reverse transcriptase-polymerase chain reaction, and endogenous Pit-1 target genes (GH, PRL, and Pit-1) were refractory to transfected Pit-1 expression vector, whereas in cotransfection experiments, Pit-1 efficiently activated reporter gene fusion constructs carrying 5'-flanking sequences of the human and rat PRL or the mouse Pit-1 genes. By transfecting reporter genes containing 8.7 kilobases of DNA flanking the hPRL pituitary-specific start site (hPRL-8700/Luc) and deletions thereof, we located a Pit-1-independent cis-active region more than 7 kilobases upstream of the start site. The most distal 1650 or 880 base pairs of the hPRL genomic fragment (which extends to -8784 base pairs), when placed directly upstream of the homologous hPRL or the heterologous thymidine kinase promoters, conferred transcriptional activation to those promoters. SKUT-1B-20 cell-specific activation of hPRL-8700/Luc could not be suppressed by the introduction of an inhibitor of protein kinase A (PKA), PKI. This is the first demonstration of pituitary-type PRL gene transcription independent of Pit-1 and activation of the PKA pathway. The SKUT-1B-20 cell line was then used in reconstitution experiments to delineate the role of Pit-1 in modulating the transcriptional effects of phorbol ester, PKA, and estrogen receptor (ER) on the hPRL gene. The low response of hPRL/luciferase fusion genes to phorbol ester was greatly enhanced by cotransfected Pit-1 and was mediated by the proximal region between -250 and -38. The catalytic subunit of PKA, C beta, was able to elicit a moderate induction of hPRL-8700/Luc even in the absence of Pit-1. A potential estrogen response element has been located in the hPRL gene sequence at a position similar to that of the estrogen response element of the rat PRL gene immediately adjacent to the distal enhancer.(ABSTRACT TRUNCATED AT 400 WORDS)

SARs on an 835 kb DNA fragment from the Drosophila genome.

We have investigated the loop organization of a 835 kilobases DNA fragment from the Drosophila genome. This analysis has focused on the periodicity of the distribution of anchoring sequences (SARs) and its relationship to the distribution of A,T-rich regions, transcription units, repeated elements, putative replication origins and topoisomerase II cleavage sites. Altogether, the data support the idea of an active participation of SARs to the structural organization and functioning of this eukaryotic genome.

Genomic structure of the mouse A-type lamin gene locus encoding somatic and germ cell-specific lamins

Mouse A-type lamin genes were isolated. Structural analyses revealed that all the three known mouse A-type lamins (A, C and C2) were coded in a single genomic locus in a 22 kilobase DNA segment. The three lamins were coded in 12, 10 and 10 exons for A, C and C2, respectively, and shared 8 exons among them. Primer extension analyses identified possible transcription start sites for both A/C and C2 genes suggesting that the locus is under the control of two separate promoters, that is a somatic cell-acting promoter (for A and C) and a testis-specific promoter (for C2) which resides in the first intron of the A/C gene. Sequence characteristics of the possible promoter regions are discussed. Divergence of the two somatic cell-type lamins (A and C) is formally accounted for by differential selection of poly(A) sites together with lamin A-specific splicing.

A germline insertion in the tuberous sclerosis (Tsc2) gene gives rise to the Eker rat model of dominantly inherited cancer

The Eker rat hereditary renal carcinoma (RC) is an excellent example of a mendelian dominant predisposition to a specific cancer in an experimental animal. We have previously established a new conserved linkage group on rat chromosome 10q and human chromosome 16p13.3, and shown that the Eker mutation is tightly linked to the tuberous sclerosis (Tsc2) gene. We now describe a germline mutation in the gene encoding Tsc2 caused by the insertion of an approximately 5 kilobase DNA fragment in the Eker rat, resulting in aberrant RNA expression from the mutant allele. The phenotype of tuberous sclerosis in humans differs from that of the Eker rat, except for the occurrence of renal tumours. The Eker rat may therefore provide insights into species-specific differences in tumourigenesis and/or phenotype-specific mutations.

High-Specificity DNA Cleavage Agent: Design and Application to Kilobase and Megabase DNA Substrates

Strategies to cleave double-stranded DNA at specific DNA sites longer than those of restriction endonucleases (longer than 8 base pairs) have applications in chromosome mapping, chromosome cloning, and chromosome sequencing--provided that the strategies yield high DNA-cleavage efficiency and high DNA-cleavage specificity. In this report, the DNA-cleaving moiety copper:o-phenanthroline was attached to the sequence-specific DNA binding protein catabolite activator protein (CAP) at an amino acid that, because of a difference in DNA bending, is close to DNA in the specific CAP-DNA complex but is not close to DNA in the nonspecific CAP-DNA complex. The resulting CAP derivative, OP26CAP, cleaved kilobase and megabase DNA substrates at a 22-base pair consensus DNA site with high efficiency and exhibited no detectable nonspecific DNA-cleavage activity.

A novel human homeobox gene distantly related to proboscipedia is expressed in lymphoid and pancreatic tissues.

A novel human homeobox gene, HB9, was isolated from a cDNA library prepared from in vitro stimulated human tonsil B lymphocytes and from a human genomic library. The HB9 gene is composed of 3 exons spread over 6 kilobases of DNA. An open reading frame of 1206 nucleotides is in frame with a diverged homeodomain. The predicted HB9 protein has a molecular mass of 41 kilodaltons and is enriched for alanine, glycine, and leucine. The HB9 homeodomain is most similar to that of the Drosophila melanogaster homeobox gene proboscipedia. Northern blot analysis of poly(A) RNA purified from the human B cell line RPMI 8226 and from activated T cells revealed a major mRNA transcript of 2.2 kilobases. Similar analysis of poly(A) RNA from a variety of adult tissues demonstrated HB9 transcripts in pancreas, small intestine, and colon. Reverse transcriptase-polymerase chain reaction was used to examine HB9 RNA transcripts in hematopoietic cell lines. HB9 RNA transcripts were most prevalent in several human B cell lines and K562 cells. In addition, transcripts were detected in RNA prepared from tonsil B cells and in situ hybridization studies localized them in the germinal center region of adult tonsil. These findings suggest the involvement of HB9 in regulating gene transcription in lymphoid and pancreatic tissues.

DNA affinity cleaving analysis of homeodomain-DNA interaction: identification of homeodomain consensus sites in genomic DNA.

We have incorporated the DNA-cleaving moiety o-phenanthroline-copper at amino acid 10 of the Msx-1 homeodomain, and we have analyzed site-specific DNA cleavage by the resulting Msx-1 derivative. We show that amino acid 10 of the Msx-1 homeodomain is close to the 5' end of the consensus DNA site 5'-(C/G)TAATTG-3' in the Msx-1-DNA complex. Our results indicate that the orientation of the Msx-1 homeodomain relative to DNA is analogous to the orientation of the engrailed and Antennapedia homeodomains. We show further that DNA affinity cleaving permits identification of consensus DNA sites for Msx-1 in kilobase DNA substrates. The specificity of the approach enabled us to identify an Msx-1 consensus DNA site within the transcriptional control region of the developmental regulatory gene Wnt-1. We propose that incorporation of o-phenanthroline-copper at amino acid 10 of a homeodomain may provide a generalizable strategy to determine the orientation of a homeodomain relative to DNA and to identify homeodomain consensus DNA sites in genomic DNA.

A putative ATP-binding protein from the che/fla locus of Bacillus subtilis.

A majority of the chemotaxis and flagellar genes of Bacillus subtilis are found in the major che/fla operon which spans over 26 kilobases of DNA and encodes at least 30 genes. In this operon, a single open reading frame, designated orf298, has been demonstrated to encode a 33,131 Dalton protein which shows no evidence of being involved in chemotaxis or motility. A strain disrupted in orf298 was assayed for motility and chemotaxis and always behaved as the wild-type strain. Inspection of the translated sequence revealed a consensus ATP-binding region. While the role of ORF298 has not yet been determined, ATP-binding and/or hydrolysis is a likely function.

The human C4b-binding protein beta-chain gene

Human complement component C4b-binding protein (C4BP) is composed of seven alpha-chains and one beta-chain. The alpha- and beta-chains are homologous and both contain multiple copies of short consensus repeats (SCR) and in addition carboxyl-terminal non-repeat regions. Each of the alpha-chains contains a binding site for C4b, whereas the beta-chain binds protein S, a vitamin K-dependent protein involved in the regulation of blood coagulation. The alpha- and beta-chain genes are closely linked in the regulators of complement activation gene cluster on the long arm of human chromosome 1, band 1q32. The human beta-chain gene which has now been characterized was found to span more than 10 kilobases of DNA. The presence of at least two different beta-chain gene transcripts was suggested by the isolation of two new cDNA clones which contained different sequences in their extended 5'-untranslated regions. Northern blot analysis demonstrated that the two clones represented distinct beta-chain mRNAs with different 5' end sequences. One class of beta-chain mRNA (denoted A19) was found to be encoded by six exons and primer extension, and S1 nuclease protection assays revealed multiple closely spaced transcription start sites for this mRNA class. Its 5'-untranslated region and signal peptide was encoded by the first exon. The second class of mRNA (denoted A12) had a different transcription start site and its 5'-untranslated region was derived from at least three exons out of which the last one was formed by utilization of an acceptor splice site within the first A19 exon. Exons encoding the mature beta-chain and the 3'-untranslated region were common to both classes of mRNA. The beta-chain contains three SCRs, out of which the first and second are encoded by individual exons, whereas two exons encode the third SCR. The exon encoding the carboxyl-terminal part of the third SCR also encodes 14 amino acids of the non-repeat region. The last exon encodes the remaining 46 carboxyl-terminal amino acids and the entire 3'-untranslated region. The elucidation of the organization of the beta-chain gene provides insight into the sophisticated molecular structure of C4BP and a basis for future structural and functional studies.

Molecular characterization of the gene encoding the gamma subunit of the human skeletal muscle 1,4-dihydropyridine-sensitive Ca2+ channel (CACNLG), cDNA sequence, gene structure, and chromosomal location

cDNA clones of the gamma subunit of the skeletal muscle 1,4-dihydropyridine-sensitive voltage-dependent Ca2+ channel were isolated from a human fetal skeletal muscle cDNA library using the rabbit gamma cDNA as a probe. The DNA sequence of the entire human cDNA was determined. Cosmids that contained the human gamma gene were isolated and used to determine the genomic organization of the coding sequences. Four exons were identified, spanning 12.5 kilobases of DNA. Reverse-transcribed polymerase chain reaction analysis detected the gamma transcript in human and mouse skeletal muscle RNAs, but not in RNA from human brain or cardiac muscle or from mouse brain, cardiac muscle, spleen, kidney, liver, or stomach. A polymorphic dinucleotide repeat within the gamma gene was identified. This repeat was used to type a subset of the Centre d'Etude du Polymorphisme Humain families. Linkage analysis indicates that the gamma gene is tightly linked (Z = 12.94, theta = 0.001) to growth hormone at chromosome 17q23, a region that also contains the adult skeletal muscle Na+ channel.

Characterization of the gene encoding human platelet glycoprotein IX.

Glycoprotein IX is a relatively small (M(r) 20,000) surface glycoprotein of human platelets; one of three (Ib alpha, Ib beta, IX) polypeptide chains present in the glycoprotein Ib-IX complex that functions as the von Willebrand factor receptor and mediates platelet adhesion in the arterial circulation. Using a cDNA for human glycoprotein IX as the probe, clones were isolated from a human genomic library, and the genomic sequence for glycoprotein IX (3.2 kilobases) was determined. The transcriptional start site was located by RNase protection and primer extension experiments. The gene includes three exons and two introns within 1.6 kilobases of DNA, and the entire open reading frame for glycoprotein IX is included within the third exon. The genes for glycoproteins IX and Ib alpha share similar exon sequences on the 5' side of their ATG start codons, and both genes possess introns in this region. The glycoprotein IX gene contains two consensus regulatory sequences (GATA and ACTTCCT [ets]) in its promoter region (5' flank, within 67 bases of the start site) that are also present in similar sites in the previously described "megakaryocyte-platelet" genes (glycoprotein IIb, platelet factor 4, beta-thromboglobulin: human and rat). Thus, the glycoprotein IX gene shares structural features with other megakaryocyte-platelet genes and contains at least two consensus cis-acting regulatory elements that may govern gene expression.

A method for recovery of high-molecular-weight DNA suitable for field-inversion gel electrophoresis from frozen tumor cells

We describe a simple method for isolation of high-molecular-weight (high-mol-wt, >800 kilobases) DNA from tumor cell lines frozen without dimethylsulfoxide (DMSO) or other protective agents. This method should be applicable to most frozen tissues and useful for molecular genetic studies such as field-inversion gel electrophoresis (FIGE), or cloning procedures that require access to intact, high-mol-wt DNA.