Nucleic Acids Research

Reiter,, Wolf-Dieter;Palm,, Peter;Zillig,, Wolfram

doi: 10.1093/nar/16.1.1pmid: 2829113

Abstract The 5'-termini were precisely mapped for five constitutive and one UV-inducible transcript from the Sulfolobus virus-like particle SSV1. The comparison of the DNA sequences around these transcriptional initiation sites revealed the presence of two conserved sequence elements: a trinucleotide sequence close to the initiation site itself and an AT-rich hexanucleotide sequence centered about 26 nucleotides upstream of it. Similar DNA sequences were found upstream of the transcriptional start sites for the ribosomal RNA genes in Sulfolobus and upstream of transcriptional start sites in other archaebacteria, allowing the derivation of a general consensus sequence for archaebacterial promoters. This consensus sequence is unlike that found in eubacteria but it resembles promoters recognized by eukaryotic RNA polymerase II. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Nordheim,, Alfred;Meese,, Klaus

doi: 10.1093/nar/16.1.21pmid: 3340525

Abstract Small DNA fragments of approximately 350 bp in length, either with or without d(CG) n tracts, are ligated into underwound DNA minicircles to generate topoisomeric rings with different topological linking numbers, Lk. These minicircles, differing by an Lk of one, can be separated by acrylamide gel electrophoresis. Furthermore, electrophoresis can be used to reveal DNA double helix conformational changes that are induced by supercoiling, such as left-handed Z-DNA. When anti-Z-DNA antibodies are added to such minicircles, their binding leads to a selective retardation of the electrophoretic migration of the Z-DNA containing circles. This effect is not seen with relaxed minicircles and those with insufficient torsional stress to induce a conformational transition. Thus the technique of ‘topoisomer gel retardation’ presents a very sensitive assay for the identification of proteins that selectively bind to DNA conformations stabilized by negative DNA supercoiling. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Jørgensen,, Jan-Elo;Stougaard,, Jens;Marcker,, Anne;Marcker, Kjeld, A.

doi: 10.1093/nar/16.1.39pmid: 3340542

Abstract The nodulin N23 gene promoter was analysed in transgenic plants using the chloramphenicol acetyltransferase (CAT) coding sequence as a reporter. A 5' flanking region of less than 1 Kb was sufficient for the organ-specific expression of a chimeric N23-CAT-3' lbc 3 gene in root nodules formed on Lotus corniculatus and Trifolium repens after infection by their respective Rhizobium symbionts. Expression was regulated at the level of RNA in both species of transgenic plants. Promoter deletion analysis defined the 5' region required for high level expression and delimited two putative regulatory sequences involved in positive control of the N23 gene in L. corniculatus . This content is only available as a PDF. © IRL Press Limited, Oxford, England

Bickmore,, W.;Christie,, S.;, van Heyningen, V.;Hastie,, N.D.;Porteous,, D.J.

doi: 10.1093/nar/16.1.51pmid: 2829125

Abstract The clinical association of Wilms' tumour with aniridia, genitourinary abnormalities and mental retardation (WAGR syndrome) is characterised cytogenetically by variable length, constitutional deletion of the short arm of chromosome 11, which always includes at least part of band 11p13. HRAS1-selected chromosome mediated gene transfer (CMGT) generated a transformant, E65–6, in which the only human genes retained map either to band 11p13 or, with HRAS1, in the region 11p15.4-pter. Human recombinants isolated from E65–6 were mapped to a panel of five WAGR deletion hybrids and two clinically related translocations. We show that E65-6 is enriched ≃400-fold for 11p15.4-pter markers and ≃200-fold for 11p13 markers. ‘Hitch-hiking’ from HRAS1 with CMGT markers has allowed us to define seven discrete intervals which subtend band 11p13. Both associated translocations co-locate within the smallest region of overlap for the WAGR locus, which has been redefined by identifying a new interval closer than FSHB. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Gafny,, Ron;Hyman, Hana, C.;Razin,, Shmuel;Glaser,, Gad

doi: 10.1093/nar/16.1.61pmid: 3340543

Abstract The 5' region of the rRNA operon, rrnA , of M. capricolum was cloned. Sequence analysis revealed two tRNA genes, tRNA leu and tRNA lys , upstream to the promoter of the rRNA operon. The in vivo transcription start sites of the rRNA operon and of the tRNA genes were mapped. The same promoters used by M. capricolum RNA polymerase are also recognized by E. coli RNA polymerase both in vivo and in vitro . We find that high levels of ppGpp in E. coll , resulting from amino acid starvation or from spoT mutation, activate rather than repress the transcription of the mycoplasma rrnA operon. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Kakkis,, Emil;Mercola,, Mark;Calame,, Kathryn

doi: 10.1093/nar/16.1.77pmid: 2829126

Abstract We have studied the transcriptional activation of translocated c-myc genes in murine plasmacytomas in which the translocation juncture occurs within the first intron of c-myc and juxtaposes c-myc with the immunoglobulin C∝ gene segment. It has been widely suggested that a novel transcriptional enhancer element located near the C∝ gene segment might activate the translocated c-myc gene. We have carried out an extensive search for such an element and find no significant transcriptional enhancer activity in a 22 kb region encompasing the translocation junction, C∝ gene segment and regions 3' of C∝. We also find that the cryptic promoter region of the translocated c-myc gene is a very weak promoter of transcription. Despite this evidence against the presence of strong transcriptional regulatory elements, the translocated c-myc gene locus is transcribed at high rates that are 25→100% of that measured for the highly active immunoglobulin genes in murine plasmacytomas. These data suggest the presence of a novel type of strong activator of transcription in the murine heavy chain locus. This content is only available as a PDF. Author notes * Present address: Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA © IRL Press Limited, Oxford, England

Haché, Robert, J.G.;Deeley, Roger, G.

doi: 10.1093/nar/16.1.97pmid: 3340544

Abstract Analysis of nuclease hypersensitivity of regions flanking the estrogendependent, chicken apoVLOLII gene has revealed an hepatic, DNaseI hypersensitive site whose sensitivity is influenced by both the developmental stage and sex of the bird. The site is located 3.0kb upstream from the gene, In a block of middle repetitive elements. Contact hybridization studies indicate that the block consists of contiguous copies of two elements with reiteration frequencies of 500–1000 and 10000–30000 copies per haploid genome. Sequencing of 1.8kb spanning the repeats has revealed that the higher frequency element is a member of the CR1 family. The adjacent lower frequency repeat can also be found next to another member of the CR1 family located in the 3' flanking region of the vitellogenin gene. The hypersensitive site has been mapped to one of the two most highly conserved regions of the CR1 element. This region displays homology with a silencer sequence recently identified in a CR1 element flanking the chicken lysozyme gene. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Puyet,, Antonio;, del Solar, Gloria H.;Espinosa,, Manuel

doi: 10.1093/nar/16.1.115pmid: 2829114

Abstract The replication origin of the fully sequenced broad-hostrange streptococcal plasmid pLSI has been determined by the use of an in vitro replication system prepared from Escherichia coli , a host in which the plasmid can be established. Replicative intermediates were isolated from reaction mixtures that contained dideoxythymidine triphosphate, thus limiting the average extent of in vitro synthesis. Analysis of Hinf I -cleaved intermediates demonstrated that the origin of replication is included within a 443-bp fragment. Replication proceeds unidirectionally in the same direction as transcription of plasmid mRNAs. Isolation of deletion derivatives allowed us to define the replication origin of pLS1 within a region of 284 bp. Replication of pLS1 occurs through single-stranded intermediates by a rolling circle mechanism. Cleavage of supercoiled plasmid DNAs with endonuclease S1 followed by restriction mapping, allowed the positioning of three major specific S1 sites in regions of high potential to form secondary structures. One of these inverted repeats is located in the region where the origin of replication of pLS1 has been defined. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Brown, James, W.;Thomm,, Michael;Beckler, Gregory, S.;Frey,, Gerhard;Stetter, Karl, O.;Reeve, John, N.

doi: 10.1093/nar/16.1.135pmid: 2829115

Abstract Transcription initiation of the his A sent in vico . in the archaebacterium Methanococcus vannielii , as determined by nuclease S 1 and primer extension analyses, occurs 73 base pairs (bp) upstream of the translation initiation site. Binding of M. vannielii RHA polymerase protects 43 bp of DNA. from 35 bp upstream (−35) to 8 bp downstream (+8) of the his A mRNA initiation site, from digestion by DNase I and exonuclease III. An A+T rich region, with a sequence which conforms to the consensus sequence for promoters of stable RNA-encoding genes in methanogens, is found at the same location (−25) upstream of the polypeptide-encoding his A gene. It appears therefore that a TATA-like sequence is also an element of promoters which direct transcription of polypeptide-encoding genes in this archaebacterium. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Thomm,, Michael;Wich,, Günter

doi: 10.1093/nar/16.1.151pmid: 2448746

Abstract The RNA polymerase of Methanococcus vannielii , in binary complex with two stable RNA operons, protects from exonuclease digestion the region from 32 bp upstream (−32) to 18 bp downstream (+18) of the transcription start site. Contained within this binding region, centered at −25, is an AT-rich sequence which is highly conserved upstream of 26 other archaebacterial tRNA and rRNA genes. We therefore propose the sequence TTTAATATA as a common element of promoters for stable RNA genes in archaebacteria. Both the similarity in sequence and the location of this conserved octanucleotide suggest homology to the eukaryotic TATA box preceding protein encoding genes transcribed by RNA polymerase B. This content is only available as a PDF. © IRL Press Limited, Oxford, England