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Jiang Q, Li Q, Yu H, Kong L. Genome-wide analysis of simple sequence repeats in marine animals-a comparative approach. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:604-619. [PMID: 24939717 DOI: 10.1007/s10126-014-9580-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/22/2014] [Indexed: 06/03/2023]
Abstract
Tandem simple sequence repeats (SSRs) are one of the most popular molecular markers in genetic analysis owing to their ubiquitous occurrence,high reproducibility, multiallelic nature, and codominant mode. High mutability makes SSRs play a role in genome evolution and correspondingly show different patterns. Comparative analysis of genomic SSRs in different taxonomic groups usually focuses on land species, while marine animals have been neglected. This study examined the abundance of genomic SSRs with repeated unit lengths of 1-6 bp in 30 marine animals including nine taxonomic groups and further compared with the land species. More than thousands of SSRs were discovered in every organism which provided a huge resource for the development of molecular markers. Thirty marine animals showed profound differences in SSR characteristics, but some group-specific trends were also found. Both similarities and differences of repeat patterns were discovered between the land and marine species. Two taxon-specific SSR types were discovered: the pentanucleotides motif AGAGG in Euteleostei and the hexanucleotide repeats of ATGTAC in Porifera and Echinodermata. Gene ontology (GO) enrichment analysis of two representative species (Amphimedon queenslandica for Porifera and Strongylocentrotus purpuratus for Echinodermata) revealed functional preference of the ATGTAC motif associated genes, and this might hint at evolutionary significance.
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Affiliation(s)
- Qun Jiang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 266003, Qingdao, China
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2
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Liu L, Payne DM, van Santen VL, Dybvig K, Panangala VS. A protein (M9) associated with monoclonal antibody-mediated agglutination of Mycoplasma gallisepticum is a member of the pMGA family. Infect Immun 1998; 66:5570-5. [PMID: 9784576 PMCID: PMC108702 DOI: 10.1128/iai.66.11.5570-5575.1998] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 62-kDa cell surface antigen (M9) of Mycoplasma gallisepticum PG31 that mediates antibody-induced agglutination of the organism was purified and subjected to N-terminal amino-acid sequencing. A 999-bp region of the cDNA encoding the M9 protein was generated by reverse transcription-PCR, and its nucleotide sequence was determined. PCR primers based on this sequence were used to screen a genomic DNA library of PG31. A full-length M9 protein-encoding gene was isolated and sequenced, revealing 96% nucleotide identity with the pMGA1.1 gene of M. gallisepticum S6. Sequence analyses of the M9 gene and flanking open reading frames that encode other pMGA family members suggest that a tandemly repeated GAA sequence may influence pMGA gene expression.
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Affiliation(s)
- L Liu
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama 36849, USA
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3
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Abstract
The coding repeat region of opa genes from Neisseria gonorrhoeae and Neisseria meningitidis determines the expression state of their respective genes through high-frequency addition of deletion of pentanucleotide coding repeat units (CRs; CTTCT). In vitro analyses of cloned opa gene CR regions using single-strand specific nucleases, oligonucleotide protection experiments, and modifications of non-B-DNA residues indicate that the regions form structures resembling H-DNA under acidic conditions in the presence of negative supercoiling. The purine/pyrimidine strand bias and H-palindromic nature of the repeat region are consistent with sequence requirements for H-DNA formation. Sequences flanking the repeat elements are required to form the H-DNA structure in vitro as judged by the pattern of exposed non-B-DNA residues in CR sequences synthesized as oligonucleotides to form beta-galactosidase::CR translational fusions. The fusions phase vary by addition and deletion of CR elements and the rate of phase variation increases upon induction of the fusion genes. The opa gene CR region is the first reported bacterial H-DNA structure and is unique in that it lies within the coding sequence for the gene.
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Affiliation(s)
- R J Belland
- Laboratory of Microbial Structure and Function, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana 59840
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4
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Bezouska K, Crichlow G, Rose J, Taylor M, Drickamer K. Evolutionary conservation of intron position in a subfamily of genes encoding carbohydrate-recognition domains. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)98999-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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5
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Abstract
A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.
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MESH Headings
- Animals
- Base Sequence
- Chromosomes/ultrastructure
- DNA/drug effects
- DNA/metabolism
- DNA/ultrastructure
- DNA Helicases/metabolism
- DNA Replication
- DNA Topoisomerases, Type I/metabolism
- DNA Topoisomerases, Type II/metabolism
- DNA, Single-Stranded/drug effects
- DNA, Single-Stranded/metabolism
- DNA, Single-Stranded/ultrastructure
- DNA, Superhelical/drug effects
- DNA, Superhelical/metabolism
- DNA, Superhelical/ultrastructure
- DNA-Binding Proteins/metabolism
- Endonucleases/metabolism
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Conformation/drug effects
- Nucleic Acid Denaturation
- Plasmids
- Transcription, Genetic
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Affiliation(s)
- G Yagil
- Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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6
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Pilch DS, Brousseau R, Shafer RH. Thermodynamics of triple helix formation: spectrophotometric studies on the d(A)10.2d(T)10 and d(C+3T4C+3).d(G3A4G3).d(C3T4C3) triple helices. Nucleic Acids Res 1990; 18:5743-50. [PMID: 2216768 PMCID: PMC332309 DOI: 10.1093/nar/18.19.5743] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We have stabilized the d(A)10.2d(T)10 and d(C+LT4C+3).d(G3A4G3).d(C3T4C3) triple helices with either NaCl or MgCl2 at pH 5.5. UV mixing curves demonstrate a 1:2 stoichiometry of purine to pyrimidine strands under the appropriate conditions of pH and ionic strength. Circular dichroic titrations suggest a possible sequence-independent spectral signature for triplex formation. Thermal denaturation profiles indicate the initial loss of the third strand followed by dissociation of the underlying duplex with increasing temperature. Depending on the base sequence and ionic conditions, the binding affinity of the third strand for the duplex at 25 degrees C is two to five orders of magnitude lower than that of the two strands forming the duplex. Thermodynamic parameters for triplex formation were determined for both sequences in the presence of 50 mM MgCl2 and/or 2.0 M NaCl. Hoogsteen base pairs are 0.22-0.64 kcal/mole less stable than Watson-Crick base pairs, depending on ionic conditions and base composition. C+.G and T.A Hoogsteen base pairs appear to have similar stability in the presence of Mg2+ ions at low pH.
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Affiliation(s)
- D S Pilch
- Graduate Group in Biophysics, School of Pharmacy, University of California, San Francisco 94143
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7
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Parniewski P, Kwinkowski M, Wilk A, Klysik J. Dam methyltransferase sites located within the loop region of the oligopurine-oligopyrimidine sequences capable of forming H-DNA are undermethylated in vivo. Nucleic Acids Res 1990; 18:605-11. [PMID: 2155405 PMCID: PMC333468 DOI: 10.1093/nar/18.3.605] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Several derivatives of pUC18 plasmid were constructed that contained oligopurine-oligopyrimidine (pur-pyr) motifs surrounded by Dam methylation sites. Inserts of two of the molecules (pPP1 and pPP2) were able to adopt the triple-stranded conformation in vitro and show in vivo a remarkable undermethylation of specific sites when grown in JM105 dam+ strain. Mapping experiments revealed that undermethylated GATC sequences were located exclusively within the single-stranded loop region of the sequence involved in H-DNA formation. Control molecules which either contained the pur-pyr tracts (pPPK and pKK42) or not (pUC18) and were not able to form the triple-stranded conformation were found to be normally methylated by the dam gene product in vivo. Location of GATC within the triplex forming sequence seems to be a prerequisite for achieving its in vivo undermethylation. E.coli host factors are involved in the observed phenomenon. This has been deduced from the fact that the undermethylated state of pPP1 and pPP2 does not depend on the phase of growth of host cells and is steadily maintained up to 50 hours, whereas the kinetics of Dam methylation in vitro of sites located within the triplex loop does not differ substantially from the kinetics of methylation of other sites on the vector. Full methylation can be readily achieved in vitro. Additional factor(s) that operate in vivo to control the undermethylated state are most likely proteins since the observed effect can be suppressed by chloramphenicol administration to the cell cultures.
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Affiliation(s)
- P Parniewski
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Lodz
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8
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Chang AC, Israel A, Gazdar A, Cohen SN. Initiation of pro-opiomelanocortin mRNA from a normally quiescent promoter in a human small cell lung cancer cell line. Gene X 1989; 84:115-26. [PMID: 2558057 DOI: 10.1016/0378-1119(89)90145-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We describe the characteristics of pro-opiomelanocortin (POMC) mRNA synthesized by a human small cell lung cancer (SCLC) cell line that secretes a peptide immunoreactive with antibodies to the POMC-derived component, adrenocorticotropin. While no alteration in restriction endonuclease pattern or structure was found for the SCLC-derived pomc gene vs. the previously described human pomc gene cloned from a fetal liver library, Northern-blot analysis of SCLC RNA using pomc-derived probes showed a hybridizing transcript more than 300 nucleotides longer than POMC mRNA isolated from human pituitaries, as well as a pomc-gene-hybridizing mRNA the same length as pituitary-derived transcripts. 5' end mapping and primer extension analyses showed that the novel mRNA species is initiated at a site 371 bp upstream from the 5' end identified for pituitary-derived POMC mRNA. We conclude that synthesis of POMC transcripts occurs from an ordinarily quiescent promoter in the SCLC cell line we have studied, as well as from the pomc promoter normally used in pituitary cells.
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Affiliation(s)
- A C Chang
- Department of Genetics, Stanford University School of Medicine, CA 94305-5120
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9
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Werner D, Neuer-Nitsche B. Site-specific location of covalent DNA-polypeptide complexes in the chicken genome. Nucleic Acids Res 1989; 17:6005-15. [PMID: 2549504 PMCID: PMC318256 DOI: 10.1093/nar/17.15.6005] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A nitrocellulose filter binding assay was applied to isolate and to analyze the fraction of chicken DNA fragments associated with residual nuclear polypeptides resistant to SDS/proteinase K treatment and phenol extraction. It is shown that the DNA-polypeptide complexes retained on nitrocellulose filters are located on a non-random sub-set of DNA sequences. (a) Southern analysis reveals that the fractions of DNA fragments from chicken erythrocytes and from hen oviduct cells associated with the resistant polypeptides have a lower sequence complexity than unfractionated DNA. Moreover, the retained DNA fractions from different cell types of the same species are highly homologous. (b) All DNA fragments of the transcriptionally active and inactive ovalbumin gene map in the DNA fraction passing the filters indicating that the tight DNA-polypeptide complexes are not remnants of transcription complexes. (c) By use of a genomic sub-set library prepared from DNA retained on filters, clones were isolated with sequences mapping specifically in the DNA fraction associated with the tight DNA-polypeptide complexes. The results are consistent with fixed covalent DNA-polypeptide complexes in the chicken genome whose location is essentially identical in different cell types of the same species and apparently determined by DNA signal-sequences.
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Affiliation(s)
- D Werner
- Institut für Zell- und Tumorbiologie, Deutsches Krebsforschungszentrum, Heidelberg, FRG
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10
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Parniewski P, Galazka G, Wilk A, Klysik J. Complex structural behavior of oligopurine-oligopyrimidine sequence cloned within the supercoiled plasmid. Nucleic Acids Res 1989; 17:617-29. [PMID: 2644622 PMCID: PMC331607 DOI: 10.1093/nar/17.2.617] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Synthetic sequence GATCC(AG)7ATCG(AT)4CG(AG)7 was cloned into plasmid and its structural behavior under the influence of supercoiling was analysed by chemical modification at variety of experimental conditions. It was found that this sequence adopts at least two different non-B conformations depending on -delta and pH values. Moreover, 12 nucleotide long non-pur.pyr spacer region separating two identical (AG)7 blocks does not provide a significant energy barrier protecting against unusual structures formation.
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Affiliation(s)
- P Parniewski
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Lodz
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11
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Hanvey JC, Shimizu M, Wells RD. Intramolecular DNA triplexes in supercoiled plasmids. Proc Natl Acad Sci U S A 1988; 85:6292-6. [PMID: 3413097 PMCID: PMC281955 DOI: 10.1073/pnas.85.17.6292] [Citation(s) in RCA: 150] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A series of inserts with oligopurine.oligopyrimidine mirror repeat sequences was investigated at the base pair level with specific chemical probes (OsO4 and diethylpyrocarbonate) to evaluate the in vitro existence of intramolecular triplexes. Two parent inserts in recombinant plasmids with (GAA)9 and (AG)12 sequences and three mutant inserts (containing transitions or transversions) revealed that base pair changes at one location affected the chemical reactivity 13 base pairs away. The specificity and nature of these reactions, as well as the thermal stability of the complexes, provide direct evidence for the existence of a triplex with a portion of the pyrimidine-rich strand folded back and Hoogsteen-paired in the major groove of the Watson-Crick duplex. The biological implications of this unorthodox DNA structure are discussed.
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Affiliation(s)
- J C Hanvey
- Department of Biochemistry, School of Medicine, University of Alabama, Birmingham 35294
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12
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Influence of DNA sequence on the formation of non-B right-handed helices in oligopurine.oligopyrimidine inserts in plasmids. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68654-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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13
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Collier DA, Griffin JA, Wells RD. Non-B right-handed DNA conformations of homopurine.homopyrimidine sequences in the murine immunoglobulin C alpha switch region. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68655-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Unusual DNA sequences located within the promoter region and the first intron of the chicken pro-alpha 1(I) collagen gene. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)45204-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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15
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Budarf M, Blackburn E. S1 nuclease sensitivity of a double-stranded telomeric DNA sequence. Nucleic Acids Res 1987; 15:6273-92. [PMID: 2819822 PMCID: PMC306083 DOI: 10.1093/nar/15.15.6273] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We examined structural properties of poly d(C4A2).d(T2G4), the telomeric DNA sequence of the ciliated protozoan Tetrahymena. Under conditions of high negative supercoiling, poly d(C4A2).d(T2G4) inserted in a circular plasmid vector was preferentially sensitive to digestion with S1 nuclease. Only the C4A2 strand was sensitive to first-strand S1 cutting, with a markedly skewed pattern of hypersensitive sites in tracts of either 46 or 7 tandem repeats. Linear poly d(C4A2).(T2G4) showed no preferential S1 sensitivity, no circular dichroism spectra indicative of a Z-DNA conformation, no unusual Tm, and no unusual migration in polyacrylamide gel electrophoresis. The S1 nuclease sensitivity properties are consistent with a model proposed previously for supercoiled poly d(CT).d(AG) (Pulleyblank et al., Cell 42:271-280, 1985), consisting of a double-stranded, protonated, right-handed underwound helix. We propose that this structure is shared by related telomeric sequences and may play a role in their biological recognition.
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16
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Wohlrab F, McLean M, Wells R. The segment inversion site of herpes simplex virus type 1 adopts a novel DNA structure. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)45585-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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17
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Müller U, Wilson C. The effect of supercoil and temperature on the recognition of palindromic and non-palindromic regions in phi X174 replicative form DNA by S1 and Bal31. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61416-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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18
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Human homologs of TU transposon sequences: polypurine/polypyrimidine sequence elements that can alter DNA conformation in vitro and in vivo. Mol Cell Biol 1987. [PMID: 3025605 DOI: 10.1128/mcb.6.11.3632] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously have shown that homologs of the outer domain segment of the inverted repeat termini (IVR-OD) of the sea urchin TU transposons are conserved among multiple eucaryotic species, including humans. We report here that two cloned human DNA IVR-OD homologs, Hut2 and Hut17, consist of a series of tandem repeats of the trimer AGG/TCC, forming segments (313 and 221 base pairs in length, respectively) of polypurine/polypyrimidine (pPu/pPy or "Puppy") asymmetry in the two DNA strands; these are punctuated at certain sites with variant trimers, which are different for the two clones. Sequences homologous to the Hut2 pPu/pPy tract exist at multiple sites in the DNA of a wide variety of eucaryotes. Hybridization of human DNA with a Hut2 probe or with a previously described chicken DNA pPu/pPy sequence indicates that pPu/pPy sequences can be grouped into families distinguishable by the extent of their homology with each probe at different hybridization stringencies. Moreover, particular pPu/pPy tracts show species-specific differences in their distribution. Both the Hut2 and Hut17 pPu/pPy tracts are cleaved by S1 nuclease when tested on supercoiled plasmids. Most if not all of the 313-base-pair Hut2 pPu/pPy tract is also sensitive to S1 in its native location in HeLa cell chromatin, indicating that the sequence contains conformational information that can be expressed in vivo. This view is supported by evidence that exogenously derived Hut2 pPu/pPy tracts introduced into mouse L cells and integrated in chromatin can assume an S1-sensitive conformation.
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19
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Hoffman-Liebermann B, Liebermann D, Troutt A, Kedes LH, Cohen SN. Human homologs of TU transposon sequences: polypurine/polypyrimidine sequence elements that can alter DNA conformation in vitro and in vivo. Mol Cell Biol 1986; 6:3632-42. [PMID: 3025605 PMCID: PMC367124 DOI: 10.1128/mcb.6.11.3632-3642.1986] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We previously have shown that homologs of the outer domain segment of the inverted repeat termini (IVR-OD) of the sea urchin TU transposons are conserved among multiple eucaryotic species, including humans. We report here that two cloned human DNA IVR-OD homologs, Hut2 and Hut17, consist of a series of tandem repeats of the trimer AGG/TCC, forming segments (313 and 221 base pairs in length, respectively) of polypurine/polypyrimidine (pPu/pPy or "Puppy") asymmetry in the two DNA strands; these are punctuated at certain sites with variant trimers, which are different for the two clones. Sequences homologous to the Hut2 pPu/pPy tract exist at multiple sites in the DNA of a wide variety of eucaryotes. Hybridization of human DNA with a Hut2 probe or with a previously described chicken DNA pPu/pPy sequence indicates that pPu/pPy sequences can be grouped into families distinguishable by the extent of their homology with each probe at different hybridization stringencies. Moreover, particular pPu/pPy tracts show species-specific differences in their distribution. Both the Hut2 and Hut17 pPu/pPy tracts are cleaved by S1 nuclease when tested on supercoiled plasmids. Most if not all of the 313-base-pair Hut2 pPu/pPy tract is also sensitive to S1 in its native location in HeLa cell chromatin, indicating that the sequence contains conformational information that can be expressed in vivo. This view is supported by evidence that exogenously derived Hut2 pPu/pPy tracts introduced into mouse L cells and integrated in chromatin can assume an S1-sensitive conformation.
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20
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Evans T, Efstratiadis A. Sequence-dependent S1 nuclease hypersensitivity of a heteronomous DNA duplex. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66939-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Fowler RF, Skinner DM. Eukaryotic DNA diverges at a long and complex pyrimidine.purine tract that can adopt altered conformations. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)84479-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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22
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Shah DM, Hironaka CM, Wiegand RC, Harding EI, Krivi GG, Tiemeier DC. Structural analysis of a maize gene coding for glutathione-S-transferase involved in herbicide detoxification. PLANT MOLECULAR BIOLOGY 1986; 6:203-11. [PMID: 24307319 DOI: 10.1007/bf00015226] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/1985] [Accepted: 11/26/1985] [Indexed: 05/20/2023]
Abstract
We have used the cDNA clone encoding maize glutathione-S-transferase (GST I) to isolate a genomic DNA clone containing the complete GST I gene. Nucleotide sequence analysis of the cDNA and genomic clones has yielded a complete amino acid sequence for maize GST I and provided the exon-intron map of its gene. The mRNA homologous sequences in the maize GST I gene consist of a 107 bp 5' untranslated region, a 642 bp coding region and ≈340 bp of the 3' untranslated region. They are divided into three exons by two introns which interrupt the coding region. The 5' untranslated spacer contains an unusual sequence of pentamer AGAGG repeated seven times. The inbred maize line (Missouri 17) contains a single gene for GST I, whereas the hybrid line (3780A) contains two genes. Nucleotide sequence analysis of the primer extended cDNA products reveals that the 5' untranslated regions of the two genes in the hybrid 3780A are identical except for a 6 bp internal deletion (or insertion). The amino acid sequence of maize GST I shares no apparent sequence homology with the published sequences of animal GST's and represents the first published sequence of a plant GST. re]19850813 ac]19851126.
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Affiliation(s)
- D M Shah
- Division of Biological Sciences, Corporate Research and Development, Monsanto Company, 700 Chesterfield Village Parkway, 63197, St. Louis, MO, U.S.A
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23
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Financsek I, Tora L, Kelemen G, Hidvégi EJ. Supercoil induced S1 hypersensitive sites in the rat and human ribosomal RNA genes. Nucleic Acids Res 1986; 14:3263-77. [PMID: 3010232 PMCID: PMC339761 DOI: 10.1093/nar/14.8.3263] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Rat and human ribosomal RNA gene fragments in supercoiled plasmids were examined for S1 nuclease hypersensitivity. In the transcribed portion of genes the number and distribution of S1 sites were found to be species specific. No S1 sites were detected in the promoter regions. In the nontranscribed spacer (NTS), downstream of the 3' end of 28S RNA gene, S1 sites appear to be conserved in rat and human rDNAs. A rat NTS fragment (2987 nucleotides long), containing three S1 sites was sequenced and the S1 sites in this region were localized in polypyrimidine . polypurine simple repeat sequences. Other types of simple sequences, two type 2 Alu repeats and an ID sequence were also found in the sequenced region. The possible role of simple sequences and S1 sites in transcription and in recombination events of rDNA is discussed.
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24
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Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD. A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn 1985; 3:327-38. [PMID: 3917024 DOI: 10.1080/07391102.1985.10508420] [Citation(s) in RCA: 127] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have inserted the 509-bp-long fragment of sea urchin P. miliaris histone gene spacer region into plasmid pUC19. The fragment contains the 60-bp-long homopurine-homopyrimidine tract that is known to be hypersensitive to the S1 endonuclease. Using two-dimensional gel electrophoresis we have observed a sharp structural transition in the insert with increasing DNA superhelicity. As in the cases of cruciform and Z form formation, the observed transition partly relaxes the superhelical stress. In contrast with the other two well documented transitions, the observed transition strongly depends on pH. At pH7 and above the transition occurs at negative superhelicities exceeding the physiological range (- sigma greater than 0.08). For pH6 the transition occurs at -sigma = 0.055, whereas for pH4.3 it takes place at -sigma = 0.001. A comprehensive analysis of the obtained data has made it possible to define the nature of the observed transition. We conclude that under superhelical stress or/and at low pH homopurinehomopyrimidine tracts adopt a novel spatial structure called the H form.
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Affiliation(s)
- V I Lyamichev
- Institute of Molecular Genetics, USSR Academy of Sciences, Moscow
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Sheflin LG, Kowalski D. Altered DNA conformations detected by mung bean nuclease occur in promoter and terminator regions of supercoiled pBR322 DNA. Nucleic Acids Res 1985; 13:6137-54. [PMID: 2995917 PMCID: PMC321943 DOI: 10.1093/nar/13.17.6137] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Mung bean nuclease was used to probe for recognizable DNA unwinding and unpairing in the plasmid pBR322. In negatively supercoiled DNA, but not relaxed DNA, cleavages occurred preferentially in non-coding regions of the genome. The types of nucleotide sequences cleaved and which non-coding regions were cleaved depended upon environmental conditions. At 37 degrees C, cleavages occurred in an 84 bp A+T-rich sequence in the terminator region of the ampicillin-resistance gene. Recognition is likely based on a novel DNA conformation which occurs in the longest, most dA+dT-rich region of pBR322. In the presence of 1 mM Mg2+, cleavages occurred in inverted repeated sequences in the promoter regions of the RNA primer for DNA replication and ampicillin- and tetracycline-resistance genes as well as the terminator of RNA-1. Potential loops of hairpin (cruciform) structures were cleaved. At 27 degrees C, cleavages occurred near a promoter activated by cAMP receptor protein in vitro and in the 3' non-coding region of the tetracycline-resistance gene. Thus, in supercoiled pBR322 DNA, recognizable DNA unwinding and unpairing occurs preferentially in regulatory regions for transcription and DNA replication.
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Christophe D, Cabrer B, Bacolla A, Targovnik H, Pohl V, Vassart G. An unusually long poly(purine)-poly(pyrimidine) sequence is located upstream from the human thyroglobulin gene. Nucleic Acids Res 1985; 13:5127-44. [PMID: 2991855 PMCID: PMC321854 DOI: 10.1093/nar/13.14.5127] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A region of human genomic DNA encompassing the 5' end of the thyroglobulin gene has been sequenced and the position of the transcriptional start site has been determined. The 5' non-translated portion of the mRNA displays a quasi-palindromic sequence which could allow this region to adopt a hairpin structure. The first exon of the gene encodes a 19 amino-acids signal peptide and the 3 first amino acids of the mature protein. Apart from the canonical TATA-Box and from a CAAT-Box homology, the promoter region contains a 209 bp-long poly(purine)-poly (pyrimidine) sequence located between positions-512 and -304 relative to the transcription start. When contained in a supercoiled plasmid, this sequence exhibits sensitivity to S1 nuclease at two distinct positions. A precise mapping of the borders of the sensitive regions was achieved by extending primers from both ends of the sequence after digestion by the enzyme. The resulting data can be explained by a model involving the formation of a triple helix structure.
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Htun H, Lund E, Westin G, Pettersson U, Dahlberg JE. Nuclease S1-sensitive sites in multigene families: human U2 small nuclear RNA genes. EMBO J 1985. [PMID: 2411549 PMCID: PMC554425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We show here that human U2 small nuclear RNA genes contain a 'strong nuclease S1 cleavage site' (SNS1 site), a sequence that is very sensitive to digestion by nuclease S1. This site is located 0.50-0.65 kb downstream of the U2 RNA coding region. It comprises a 0.15-kb region in which (dC-dT)n:(dA-dG)n co-polymeric stretches represent greater than 90% of the sequence. Nuclease S1 is able to excise unit length repeats of the human U2 RNA genes both from cloned fragments and total human genomic DNA. The precise locations of the cleavage sites are dependent on the superhelicity of the substrate DNA. In negatively supercoiled substrates, cleavages are distributed over the entire 0.15-kb region, but in linearized substrates, they occur within a more limited region, mainly at the boundary of the SNS1 site closest to the human U2 RNA coding region. Nuclease S1 cleavage of negatively supercoiled substrates occurs at pHs as high as 7.0; in contrast, cleavage of linearized substrates requires a pH less than 5.0, indicating that supercoiling contributes to the sensitivity of this site. Mung bean nuclease gives results similar to that observed with nuclease S1.
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Trifonov EN, Konopka AK, Jovin TM. Unusual frequencies of certain alternating purine-pyrimidine runs in natural DNA sequences: relation to Z-DNA. FEBS Lett 1985; 185:197-202. [PMID: 3996596 DOI: 10.1016/0014-5793(85)80769-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Prokaryotic, eukaryotic and mitochondrial DNA sequences of total Length 300 000 nucleotides have been analyzed to find out whether stretches of alternating purines and pyrimidines are unusual in terms of occurrence, composition and base sequence. Alternating runs longer than 5 nucleotides are significantly under-represented in the natural sequences as compared to random ones. Octanucleotides are the most deficient, occurring at only 60% of the frequency expected in random sequences. An unexpectedly high proportion of these octamers consists of alternating tetramers with the repeat structure (PuPyPuPy)2 or (PyPuPyPu)2. DNA stretches containing such sequences can potentially form a S1 nuclease sensitive slippage (staggered loop) structure, which might serve as a locally unstacked intermediate in the B- to Z-DNA conformational transition.
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Brown DM, Gray DM, Patrick MH, Ratliff RL. Photochemical demonstration of stacked C.C+ base pairs in a novel DNA secondary structure. Biochemistry 1985; 24:1676-83. [PMID: 4005222 DOI: 10.1021/bi00328a016] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The secondary structure of the alternating polydeoxynucleotide sequence poly[d(C-T)] was studied as a function of pH by ultraviolet absorbance and circular dichroism spectroscopy and by the analysis of UV-induced photoproducts. As the pH was lowered, poly[d(C-T)] underwent a conformational transition that was characterized by changes in the long-wavelength region (280-320 nm) of the CD spectrum. These changes have previously been interpreted as evidence for the formation of a core of stacked, protonated C X C+ base pairs in a double-helical complex of poly[d(C-T)], with the thymidyl residues being looped out into the solvent [Gray, D. M., Vaughan, M., Ratliff, R. L., & Hayes, F. N. (1980) Nucleic Acids Res. 8, 3695-3707]. In the present work, poly[d(C-T)] was labeled with [U-14C]cytosine and [methyl-3H]thymine and irradiated at pH values both above and below the conformational transition point (monitored by CD spectroscopy). The distribution of radioactivity in uracil means value of uracil dimers, uracil means value of thymine dimers (the deamination products of cytosine means value of cytosine and cytosine means value of thymine dimers, respectively), and thymine-means value of thymine dimers was then determined. As the pH was decreased, we found an increase in the yield of uracil means value of uracil dimers and a decrease in the yield of uracil means value of thymine dimers, which occurred concomitantly with the change in the CD spectrum.(ABSTRACT TRUNCATED AT 250 WORDS)
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Htun H, Lund E, Dahlberg JE. Human U1 RNA genes contain an unusually sensitive nuclease S1 cleavage site within the conserved 3' flanking region. Proc Natl Acad Sci U S A 1984; 81:7288-92. [PMID: 6209712 PMCID: PMC392131 DOI: 10.1073/pnas.81.23.7288] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We find that the cloned DNAs of human U1 small nuclear RNA genes contain two nuclease S1-sensitive sites, one about 1.8 kilobases downstream of the U1 RNA coding region and the other around 0.3 kilobase upstream. The downstream site is unusually sensitive to the nuclease, being cleaved in both linear and negatively supercoiled DNAs. The extent of cleavage at this site is enhanced at lower pH and reduced concentrations of NaCl; the effects of salt are more apparent on linear than supercoiled DNAs. The nuclease S1 sensitivity of this downstream site is dependent on the presence of the sequence (dC-dT)n X (dA-dG)n, where n = 15-25. (One gene with n = 5 is resistant to nuclease S1 cleavage in this region.) In contrast, the nuclease S1 site upstream of the coding region is cleaved only when the DNA is supercoiled. This site also has a homopyrimidine X homopurine bias in the DNA strands, but the sequence is less regular. In the course of these studies, we detected several discrepancies between our restriction maps of some U1 RNA genes and those published by others. Our maps demonstrate that all seven cloned human U1 RNA genes are very similar in sequence for as much as 2.3 kilobases downstream of the U1 RNA coding region.
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Evans T, Schon E, Gora-Maslak G, Patterson J, Efstratiadis A. S1-hypersensitive sites in eukaryotic promoter regions. Nucleic Acids Res 1984; 12:8043-58. [PMID: 6095186 PMCID: PMC320272 DOI: 10.1093/nar/12.21.8043] [Citation(s) in RCA: 153] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We have examined by fine mapping the S1 nuclease-hypersensitivity of the 5' flanking regions of the human beta-globin and rat preproinsulin II genes and of the SV40 origin/enhancer region. In all cases S1-hypersensitive sites are located in known or presumed promoter/regulatory regions. Though a consensus DNA sequence is not evident, all of these sites reside in predominantly homopurine-homopyrimidine stretches. The alternate (non-B) DNA structure which is revealed by the enzymatic probe is a sequence-dependent feature of a short stretch of DNA, which is retained upon transplantation into a foreign environment. The alternate structure exhibits S1-nicking patterns uniquely different from those associated with the presence of Z-DNA.
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Sheflin LG, Kowalski D. Mung bean nuclease cleavage of a dA + dT-rich sequence or an inverted repeat sequence in supercoiled PM2 DNA depends on ionic environment. Nucleic Acids Res 1984; 12:7087-104. [PMID: 6091054 PMCID: PMC320144 DOI: 10.1093/nar/12.18.7087] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We have determined the nucleotide sequences around two alternative sites cleaved in supercoiled PM2 DNA by single-strand-specific mung bean nuclease in different ionic environments. In 10 mM Tris-HC1 (pH 7.0, 37 degrees C), the major site is a dA+dT-rich sequence which maps with a known early denaturation region at 0.75 map units. About 30 cleavages occurred in a 135 bp region. Cleavages were largely excluded at (dA)n . (dT)n (n = 3-7) sequences. Cleavage patterns of this type have not been previously observed in dA+dT-rich sequences. With the addition of 0.1 M NaC1 the major alternative site occurred in a hyphenated inverted repeat sequence 500 bp away (0.70 map units) and did not map to an early denaturation region. One major and 4 minor cleavages occurred in the region between the repeats, suggesting that a hairpin containing at most a 12 bp stem and 10 base loop is recognized. The basis for nuclease recognition of the dA+dT-rich sequence is not clear. The differences in the sequences and cleavage patterns at the alternative sites indicate that their secondary structures differ.
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Abstract
The potential of the cloned histone H5 gene to form altered DNA structures has been examined by S1 nuclease digestion of supercoiled recombinant plasmids containing up to 8.8 kbp of chicken DNa. The three main nicking sites map at the upstream and downstream sequences flanking the structural gene. The cleavage sites share sequence homology, strand specificity, and do not seem to be single-stranded. The sequence of the S1-sensitive sites does not suggest that the fragments can adopt any of the known DNA secondary structures.
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