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G P Holmquist

Publications and source records attributed to G P Holmquist.

16 recordsLinked to original sources
PubMed1992

Binding of transcription factors creates hot spots for UV photoproducts in vivo.

Cyclobutane dipyrimidines and less than mean value of 6-4 dipyrimidines are the two major classes of mutagenic DNA photoproducts produced by UV irradiation of cells. We developed a method to map cyclobutane dipyrimidines at the DNA sequence level in mammalian cells. The frequency of this class of photoproducts was determined at every dipyrimidine along the human phosphoglycerate kinase-1 (PGK1) promoter sequence and was compared to the UV-induced frequency distribution of mean value of 6-4 dipyrimidines. After irradiation of living cells containing active or inactive PGK1 genes, enzymatic or chemical cleavage at UV photoproducts, and amplification by ligation-mediated polymerase chain reaction, photofootprints were seen in all regions which bind transcription factors and appear as DNase I footprints. Photoproduct frequency within transcription factor binding sites was suppressed or enhanced relative to inactive genes or naked DNA with enhancements of up to 30-fold. Since photoproducts are mutagenic, this indicates that photoproduct (mutation?) hot spots may be tissue specific in mammals.

Animals↗
PubMed1992

Chromosome bands, their chromatin flavors, and their functional features.

To show that the input pattern of chromosomal mutations is highly organized relative to the band patterns along human chromosomes, a new term, "metaphase chromatin flavor," is introduced. Five different flavors of euchromatic metaphase bands are cytologically identified along a human ideogram. These are G-bands and, based upon combinations of extreme Alu richness and GC richness, four different R-band flavors. The two flavors with extremely GC-rich components, traditionally called "T-bands," represent only 15% of all bands. However, they contain 65% of mapped genes, 19 of 25 mapped oncogenes, most cancer-associated rearrangements, evolutionary rearrangements, meiotic chiasmata, and X-ray-induced breaks. Flavors with extremely Alu-rich flavors are also involved in melphalan-induced rearrangements, pachytene stretching, and mitotic chiasmata. Frequencies of CpG islands, CCGCCC boxes, retroposon families, and genes are characteristic to each chromatin flavor and will facilitate alignment of genome sequences onto ideograms of chromatin flavor. The influence of chromatin flavor on the evolution of a gene's sequence is so strong that one can infer the flavor of the band in which a gene resides from the sequence of the gene itself. Correlation coefficients for many pairs of mapped genetic variables, while globally high, are quite low within bands of one flavor, implicating a concerted mode of evolution for bands of one chromatin flavor.

Biological Evolution↗
PubMed1991

In vivo mapping of a DNA adduct at nucleotide resolution: detection of pyrimidine (6-4) pyrimidone photoproducts by ligation-mediated polymerase chain reaction.

DNA adducts in unique sequences along the mammalian genome are mapped in vivo at single-nucleotide resolution. Pyrimidine (6-4) pyrimidone photoproducts [(6-4) photoproducts] represent one of the two major adduct classes found after UV irradiation of DNA and were shown to play an important role in UV-induced mutagenesis. After UV light treatment of cells, DNA is prepared and chemically cleaved at (6-4) photoproducts with piperidine. Gene-specific fragments are then amplified from total genomic DNA by use of a ligation-mediated polymerase chain reaction. Analysis of the human chromosome X-linked phosphoglycerate kinase (PGK1) gene's promoter has shown that the frequency of (6-4) photoproducts expressed as piperidine-labile sites is (i) high at TpC and CpC dinucleotides, (ii) dependent on the nearest-neighbor bases, (iii) inhibited by the binding of a transcription factor, and (iv) different for DNA derived from the active and inactive X chromosome. This latter difference is mainly a consequence of the presence of 5-methylcytosine (m5C) in CpG dinucleotides on the inactive X chromosome. 5-Methylcytosine in the sequences Tm5CG and Cm5CG inhibits the formation of (6-4) photoproducts. Thus, in addition to in vivo mapping of a DNA adduct at nucleotide resolution, we also report another method for methylation analysis and photofootprinting.

Animals↗
PubMed1989

Evolution of chromosome bands: molecular ecology of noncoding DNA.

Giemsa dark bands, G-bands, are a derived chromatin character that evolved along the chromosomes of early chordates. They are facultative heterochromatin reflecting acquisition of a late replication mechanism to repress tissue-specific genes. Subsequently, R-bands, the primitive chromatin state, became directionally GC rich as evidenced by Q-banding of mammalian and avian chromosomes. Contrary to predictions from the neutral mutation theory, noncoding DNA is positionally constrained along the banding pattern with short interspersed repeats in R-bands and long interspersed repeats in G-bands. Chromosomes seem dynamically stable: the banding pattern and gene arrangement along several human and murine autosomes has remained constant for 100 million years, whereas much of the noncoding DNA, especially retroposons, has changed. Several coding sequence attributes and probably mutation rates are determined more by where a gene lives than by what it does. R-band exons in homeotherms but not G-band exons have directionally acquired GC-rich wobble bases and the corresponding codon usage: CpG islands in mammals are specific to R-band exons, exons not facultatively heterochromatinized, and are independent of the tissue expression pattern of the gene. The dynamic organization of noncoding DNA suggests a feedback loop that could influence codon usage and stabilize the chromosome's chromatin pattern: DNA sequences determine affinities of----proteins that together form----a chromatin that modulates----rate constants for DNA modification that determine----DNA sequences. Theories of hierarchical selection and molecular ecology show how selection can act on Darwinian units of noncoding DNA at the genome level thus creating positionally constrained DNA and contributing minimal genetic load at the individual level.

Base Sequence↗
PubMed1988

An equation for DNA electrophoretic mobility in agarose gels.

Assignment of molecular weight to DNA fragments on the basis of electrophoretic mobility in agarose gels is complicated by nonlinearity of the relationship between mobility and molecular weight. Graphical methods that linearize sigmoidal curves provide a simplified description of the mobility function when applied to normalized mobility data. This description is valid over a wide range of molecular weights. Linear duplex molecules of lengths ranging from 118 to 169,200 base pairs were electrophoresed at voltage gradients of 1 to 6 V/cm through horizontal slab gels ranging from 0.2 to 1.6% agarose. A logit transformation of the mobility graphed versus the logarithm of molecular weight, analogous to a Hill plot of enzyme kinetics, is a straight line. Changes in the voltage gradient or gel composition alter the position but not the slope or linearity of the data plotted by this method. The logistic representation is compared with the conventional graph of log molecular weight versus mobility, with the graph of molecular weight versus reciprocal mobility, and with Probit analysis of the mobility function. Parameters were determined for one equation that accurately describes DNA mobility as a function of the three tested variables. Curves are presented that are useful in predicting fragment length, migration, resolution, and gel performance.

DNA, Viral↗
PubMed1987

Role of replication time in the control of tissue-specific gene expression.

Late-replicating chromatin in vertebrates is repressed. Housekeeping (constitutively active) genes always replicate early and are in the early-replicating R-bands. Tissue-specific genes are usually in the late-replicating G-bands and therein almost always replicate late. Within the G-bands, however, a tissue-specific gene does replicate early in those cell types that express that particular gene. While the condition of late replication may simply be coincident with gene repression, we review evidence suggesting that late replication may actively determine repression. As mammals utilize a developmental program to Lyonize (facultatively heterochromatinize) whole X chromosomes to a late-replicating and somatically heritable repressed state, similarly another program seems to Lyonize individual replicons. In frogs, all genes begin embryogenesis by replicating during a very short interval. As the developmental potency of embryonic cells becomes restricted, late-replicating DNA gradually appears. This addition to the repertoire of gene control--i.e., repression via Lyonization of individual replicons--seems to have evolved in vertebrates with G-bands being a manifestation of the mechanism.

Animals↗
PubMed1986

Replication time of interspersed repetitive DNA sequences in hamsters.

The replication time of 34 hamster genomic DNA segments containing interspersed repeat sequences was determined by probing the cloned segments with nick-translated early- and late-replicating hamster DNA. One-third of these cloned families replicated early, one-third replicated late, and one-third replicated without temporal bias. 19 different inserts from these clones along with the SINE, Alu, and the LINE, A36Fc, were used to probe Southern blots of early- and late-replicating hamster or human DNA. We report long interspersed repeats, LINEs, are selectively partitioned into late-replicating DNA and are often concertedly hypomethylated, while short interspersed repeats, SINEs, are selectively partitioned into early-replicating DNA. For some interspersed repeat families, this partitioning is complete or almost complete. The CCGG frequency is very low in late-replicating DNA. The mammalian chromosome's pattern of early-replicating R-bands and late-replicating G-bands reflects a differential distribution of LINEs and SINEs.

Animals↗
PubMed1985

Fra(10)(q25): the BrdU effect is substitution-dependent.

Expression in the majority of fra(10)(q25) cases is either induced or enhanced by the presence of bromodeoxyuridine (BrdU) in the culture medium. BrdU is known to exert its effects on cells via two primary mechanisms: substitution-dependent and concentration-dependent. BrdU incorporation into DNA and BrdU concentration in the culture medium can be resolved as independent variables. The results of such experiments indicate that at three fixed levels of BrdU substitution, 100-fold variation of BrdU concentration had little or no effect on fra(10)(q25) expression. At a fixed BrdU concentration, the level of fra(10)(q25) expression rises as a function of increased BrdU substitution, approaching 100% expression at 100% substitution. Thus, BrdU induction or enhancement of fra(10)(q25) expression is clearly substitution-dependent. Iododeoxyuridine, another halogenated pyrimidine, has a similar effect. The critical time of incorporation is between 8 and 9 hrs before mitosis. After this time, removal of BrdU (and fluorodeoxyuridine [FdU]) from the culture medium followed by addition of deoxythymidine does not reverse the BrdU effect on fra(10)(q25) expression.

Bromodeoxyuridine↗
PubMed1984

Replication timing of genes and middle repetitive sequences.

DNA replication in mammals is temporally bimodal. "Housekeeping" genes, which are active in all cells, replicate during the first half of the S phase of cell growth. Tissue-specific genes replicate early in those cells in which they are potentially expressed, and they usually replicate late in tissues in which they are not expressed. Replication during the first half of the S phase is, therefore, a necessary but not sufficient condition for gene transcription. A change in the replication timing of a tissue-specific gene appears to reflect the commitment of that gene to transcriptional competence or to quiescence during ontogeny. Most families of middle repetitive sequences replicate either early or late. These data are consistent with a model in which two functionally distinct genomes coexist in the nucleus.

Animals↗
PubMed1980

Ring chromosome 15: phenotype, Ag-NOR analysis, secondary aneuploidy, and associated chromosome instability.

Cytogenetic analysis of a 15 month old girl evaluated for severe developmental delay and acral skeletal hypoplasia revealed a predominant 46,XX,r(15) karyotype. Prophase banding analysis showed minimal deletion of the ring chromosome (breakpoints p12 and q26), while silver staining showed it to have an active nucleolus organizing region, multiple abnormal secondary configurations, and decreased satellite association. Although there was no spontaneous instability in the rest of the karyotype, gentian violet-induced chromosome breakage was significantly increased. The rate of spontaneous sister chromatid exchange was not elevated. Cellular mosaicism for chromosome 15 aneuploidy most likely accounts for the patient's phenotypic abnormalities.

Abnormalities, Multiple↗
PubMed1979

Telomere replication, kinetochore organizers, and satellite DNA evolution.

Robertsonian rearrangements demonstrate one-break chromosome rearrangement and the reversible appearance and disappearance of telomeres and centromeres. Such events are quite discordant with classical cytogenetic theories, which assume all chromosome rearrangements to require at least two breaks and consider centromeres and telomeres as immutable structures rather than structures determined by mutable DNA sequences. Cytogenetic data from spontaneous and induced telomere-telomere fusions in mammals support a molecular model of terminal DNA synthesis in which all telomeres are similar and recombine before replication and subsequent separation. This, along with evidence for a hypothetical DNA sequence, the kinetochore organizer, readily explains latent telomeres, latent centromeres, and reversible (one-break) Robertsonian rearrangements. A second model, involving simply recombination between like satellite DNA sequences on different chromosomes, explains not only how one satellite can simultaneously evolve on different chromosomes, but also why satellite DNA is usually located near centromeres or telomeres and why it maintains a preferred orientation with respect to the centromere.

Base Sequence↗
PubMed1979

Partial triplication and deletion of 13q: study of a family presenting with bilateral retinoblastomas.

This report compares the pathogenetic influences of selective deletion and triplicaton of chromosome 13 derived from a familial 12;13 insertional translocation. In the proband a heritable chromosomal basis for his bilateral retinoblastomas is established [46,XY,del (13) (pter leads to q12.5: :q22.1 leads to qter)mat], and in his sister the relatively modest effects of triplication of the mid-portions of 13q are demonstrated [46,XX,ins(12;13) (12pter leads to 12p11.2: :13q22.1 leads to 13q12.5: :12p11.2 leads to 12qter)mat]. Qualitative and quantitative gene marker studies and chromosomal staining techniques to differentiate timing of DNA replication failed to indicate functional gene changes about the breakpoints.

Child, Preschool↗
PubMed1979

De novo 13q paracentric inversion in a boy with cleft palate and mental retardation.

A paracentric inversion in chromosome 13, inv(13)(q12q22), is described in a boy with mild mental retardation and multiple minor anomalies. Bromodeoxyuridine-late replication studies showed no changes in the replication pattern of bands in the abnormal chromosome 13. The relation between the proband's phenotype and his inv(13) is unclear.

Child, Preschool↗
PubMed1976

Histones and G banding of chromosomes.

Polylysine, polyarginine, and histones H1, H2A, H2B, and H3 inhibit Giemsa staining and chromosome banding by binding to DNA and preventing side stacking of the positively charged thiazine dyes to the negatively charged phosphate groups on DNA. This is a nonspecific effect and does not of itself provide evidence for a role of histones in G banding. The question of whether histones are involved in chromosome banding is reviewed.

Arginine↗
PubMed1975

Sister chromatid exchange and chromosome organization based on a bromodeoxyuridine Giemsa-C-banding technique (TC-banding).

Hoechst 33258 fluorescent staining of bromodeoxyuridine substituted chromosomes provided a high resolution technique for following the segregation of replicated chromosomal DNA (Latt, 1973). Modifications have produced the same results after Giemsa staining (Wolff and Perry, 1975). Since this does not necessarily require Hoechst (Korenberg and Freedlander, 1975), we call this bromodeoxyuridine-Giemsa banding (BG-banding). We here describe a further modification which allows one to follow the T-rich strand of the AT-rich satellite DNA of C-band heterochromatin. We call this TC-banding. This technique was used to examine metacentric marker chromosomes found in mouse L-cells that contain many interstitial blocks of centromeric-type heterochromatin in each arm plus the usual two blocks of centromeric heterochromatin. One of the advantages of this technique for such chromosomes is that it is possible to distinguish first from second cell cycle sister chromatid exchange and unambiguously detect centromeric sister chromatid exchange. We found some chromosomes to have high rates of centromeric sister chromatid exchange. After one cycle in bromodeoxyuridine we could examine the satellite polarity of the heterochromatic DNA. Since there was no change in satellite polarity in any of the heterochromatic blocks, marker chromosomes could not have been formed by paracentric inversions, inverted insertions or inverted translocations. These results allow the formulation of several rules of chromosome organization.

Animals↗