scholarly journals Supercoiling Theory and Model of Chromosomal Structures in Eukaryotic Cells

2019 ◽  
Author(s):  
Hao Zhang ◽  
Tianhu Li
Keyword(s):  
Driving Forces ◽  
Histone H1 ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Negative Supercoils ◽  
Current Report ◽  
Theory And Model

About six billion base pairs of DNA reside highly orderly in each human cell’s nucleus through their manifestation as twenty-three pairs of chromosomes. Delicate patterns of spatial organizations of DNA macromolecules in these eukaryotic chromosomes as well as their associated physical driving forces have, however, not been fully understood thus far. On the basis of (1) our four recent discoveries about supercoiling properties of histone H1, nucleosomes, linker DNA and polynucleosomes, (2) well-accepted six axioms about signs, shapes and handedness of DNA supercoils, and (3) our three new prepositions about correlations between DNA supercoils and chromosomal structures, we formulate new theories and models of eukaryotic chromosomal structures in the current report. It is our conclusion that all levels of chromosomal structures in eukaryotic cells are governed mainly by negative supercoils that are present in their naked linker DNA regions.

scholarly journals New Supercoiling Theory and Model of Chromosomal Structures in Eukaryotic Cells

2018 ◽  
Author(s):  
Hao Zhang ◽  
Tianhu Li
Keyword(s):  
Driving Forces ◽  
Histone H1 ◽  
Dna Supercoiling ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Genetic Events ◽  
Current Report ◽  
Theory And Model

About six billion base pairs of DNA reside highly orderly in each human cell’s nucleus through their manifestation as twenty-three pairs of chromosomes. Delicate patterns of spatial organizations of DNA macromolecules in these eukaryotic chromosomes as well as their associated driving forces have, however, not been fully understood thus far. On the basis of (1) our four recent discoveries about supercoiling properties of histone H1, nucleosomes, linker DNA and polynucleosomes, (2) well-established axioms about sign, shapes and handedness of DNA supercoils, as well as (3) the fact that alterations of DNA supercoils are affiliated with every single steps of cellular genetic events, we analyze effects of DNA supercoils on eukaryotic chromosomal structures in systematical and comprehensive manners in the current report, and present new theory and models of eukaryotic chromosomal structures from the DNA supercoiling perspective. It is our hope that our current presentation of new supercoiling theory and models could provoke future new efforts to unravel exquisite eukaryotic chromosomal architectures in an all-inclusive manner.

scholarly journals Supercoiling Theory and Model of Chromosomal Structures in Eukaryotic Cells

2018 ◽  
Author(s):  
Hao Zhang ◽  
Tianhu Li
Keyword(s):  
Driving Forces ◽  
Three Dimensional ◽  
Histone H1 ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Negative Supercoils ◽  
Theory And Model

About six billion base pairs of DNA reside highly orderly in each human cell’s nucleus through their manifestation as twenty-three pairs of chromosomes. Delicate patterns of spatial organizations of DNA macromolecules in these eukaryotic chromosomes as well as their associated physical driving forces have, however, not been fully understood thus far. On the basis of (1) our four recent discoveries about supercoiling properties of histone H1, nucleosomes, linker DNA and polynucleosomes and (2) well-established axioms about signs, shapes and handedness of DNA supercoils, we formulate new theories and models of eukaryotic chromosomal structures. It is our conclusion that three-dimensional structures of eukaryotic chromosomes and their sublevel architectures are govern mainly by negative supercoils that are present in their naked linker DNA regions.

scholarly journals Adding toYersinia enterocoliticaGene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Daniela Lepka ◽  
Tobias Kerrinnes ◽  
Evelyn Skiebe ◽  
Birgitt Hahn ◽  
Angelika Fruth ◽  
...  
Keyword(s):  
Hypothetical Protein ◽  
Replication Initiation ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Significant Similarity ◽  
Replication Initiation Protein ◽  
Cryptic Plasmids ◽  
Reading Frames

We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs) carried by aYersinia enterocoliticabiotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs) encoding the first CcdA/CcdB-like antitoxin/toxin system described for aYersiniaplasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described inSalmonella(CcdA/B),Klebsiella(RepA), andPlesiomonas(MobA/C) indicating genomic fluidity among members of theEnterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9%) was similar to that of pYe4449-1 (53.7%) and differed from that of theY. enterocoliticagenome (47.3%). Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at4°Cbut not at or above27°Csuggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing theDxxGN(x)nDxxGNmotif. Our findings illustrate the exceptional gene pool diversity within the speciesY. enterocoliticadriven by horizontal gene transfer events.

scholarly journals Regulation of the higher-order structure of chromatin by histones H1 and H5.

1981 ◽  
Vol 90 (2) ◽  
pp. 279-288 ◽  
Author(s):  
J Allan ◽  
G J Cowling ◽  
N Harborne ◽  
P Cattini ◽  
R Craigie ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Single Species ◽  
Histone H1 ◽  
Higher Order ◽  
Linker Histone ◽  
Micrococcal Nuclease ◽  
Order Structure ◽  
Chicken Erythrocyte ◽  
Base Pairs ◽  
Native Chicken

Chicken erythrocyte chromatins containing a single species of linker histone, H1 or H5, have been prepared, using reassembly techniques developed previously. The reconstituted complexes possess the conformation of native chicken erythrocyte chromatin, as judged by chemical and structural criteria; saturation is reached when two molecules of linker histone are bound per nucleosome, as in native erythrocyte chromatin, which the resulting material resembles in its appearance in the electron microscope and quantitatively in its linear condensation factor relative to free DNA. The periodicity of micrococcal nuclease-sensitive sites in the linker regions associated with histone H1 or H5 is 10.4 base pairs, suggesting that the spatial organization of the linker region in the higher-order structure of chromatin is similar to that in isolated nucleosomes. The susceptible sites are cut at differing frequencies, as previously found for the nucleosome cores, leading to a characteristic distribution of intensities in the digests. The scission frequency of sites in the linker DNA depends additionally on the identity of the linker histone, suggesting that the higher-order structure is subject to secondary modulation by the associated histones.

Structural studies of DNA gyrase

1984 ◽  
Vol 42 ◽  
pp. 164-167
Author(s):  
T. Kirchhausen ◽  
J. Wang ◽  
S. C. Harrison
Keyword(s):  
Microscopic Study ◽  
Dna Gyrase ◽  
Staphylococcal Nuclease ◽  
Dependent Manner ◽  
Type Ii ◽  
Structural Studies ◽  
Electron Microscopic ◽  
Base Pairs ◽  
Gyrase A ◽  
Negative Supercoils

DNA gyrase, a prokaryotic type II topoisomerase, can introduce negative supercoils into DNA in an ATP-dependent manner and relax negative supercoils in the absence of ATP. Gyrase is a tetramer of two A subunits (MW 105,000) and two B subunits (MW 95,000), and it interacts with about 140 base pairs of DNA (based on staphylococcal nuclease and DNase I protection experiments). We have undertaken an electron microscopic study of gyrase and its binding to DNA, in order to determine how DNA wraps in its complex with the protein.

scholarly journals Mechanistic Analyses of Supercoiling Behaviors of DNA in Nucleosomes and Chromatins

2019 ◽  
Author(s):  
Hao Zhang ◽  
Tianhu Li
Keyword(s):  
Dna Sequences ◽  
Base Pair ◽  
Histone H1 ◽  
Molecular Pathways ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nucleosome Core ◽  
Histone Octamers ◽  
Dynamic Structures ◽  
Current Report

AbstractBesides those in 146-base pair nucleosome core particle DNA, supercoils have been known to be present in 10-base pair arm DNA segments and naked linker DNA segments. The interacting patterns among histone octamers, histone H1, 10-base pair arm DNA segments and linker DNA have, however, not yet been elucidated. In the current report, we examine correlations among constituents of nucleosomes from the mechanistic perspectives and present molecular pathways for elucidating supercoiling behaviors of their component DNA sequences. It is our hope that our new analyses could serve as incentives to further clarify correlations between histones and DNA in the dynamic structures of chromatins in the future.

scholarly journals Histone H1 represses transcription from minichromosomes assembled in vitro.

1989 ◽  
Vol 9 (12) ◽  
pp. 5573-5584 ◽  
Author(s):  
A Shimamura ◽  
M Sapp ◽  
A Rodriguez-Campos ◽  
A Worcel
Keyword(s):  
Transcriptional Activation ◽  
Transcriptional Repression ◽  
Histone H1 ◽  
Rrna Gene ◽  
Base Pairs ◽  
Dna Templates ◽  
5S Rrna Gene ◽  
In Trans ◽  
Transcription Complexes

We have previously shown that transcription from a Xenopus 5S rRNA gene assembled into chromatin in vitro can be repressed in the absence of histone H1 at high nucleosome densities (one nucleosome per 160 base pairs of DNA) (A. Shimamura, D. Tremethick, and A. Worcel, Mol. Cell. Biol. 8:4257-4269, 1988). We report here that transcriptional repression may also be achieved at lower nucleosome densities (one nucleosome per 215 base pairs of DNA) when histone H1 is present. Removal of histone H1 from the minichromosomes with Biorex under conditions in which no nucleosome disruption was observed led to transcriptional activation. Transcriptional repression could be restored by adding histone H1 back to the H1-depleted minichromosomes. The levels of histone H1 that repressed the H1-depleted minichromosomes failed to repress transcription from free DNA templates present in trans. The assembly of transcription complexes onto the H1-depleted minichromosomes protected the 5S RNA gene from inactivation by histone H1.

Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II

Science ◽  
1991 ◽  
Vol 254 (5029) ◽  
pp. 238-245
Author(s):  
PJ Laybourn ◽  
JT Kadonaga
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Histone H1 ◽  
Regulation Of Transcription ◽  
Base Pairs ◽  
Transcription Analysis ◽  
Dna Templates ◽  
Naked Dna

The relation between chromatin structure and transcriptional activity was examined by in vitro transcription analysis of chromatin reconstituted in the absence or presence of histone H1. To maintain well-defined template DNA, purified components were used in the reconstitution of chromatin. Reconstitution of nucleosomal cores to an average density of 1 nucleosome per 200 base pairs of DNA resulted in a mild reduction of basal RNA polymerase II transcription to 25 to 50 percent of that obtained with naked DNA templates. This nucleosome-mediated repression was due to nucleosomal cores located at the RNA start site and could not be counteracted by the sequence-specific transcription activators Sp1 and GAL4-VP16. When H1 was incorporated into the chromatin at 0.5 to 1.0 molecule per nucleosome (200 base pairs of DNA), RNA synthesis was reduced to 1 to 4 percent of that observed with chromatin containing only nucleosomal cores, and this H1-mediated repression could be counteracted by the addition of Sp1 or GAL4-VP16 (antirepression). With naked DNA templates, transcription was increased by a factor of 3 and 8 by Sp1 and GAL4-VP-16, respectively (true activation). With H1-repressed chromatin templates, however, the magnitude of transcriptional activation mediated by Sp1 and GAL4-VP16 was 90 and more than 200 times higher, respectively, because of the combined effects of true activation and antirepression. The data provide direct biochemical evidence that support and clarify previously proposed models in which there is depletion or reconfiguration of nucleosomal cores and histone H1 at the promoter regions of active genes.

On the structure of cellular and viral chromatin

1978 ◽  
Vol 283 (997) ◽  
pp. 275-285 ◽  
Keyword(s):  
Ionic Strength ◽  
Simian Virus 40 ◽  
Histone H1 ◽  
Staphylococcal Nuclease ◽  
Dna Fragments ◽  
Base Pairs ◽  
Nuclease Digestion ◽  
Dna Fragment ◽  
Histone H5 ◽  
Low Ionic Strength

Some of the recent experimental data obtained in our laboratory are briefly reviewed. 1. A mild staphylococcal nuclease digestion of either chromatin or nuclei from mouse Ehrlich tumour cells results in chromatin subunits (mononucleosomes) of three discrete kinds. The smallest mononucleosome (MN 1 contains all histones except H1 and a DNA fragment 140 base pairs long. The intermediate mononucleosome (MN 2 ) contains all five histones and a DNA fragment 170 base pairs long. The third mononucleosome (MN 3 ) also contains all five histones, but its associated DNA is longer and somewhat heterogeneous in size (180-200 base pairs). Most of the MN 3 particles are rapidly converted to mononucleosomes MN 2 and MN 1 by nuclease digestion. However, there exists a relatively nuclease-resistant subpopulation of the MN 3 mononucleosomes. These 200 base-pair MN 3 particles contain not only histones but also non-histone proteins and are significantly more resistant to nuclease then even the smaller mononucleosomes MN 1 and MN 2 . 2. Nuclease digestion of hen erythrocyte nuclei or chromatin, in which histone H1 is partially replaced by histone H5 produces the mononucleosomes MN 1 and two electrophoretically resolvable kinds of MN 2 mononucleosomes, one containing histone H1 and the other one histone H5. A relatively nuclease-resistant subset of the mononucleosomes MN 3 is preferentially accumulated at later stages of the digestion. 3. Although pancreatic DNase (DNase I) and spleen acid DNase (DNase II) attack the DNA in chromatin in a manner different from that of staphylococcal nuclease, the deoxyribonucleoprotein (DNP) products of digestion are similar for all three enzymes under identical solvent conditions, as revealed by gel electrophoresis of the DNP at low ionic strength. 4. There are eight major kinds of staphylococcal nuclease-produced soluble subnucleosomes (i.e. particles smaller than the mononucleosomes). In particular, the subnucleosome SN 1 is a set of naked double-stranded DNA fragments ca. 20 base pairs long. Subnucleosome SN 2 is a complex of a specific highly basic non-histone protein and a DNA fragment ca. 27 base pairs long. Subnucleosomes SN 7 and SN 8 each contain all of the histones except H1 and DNA fragments ca. 100 and 120 base pairs long, respectively. 5. Nuclease digestion of isolated mono- and dinucleosomes does not produce all of the subnucleosomes. These and related findings indicate that the cleavages required to generate these subnucleosomes result from some aspect of chromatin structure which is lost upon digestion to mono- or dinucleosomes. Nuclease digestion of isolated minichromosomes of Simian virus 40 (SV40) (which contain all five histones including H1) produces mononucleosomes MN 1 and MN 2 but does not produce some of the subnucleosomes or the relatively nuclease-resistant subset of the MN 3 mononucleosomes. 6. The rate of sedimentation of the SV40 minichromosomes ( ca. 60 S ) under ‘physiological’ ionic conditions ( μ ≈ 0.15) is about two times higher than that in a low ionic strength buffer ( μ ≈ 0.005). Occurrence of the compact state of the minichromosome critically depends upon the presence of histone H1 and can be irreversibly fixed by treatment with formaldehyde.

Histone H1 represses transcription from minichromosomes assembled in vitro

1989 ◽  
Vol 9 (12) ◽  
pp. 5573-5584
Author(s):  
A Shimamura ◽  
M Sapp ◽  
A Rodriguez-Campos ◽  
A Worcel
Keyword(s):  
Transcriptional Activation ◽  
Transcriptional Repression ◽  
Histone H1 ◽  
Rrna Gene ◽  
Base Pairs ◽  
Dna Templates ◽  
5S Rrna Gene ◽  
In Trans ◽  
Transcription Complexes

We have previously shown that transcription from a Xenopus 5S rRNA gene assembled into chromatin in vitro can be repressed in the absence of histone H1 at high nucleosome densities (one nucleosome per 160 base pairs of DNA) (A. Shimamura, D. Tremethick, and A. Worcel, Mol. Cell. Biol. 8:4257-4269, 1988). We report here that transcriptional repression may also be achieved at lower nucleosome densities (one nucleosome per 215 base pairs of DNA) when histone H1 is present. Removal of histone H1 from the minichromosomes with Biorex under conditions in which no nucleosome disruption was observed led to transcriptional activation. Transcriptional repression could be restored by adding histone H1 back to the H1-depleted minichromosomes. The levels of histone H1 that repressed the H1-depleted minichromosomes failed to repress transcription from free DNA templates present in trans. The assembly of transcription complexes onto the H1-depleted minichromosomes protected the 5S RNA gene from inactivation by histone H1.

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