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> Anatomy > Cell Component > Chromosome Structures

Chromosome Structures

Chromosome Structures are the physical organization and architecture of chromosomes, the structures within cells that contain the genetic material.
This includes the various components and features that make up the overall structure and organization of chromosomes, such as the chromatin, centromeres, telomeres, and chromosomal domains.
Understanding Chromosome Structures is crucial for studying genetic inheritance, genome organization, and cellular processes like cell division.
PubCompare.ai's AI-powered platform can help researchers easily identify the most effective protocols and methods for investigating Chrosome Structures from the scientific literature, preprints, and patents, enhancing reproducibility and accuracy in this important area of biological research.

Most cited protocols related to «Chromosome Structures»

1
Genetic Manipulation of M. extorquens AM1
M. extorquens AM1 strains were grown at 30°C on agar plates with "Hypho" minimal salts medium [15 (link)]; E. coli were grown at 37°C on Luria-Bertani agar [16 ]. Substrates and antibiotics were used at the following concentrations: methanol (125 mM), succinate (15 mM), sucrose (5% w/v unless otherwise stated), 50 μg/ml Ap (ampicillin), 20 μg/ml Cm, 50 μg/ml Km, 50 μg/ml Rif (rifamycin), 35 μg/ml Sm, and 10 μg/ml Tc.
Tri-parental conjugations were performed by mixing the E. coli strain with the donor plasmid, the M. extorquens AM1 recipient strain, and an E. coli strain with the helper plasmid pRK2073 [17 (link)]. This mixture was grown overnight on permissive Nutrient agar [16 ] plates at 30°C before introducing some of the mix (either by streaking with a loop or by washing with Hypho and re-plating) onto selective medium containing an appropriate C source, Rif for counter-selection against E. coli [9 (link)], and the selective antibiotic (Tc for pCM433-based donors; neither Ap nor Cm works effectively in M. extorquens AM1, Marx, unpublished). Sucrose selection was accomplished by suspending a loop of a given strain in 100 μl Hypho (approximately 109 ml-1) and plating 50 μl of a 10-2 dilution of this suspension onto Hypho plates containing an appropriate C source (generally succinate) and 5% sucrose. Resulting strains were tested for Tc sensitivity, additional expected phenotypes (depending on the locus and allele being exchanged), and additionally, the chromosomal organization of all strains constructed was confirmed through PCR analysis. DNA concentrations were determined using a ND-1000 spectrophotometer (NanoDrop).
, & Marx C.J. (2008). Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Research Notes, 1, 1.
Publication 2008
A-Loop Agar Alleles Antibiotics Antibiotics, Antitubercular Chromosome Structures Donors Escherichia coli Hypersensitivity Methanol Nutrients Parent Phenotype Plasmids rifamycin SV Salts Strains Succinate Sucrose Technique, Dilution
2
Detecting Chromosomal Amplifications in Breast Cancer
This kind of analysis pinpoints continuous clusters of co-expressed genes and permits to visualize their chromosomal organization. For all following tests, TCA was performed to verify the robustness of clusters.
An in silico study conducted by Buness et al. (14 (link)) identified 32 series of 20 characteristic overexpressed genes for amplified chromosomal regions. Six hundred and forty genes were tested for all patients and molecular subtypes. We considered as positive results continuous clusters of correlated co-expressed genes composed of at least three genes with r ≥ 0.30 and P ≤ 0.05. To quantify the global relationship among a cluster of co-expressed genes, eigenvalues of the correlation matrix were computed, and the ratio of the largest one to the sum of all eigenvalues multiply by 100 was taken (i.e. it comes to perform a principal component analysis based on the correlation matrix and take the percentage of variance explained by the first principal component) (Supplementary Method). This value is called multicorrelation score (MCS).
ESR1: A recent study showed that ESR1 was co-expressed with closely adjacent genes at 6q25.1 (15 (link)).
8p11-12 amplicon: At 8p11-12, one of the most frequently amplified regions in breast cancer (10–15% of cases), Bernard-Pierrot et al. identified five genes (LSM1, BAG4, DDHD2, PPAPDC1B and WHSC1L1) as consistently overexpressed due to an increased gene copy number (16 (link), 17 (link)).
Chromosome 17: Chromosome 17 is highly amplified in breast cancer, especially in HER2+ molecular subtype. Its amplified regions permit to distinguish HER2+ and luminal A (5 (link), 18 (link)). We chose three genes in different regions of chromosome 17 to test bc-GenExMiner analyses: TRAF4 at 17q11-q12, MED24 at 17q21.1 and GGA3 at 17q25.1 (14 (link)).
ER status: Numerous studies showed that CNA varied among breast tumours with different ER status (4 (link), 5 (link), 19–21 (link)). A list of 59 genes, which demonstrated different expression profile according to ER status in gained regions, was tested to screen for DNA continuous clusters of correlated co-expressed genes (20 (link)). We chose the following criterion: at least two DNA continuous genes with correlated gene-expressions, to define clusters of correlated co-expressed genes. MCS was used to compare clusters of co-expressed genes.
Jézéquel P., Frénel J.S., Campion L., Guérin-Charbonnel C., Gouraud W., Ricolleau G, & Campone M. (2013). bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses. Database: The Journal of Biological Databases and Curation, 2013, bas060.
Publication 2013
BAG4 protein, human Breast Carcinoma Breast Neoplasm Chromosomes Chromosomes, Human, Pair 17 Chromosome Structures ERBB2 protein, human Gene Expression Genes Genes, vif MED24 protein, human Patients Phenobarbital TNF Receptor-Associated Factor 4 WHSC1L1 protein, human
3
Chromosomal Verification by PCR
Two PCR reactions were carried out to test for correct chromosomal structures. Eight independent colonies were transferred into 150-μl LB medium with kanamycin in 96-well microplates and incubated overnight at 37°C without shaking. A measure of 1 μl of each culture was separately examined in 20-μl PCR reactions following 2-min ‘hot start' at 95°C. PCR verification with kanamycin-specific primers k1 and k2 and locus-specific primers U and D (Figure 2) was carried out as described previously (Datsenko and Wanner, 2000 (link)). PCR products were analyzed by 1% agarose gel electrophoresis as above.
Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., Datsenko K.A., Tomita M., Wanner B.L, & Mori H. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Molecular Systems Biology, 2, 2006.0008.
Publication 2006
Chromosome Structures Electrophoresis, Agar Gel Kanamycin Oligonucleotide Primers
4
Optimizing Synteny Block Scale for Ragout 2
Synteny block scale is an important parameter for the Ragout 2 pipeline. As synteny blocks breakpoints are defined by the structural rearrangements between genomes, longer blocks represent more conserved and reliable markers. Additionally, increasing block size helps to filter out common repetitive sequence (such as SINE/LINE repeats). On the other hand, synteny blocks computed for draft assemblies might be artificially shortened because of contig fragmentation.
Through our experiments we found that blocks of size 10 kb represent a good trade-off for improving an NGS draft using reference genomes from the same species or genus. Intuitively, it is larger than typical LINE repeat size (7 kb) and covers most of the NGS contig sequence but is yet reliable enough for homologous markers comparison. The default settings for mammalian genomes additionally include two iterations with synteny block sizes 500 bp (longer than most of the of SINE repeats) and 100 bp. These additional iterations are aimed to fill assembly gaps and do not change the structure of the final chromosomes. The default synteny block size could be changed by the user. For example, one might increase it for analysis of the highly contiguous assemblies using relatively distant reference genomes.
Kolmogorov M., Armstrong J., Raney B.J., Streeter I., Dunn M., Yang F., Odom D., Flicek P., Keane T.M., Thybert D., Paten B, & Pham S. (2018). Chromosome assembly of large and complex genomes using multiple references. Genome Research, 28(11), 1720-1732.
Publication 2018
Chromosome Structures Gene Rearrangement Genome Mammals Repetitive Region Short Interspersed Nucleotide Elements Synteny
5
Mitotic Chromosome Structure Dissection
DT40 Cell cultures synchronously entering mitosis were analyzed by Hi-C, imaging and proteomics to determine the structure of chromosomes. Hi-C data were used to quantify chromosome compartmentalization and to derive relationships between contact frequency P and genomic distance s. Coarse grained models and equilibrium polymer simulations were performed to test models of prophase and prometaphase chromosome organization against Hi-C data, and to identify best fitting parameters for size of loops, helical turn and pitch, linear density (Mb/micron chromosome length). Imaging of chromosome dimensions and condensin localization were performed to validate model predictions. Cell lines expressing condensin subunits fused to auxin-inducible degron domains were used to efficiently deplete these subunits prior to cells entering mitosis. Hi-C and imaging analysis were then performed to assess the effects of depletion of condensins on mitotic chromosome formation. Detailed procedures for all methods are described in the Supplementary Materials.
Gibcus J.H., Samejima K., Goloborodko A., Samejima I., Naumova N., Nuebler J., Kanemaki M., Xie L., Paulson J.R., Earnshaw W.C., Mirny L.A, & Dekker J. (2018). A pathway for mitotic chromosome formation. Science (New York, N.Y.), 359(6376), eaao6135.
Publication 2018
Auxins Cell Culture Techniques Cell Lines Cells Chromosomes Chromosome Structures condensin complexes Genome Helix (Snails) Mitosis Polymers Prometaphase Protein Subunits

Most recents protocols related to «Chromosome Structures»

1
Defining Chromosomal Regions in P. pacificus
The chromosome regions ChrIL and ChrIR are defined as the homologous regions to the left and right of position 21.05 Mb of chromosome 1 in P. pacificus, respectively. The three chromosomal elements ChrIL, ChrIR, and ChrX regions correspond to the conserved chromosome elements recently named as NigonE, NigonN and NigonX, respectively59 (link) (see detail, Supplementary Note). Note that we refrained from using this terminology as it was differently applied in recent publications50 (link),60 (link).
Yoshida K., Rödelsperger C., Röseler W., Riebesell M., Sun S., Kikuchi T, & Sommer R.J. (2023). Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. Nature Ecology & Evolution, 7(3), 424-439.
Publication 2023
Chromosomes Chromosomes, Human, Pair 1 Chromosome Structures
2
Site-Directed Mutagenesis of Fis Binding Site
Site-directed mutagenesis was performed using the Quikchange II (Stratagene) site-directed mutagenesis kit, according to the manufacturer’s recommendations. The oligonucleotides used to mutate the Fis binding site (FBSFOR2 and FBSREV2) are described in Table 2, and were supplied by MWG Biotech. Plasmid pMMC108 [20 (link)] was used as the substrate for the mutagenesis. The method of allele replacement was as described previously [24 (link)]. Briefly, the mutated Fis binding site was introduced to the chromosome by cloning an MfeI-SnaBI fragment of fimS, containing the disrupted site into pSGS501, a plasmid containing the cat chloramphenicol resistance gene (Table 1). The resulting plasmid was digested with EcoRV and an 8 kb fragment containing the mutated fimS region was gel extracted. Two micrograms of this fragment were electroporated into strain VL386recD. Loss of plasmid sequences following homologous recombination with the chromosome was confirmed by testing the transformants for chloramphenicol sensitivity. The presence of the disrupted Fis binding site in the chromosomal fimS element was confirmed by PCR amplification followed by DNA sequencing.
Conway C., Beckett M.C, & Dorman C.J. (2023). The DNA relaxation-dependent OFF-to-ON biasing of the type 1 fimbrial genetic switch requires the Fis nucleoid-associated protein. Microbiology, 169(1), 001283.
Publication 2023
Alleles Binding Sites Chloramphenicol Chloramphenicol Resistance Chromosomes Chromosome Structures Genes Homologous Recombination Hypersensitivity Mutagenesis Mutagenesis, Site-Directed Oligonucleotides Plasmids Strains
3
Genetic Algorithm Solution Representation
The structure of chromosomes and genes in the population may vary depending on the type of problem. Binary, integer, float and permutation are some of the solution representations used in the algorithm [37 ]. Float solution representation is used in this article and the related chromosome structure is shown in Fig. 7 is also shown.

Solution representation used in Genetic Algorithm

The chromosome in Fig. 7 consists of five genes and each gene corresponds to the coefficients in the prediction model.
UÇAR U.U., Aygun H, & Tanyeri B. (2023). Optimized modeling of energy and environmental metrics of mixed flow turbofan engine used regional aircraft. Journal of Thermal Analysis and Calorimetry, 148(10), 4495-4511.
Publication 2023
Chromosomes Chromosome Structures Genes Reproduction
4
Chromosome Conformational Dynamics Modeling
The 3D structure of individual chromosomes was constructed using a home-built C++ software, motivated by studies Chrom3D34 (link) and NucDynamics.35 (link),36 (link) Each chromosome has a beads-on-a-string representation and starts with a randomized conformation. Then, the time evolution of chromosome conformation is governed by the Newton equation of motion, with forces (detailed below) implemented to characterize the chromosome structural integrity ( F→iten ), volume exclusion between spatially overlapping genomic sites ( F→irep ), drag by nucleoplasm ( −γv→i ), and genomically distant interactions suggested by Hi-C ( F→iHi−C ).
Clarence T., Robert N.S., Sarigol F., Fu X., Bates P.A, & Simakov O. (2023). Robust 3D modeling reveals spatiosyntenic properties of animal genomes. iScience, 26(3), 106136.
Publication 2023
Biological Evolution Chromosomes Chromosome Structures Genome
5
Genetic Manipulation of Ribosomal Proteins
The primers rpsTREPF-rpsTREPR (for rpsT) and rpsBHISF-rpsFR (for rpsB) were used to amplify the KanR gene from pKD4 [24 (link)]. The PCR products were then recombined into the E. coli MG1655 chromosomes using their protocol. MG1655 carrying the pKD46 plasmid was grown in LB medium with ampicillin and L-arabinose at 30 °C to an approximate OD600 of 0.6, then made electrocompetent [47 ]. PCR products were gel-purified, digested with DpnI, re-purified, and then suspended in 10 mM Tris (pH 8.0). Electroporation was performed according to the manufacturer’s instructions in a BIO-RAD Gene Pulser II (2.5 kV, 25 µF, 200 Ω) with 0.25-cm chambers. Transformants were selected on LB-kanamycin plates at 42 °C. To check for possible loss of the pKD46 plasmid, the colonies were tested for ampicillin sensitivity. The chromosomal structure of mutants was confirmed by PCR (Supplementary Figure S1). KanR colonies were then transformed with pCP20 plasmid. The resulting AmpR transformants were selected at 30 °C, incubated at 42 °C, and tested for antibiotic resistance. A PCR was also used to confirm the mutations of rpsB and rpsT (Supplementary Figure S1). The rpsB:his and rpsT:strep strains were named ‘E6001’ and ‘E6004’, respectively. The rpsB-KanR mutation was transduced into E6004. Transductants were selected as KanR colonies, and then pCP20 was introduced by transformation. The KanR-AmpR colonies were isolated and their chromosomal structures were confirmed by PCR. Finally, KanR was deleted after induction of Flp recombinase, resulting in an ‘E6006’ strain containing both rpsT:his and rpsB:strep.
Giudice E., Georgeault S., Lavigne R., Pineau C., Trautwetter A., Ermel G., Blanco C, & Gillet R. (2023). Purification and Characterization of Authentic 30S Ribosomal Precursors Induced by Heat Shock. International Journal of Molecular Sciences, 24(4), 3491.
Publication 2023
Ampicillin Antibiotic Resistance, Microbial Arabinose Autosomal Recessive Polycystic Kidney Disease Chromosomes, Human, 16-18 Chromosome Structures Electroporation FLP recombinase Genes Hypersensitivity Kanamycin Mutation Oligonucleotide Primers Plasmids Strains Streptococcal Infections Tromethamine

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More about "Chromosome Structures"

Chromosome Structure refers to the physical organization and architecture of chromosomes, the cellular structures that contain the genetic material.
This includes the various components and features that make up the overall structure and arrangement of chromosomes, such as chromatin, centromeres, telomeres, and chromosomal domains.
Understanding the intricate Chromosome Structure is crucial for studying genetic inheritance, genome organization, and vital cellular processes like cell division.
Researchers can utilize PubCompare.ai's AI-powered platform to easily identify the most effective protocols and methods for investigating Chromosome Structure from the scientific literature, preprints, and patents.
This can help enhance the reproducibility and accuracy of studies in this important area of biological research.
Related terms and subtopics include: Chromosome, Chromatid, Chromatin, Centromere, Telomere, Chromosomal Domain, Genetic Inheritance, Genome Organization, Cell Division, Cytogenetics, Karyotype, Chromatin Remodeling, Epigenetics, Fluorescence In Situ Hybridization (FISH), Metaphase Spread, Accutase, PS.1 Microscope System, CLC Assembly Cell Software, DNAzol Reagent, Anti-CB1R, Colchicine, Fluorescence Microscope, Ficoll, DNeasy Kit, Anti-SCP3.
PubCompare.ai's platform can help researchers optimize their investigative protocols and ensure the higheest level of reproducibility and accuracy in their Chromosome Structure studies.