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89 results for “Chromosome conformation”
Data from: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms
Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Not only can meta3C be applied to species already sequenced, but a single meta3C library can be used for assembling, scaffolding and characterizing the tridimensional organization of unknown genomes. By applying meta3C to a semi-complex environmental sample, we confirmed its promising potential. Overall, this first meta3C study highlights the remarkable diversity of microorganisms chromosome organization, while providing an elegant and integrated approach to metagenomic analysis. - See more at: http://elifesciences.org/content/3/e03318#sthash.Yx6nSY4J.dpuf
Data from: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms
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Data from: Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling
Inherently dynamic, chromosomes adopt many different conformations in response to DNA metabolism. Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to reveal features from dynamic or transient events that are only visible in a fraction of cells at any given moment. We developed a method to determine chromosome conformation from relative positions of three fluorescently tagged DNA in living cells imaged in 3D. Cell type specific chromosome folding properties could be assigned based on positional combinations between three loci on yeast chromosome 3. We determined that the shorter left arm of chromosome 3 is extended in MATα cells, but can be crumpled in MATa cells. Furthermore, we implemented a new mathematical model that provides for the first time an estimate of the relative physical constraint of three linked loci related to cellular identity. Variations in this estimate allowed us to predict functional consequences from chromatin structural alterations in asf1 and recombination enhancer deletion mutant cells. The computational method is applicable to identify and characterize dynamic chromosome conformations in any cell type.
Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation
<p><i>Pogona vitticeps</i> has female heterogamety (ZZ/ZW) but the master sex determining gene is unknown, as is the case for all reptiles. We show that <i>nr5a1</i>, a gene that is essential in mammalian sex determination, has alleles on the Z and W chromosomes (Z-<i>nr5a1</i> and W-<i>nr5a1</i>), which are both expressed and can recombine. Three transcript isoforms of Z-<i>nr5a1</i> were detected in gonads of adult ZZ males, two of which encode a functional protein. However, ZW females produced sixteen isoforms, most of which contained premature stop codons. The array of transcripts produced by the W-borne allele (W-<i>nr5a1</i>) is likely to produce truncated polypeptides that could act as a competitive inhibitor to the full-length intact protein. We hypothesize that an altered configuration of the W chromosomes affects the conformation of the primary transcript generating inhibitory W-borne isoforms that suppress testis determination. Under this hypothesis, the GSD system of <i>P. vitticeps</i> is a W-borne dominant female-determiner that may be controlled epigenetically.</p>
Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation
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Data from: Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling
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A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation
GEO Series GSE67516. Mus musculus. 42 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Determination of the spatial organization of the FXN gene locus by using Chromosome Conformation Capture technique coupled with High-throughtput sequencing (3C-seq).
GEO Series GSE42961. Homo sapiens. 5 samples. Type: Other.
Chromosome conformation capture (Hi-C) of the turquoise killifish
GEO Series GSE218971. Nothobranchius furzeri. 2 samples. Type: Other.
HiChIRP reveals RNA-associated chromosome conformation
GEO Series GSE115524. Mus musculus; Homo sapiens. 42 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [Hi-C]
GEO Series GSE221497. Zymomonas mobilis. 10 samples. Type: Other.
Chromosome conformation capture-on-chip analysis of long-range cis interactions of the SOX9 promoter
GEO Series GSE50449. Homo sapiens. 6 samples. Type: Other.
Multiplexed analysis of chromosome conformation at vastly improved sensitivity
GEO Series GSE67959. Mus musculus. 14 samples. Type: Other.
Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids
GEO Series GSE77237. Homo sapiens. 4 samples. Type: Other.
HI-C 2.0: AN OPTIMIZED HI-C PROCEDURE FOR HIGH-RESOLUTION GENOME-WIDE MAPPING OF CHROMOSOME CONFORMATION
GEO Series GSE98161. Homo sapiens. 3 samples. Type: Other.
Characterization of chromosomal architecture in Arabidopsis thaliana by Chromosome Conformation Capture
GEO Series GSE50181. Arabidopsis thaliana. 26 samples. Type: Other.
Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [RNA-Seq]
GEO Series GSE221498. Zymomonas mobilis. 15 samples. Type: Expression profiling by high throughput sequencing.
Mapping the inter- and intra-chromosomal interactions of specific insulator binding sites with circular chromosome conformation capture (4C) assay (Gondor et al., 2008 Nature Protocol) [NimbleGen Arra
GEO Series GSE50768. Drosophila melanogaster. 3 samples. Type: Genome binding/occupancy profiling by genome tiling array.
5C-ID: Increased resolution Chromosome-Conformation-CaptureCarbon-Copy with in situ 3C and double alternating primer design
GEO Series GSE114121. Mus musculus. 7 samples. Type: Other.
Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [TT-Seq]
GEO Series GSE281416. Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing.
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International Brain Laboratory public data
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OpenNeuro
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