Acquiring and sequencing of all 24 single human chromosomes
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001003300 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Gene dosage imbalance of heteromorphic sex chromosomes (XY or ZW) exists between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds brought sex chromosome dosage compensation into question. This study examines transcriptomic and proteomic levels of dosage compensation in platypus and chicken compared to mouse, a model eutherian species. We analyzed mRNA and protein levels in heart and liver tissues of chicken, mouse and platypus.
2024-07-30 | PXD040182 | Pride
Project description:Sex chromosomes evolved many times independently in many different organisms. According to the currently accepted model, X- and Y-chromosomes evolve from a pair of autosomes via a series of inversions leading to step-wise expansion of a non-recombining region on the Y chromosome (NRY) and the consequential degeneration of genes trapped in the NRY. Our results suggest that plants represent an exception to this rule due to their unique life-cycle that includes alteration of diploid and haploid generations and widespread haploid expression of genes in plant gametophytes. Using a new high-throughput approach we identified over 400 new genes expressed from X- and Y- chromosomes in Silene latifolia, a plant that evolved sex chromosomes about 10 million years ago. Y-linked genes show faster accumulation of amino-acid replacements and loss of expression, compared to X-linked genes. These degenerative processes are significantly less pronounced in more constrained genes and genes that are likely exposed to haploid-phase selection. This may explain why plants retain hundreds of expressed Y-linked genes despite millions of years of Y-chromosome degeneration, while animal Y-chromosomes are almost completely degenerate. We used a combination of Illumina sequencing of cDNA (RNAseq) and segregation analysis of SNPs identified from RNAseq to identify sex-linked genes in plant Silene latifolia. The experiment involved RNAseq from male and female parents and F1 progeny for two genetic crosses. We submit raw data in fastq format for 11 samples. Four of these samples are single end Solexa reads (a single file per sample) and seven samples were sequenced with paired end Solexa sequencing (two fastq files per sample) - 18 files in total.
2012-07-30 | E-GEOD-30958 | biostudies-arrayexpress
Project description:The three-dimensional (3D) organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure or how structure influences gene expression. Here we exploit the X-chromosome-wide process of dosage compensation to dissect these mechanisms. The dosage compensation complex (DCC) of C. elegans, a condensin complex, binds to both X chromosomes of hermaphrodites via sequence-specific recruitment sites (rex sites) to reduce chromosome-wide gene expression by half. Using genome-wide chromosome conformation capture and single-cell FISH to compare chromosome structure in wild-type and DCC-defective embryos (DC mutants), we show that the DCC remodels X chromosomes of hermaphrodites into a spatial conformation distinct from autosomes. The dosage-compensated X chromosomes are composed of Topologically Associating Domains (TADs) that have sharper boundaries and more regular spacing than TADs on autosomes. Most TAD boundaries on X coincide with the highest-affinity rex sites, and these boundaries are lost or diminished in DC mutants, thereby restoring the topology of X to a native conformation resembling that of autosomes. Although most rex sites engage in multiple strong DCC-dependent long-range interactions, the strongest interactions occur between rex sites at the DCC-dependent TAD boundaries. We propose the DCC actively shapes the topology of the entire X chromosome by forming new TAD boundaries and reinforcing pre-existing weak TAD boundaries through interactions between its highest affinity sites. Such changes in higher-order X-chromosome structure then influence gene expression over long distances.
2015-06-03 | GSE59715 | GEO
Project description:The three-dimensional (3D) organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure or how structure influences gene expression. Here we exploit the X-chromosome-wide process of dosage compensation to dissect these mechanisms. The dosage compensation complex (DCC) of C. elegans, a condensin complex, binds to both X chromosomes of hermaphrodites via sequence-specific recruitment sites (rex sites) to reduce chromosome-wide gene expression by half. Using genome-wide chromosome conformation capture and single-cell FISH to compare chromosome structure in wild-type and DCC-defective embryos (DC mutants), we show that the DCC remodels X chromosomes of hermaphrodites into a spatial conformation distinct from autosomes. The dosage-compensated X chromosomes are composed of Topologically Associating Domains (TADs) that have sharper boundaries and more regular spacing than TADs on autosomes. Most TAD boundaries on X coincide with the highest-affinity rex sites, and these boundaries are lost or diminished in DC mutants, thereby restoring the topology of X to a native conformation resembling that of autosomes. Although most rex sites engage in multiple strong DCC-dependent long-range interactions, the strongest interactions occur between rex sites at the DCC-dependent TAD boundaries. We propose the DCC actively shapes the topology of the entire X chromosome by forming new TAD boundaries and reinforcing pre-existing weak TAD boundaries through interactions between its highest affinity sites. Such changes in higher-order X-chromosome structure then influence gene expression over long distances.
2015-06-03 | GSE59597 | GEO
Project description:The three-dimensional (3D) organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure or how structure influences gene expression. Here we exploit the X-chromosome-wide process of dosage compensation to dissect these mechanisms. The dosage compensation complex (DCC) of C. elegans, a condensin complex, binds to both X chromosomes of hermaphrodites via sequence-specific recruitment sites (rex sites) to reduce chromosome-wide gene expression by half. Using genome-wide chromosome conformation capture and single-cell FISH to compare chromosome structure in wild-type and DCC-defective embryos (DC mutants), we show that the DCC remodels X chromosomes of hermaphrodites into a spatial conformation distinct from autosomes. The dosage-compensated X chromosomes are composed of Topologically Associating Domains (TADs) that have sharper boundaries and more regular spacing than TADs on autosomes. Most TAD boundaries on X coincide with the highest-affinity rex sites, and these boundaries are lost or diminished in DC mutants, thereby restoring the topology of X to a native conformation resembling that of autosomes. Although most rex sites engage in multiple strong DCC-dependent long-range interactions, the strongest interactions occur between rex sites at the DCC-dependent TAD boundaries. We propose the DCC actively shapes the topology of the entire X chromosome by forming new TAD boundaries and reinforcing pre-existing weak TAD boundaries through interactions between its highest affinity sites. Such changes in higher-order X-chromosome structure then influence gene expression over long distances.
2015-06-03 | GSE63717 | GEO
Project description:Dosage compensation restores a balanced network of gene expression between autosomes and sex chromosomes in males (XY) and females (XX). In mammals, this is achieved by doubling the expression of X-linked genes in both sexes, together with X inactivation in females. X up-regulation may be controlled by DNA sequence based and/or epigenetic mechanisms that double the X output potentially in response to an autosomal counting factor. Human triploids with either one or two active X chromosomes (Xa) provide a mean to test X chromosome expression in the presence of three sets of autosomes, which will help understand the underlying mechanisms of X up-regulation. We measured whole genome gene expression in human triploid cell cultures with either one or two active X. We found that overall X-linked gene expression is not tripled in the presence of three sets of autosomes. However, in triploid cells with a single active X chromosome, its expression is adjusted upward, presumably by an epigenetic mechanism that senses the active X-autosome ratio.
2009-11-06 | GSE18877 | GEO
Project description:Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs), some of them being attached to the nuclear lamina (NL) in lamina-associated domains (LADs). Here, we identified LADs and TADs at two consecutive stages of Drosophila spermatogenesis – in spermatogonia (SpG) and spermatocytes (SpCs). We found that launching of SpC-specific transcription frequently correlates with promoters’ detachment from the NL accompanied by spatial insulation of adjacent regions. We also revealed an increased contact frequency between SpC-specific genes implying their de novo gathering into “transcription factories”. In SpG and SpCs, single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.
2022-02-01 | GSE156567 | GEO
Project description:Sex chromosomes evolved many times independently in many different organisms. According to the currently accepted model, X- and Y-chromosomes evolve from a pair of autosomes via a series of inversions leading to step-wise expansion of a non-recombining region on the Y chromosome (NRY) and the consequential degeneration of genes trapped in the NRY. Our results suggest that plants represent an exception to this rule due to their unique life-cycle that includes alteration of diploid and haploid generations and widespread haploid expression of genes in plant gametophytes. Using a new high-throughput approach we identified over 400 new genes expressed from X- and Y- chromosomes in Silene latifolia, a plant that evolved sex chromosomes about 10 million years ago. Y-linked genes show faster accumulation of amino-acid replacements and loss of expression, compared to X-linked genes. These degenerative processes are significantly less pronounced in more constrained genes and genes that are likely exposed to haploid-phase selection. This may explain why plants retain hundreds of expressed Y-linked genes despite millions of years of Y-chromosome degeneration, while animal Y-chromosomes are almost completely degenerate.
2012-07-30 | GSE30958 | GEO
Project description:Dosage compensation restores a balanced network of gene expression between autosomes and sex chromosomes in males (XY) and females (XX). In mammals, this is achieved by doubling the expression of X-linked genes in both sexes, together with X inactivation in females. X up-regulation may be controlled by DNA sequence based and/or epigenetic mechanisms that double the X output potentially in response to an autosomal counting factor. Human triploids with either one or two active X chromosomes (Xa) provide a mean to test X chromosome expression in the presence of three sets of autosomes, which will help understand the underlying mechanisms of X up-regulation. We measured whole genome gene expression in human triploid cell cultures with either one or two active X. We found that overall X-linked gene expression is not tripled in the presence of three sets of autosomes. However, in triploid cells with a single active X chromosome, its expression is adjusted upward, presumably by an epigenetic mechanism that senses the active X-autosome ratio. Six human XXX triploid fibroblast clones with either one or two active X, three XYY triploid fibroblast cultures, and two male (XY) and two female (XaXi) control diploid fibroblast cultures were selected for RNA extraction and hybridization on Affymetrix whole genome expression arrays (HG-U133 2.0 plus chip). Probe labeling, array hybridization and scanning were done by the University of Washington Microarray Center.
2009-11-06 | E-GEOD-18877 | biostudies-arrayexpress
Project description:This dataset contains the genotypes jointly-called from whole genome sequencing data of 177 self-reported Peranakans in Singapore. Reads were aligned to GRCh37 reference genome and jointly-called with other WGS samples. Basic quality control measures and population phasing without reference were performed on the called genotypes. The data are stored in VCF v 4.3 format, and one .vcf.gz file stored the genotypes from one of the 23 chromosomes (22 autosomes+X chromosome).
| EGAD00001007786 | EGA