Small chromosomal regions position themselves autonomously according to their chromatin class
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA330838 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3939190.fastq.gz | Fastqsanger.gz | |||
| SRR3939200.fastq.gz | Fastqsanger.gz | |||
| SRR3939210.fastq.gz | Fastqsanger.gz | |||
| SRR3939191.fastq.gz | Fastqsanger.gz | |||
| SRR3939201.fastq.gz | Fastqsanger.gz |
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Project description:The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatin and euchromatin domains. The mechanisms of this chromatin segregation are still poorly understood. In this work we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background and compared it to an orthologous region in the context of its native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (i) gene-rich and SINE-rich euchromatin, (ii) gene-poor and LINE/LTR-rich heterochromatin and (iii) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show using FISH and 4C-seq technologies that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespectively of their chromosomal context, thus rendering this a chromosome segment autonomous property. Interactions with the nuclear lamina are also partially retained in the HAC but demonstrate less autonomy. Taken together, our results show that genomic segments autonomously fold and position themselves relative to other genomic parts, suggesting that the three major classes of chromatin constitute a blueprint for the overall nuclear architecture.
2017-03-22 | GSE84952 | GEO
Project description:The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatin and euchromatin domains. The mechanisms of this chromatin segregation are still poorly understood. In this work we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background and compared it to an orthologous region in the context of its native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (i) gene-rich and SINE-rich euchromatin, (ii) gene-poor and LINE/LTR-rich heterochromatin and (iii) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show using FISH and 4C-seq technologies that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespectively of their chromosomal context, thus rendering this a chromosome segment autonomous property. Interactions with the nuclear lamina are also partially retained in the HAC but demonstrate less autonomy. Taken together, our results show that genomic segments autonomously fold and position themselves relative to other genomic parts, suggesting that the three major classes of chromatin constitute a blueprint for the overall nuclear architecture.
2017-03-21 | GSE84685 | GEO
Project description:The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes.
| S-EPMC5453326 | biostudies-literature
Project description:Small chromosomal regions position themselves autonomously according to their chromatin class
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Project description:The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects is still controversial. To determine how changes in chromosome positioning affect transcription we characterized nuclear organization and global gene expression after large-scale chromosomal rearrangements in budding yeast. We used computational modelling and single cell imaging to determine chromosome position and integrated these data with genome-wide transcriptional profiles from RNA sequencing. Chromosome displacement relative to the nuclear periphery has mild but widespread and significant effects on transcription. Our study suggests that basal transcriptional activity is sensitive to radial changes on chromosomal position, and provides support for the functional relevance of budding yeast chromosome-level 3D organization in gene expression.
2017-12-20 | GSE108261 | GEO
Project description:When some genes are silenced, their positions within the nucleus can change dramatically [1] [2]. It is unclear, however, whether genes move to new positions when they are activated [3]. The chromosomes within the polarized nuclei of the fruit fly Drosophila have a well-characterized apical-basal orientation (the Rabl configuration [4]). Using a high-resolution in situ hybridization method [5], we found that each of 15 transcribed genes was localized as predicted by their chromosomal position and by the known polarized organization of the chromosomes. We also found that, within their specific apical-basal plane, most nascent transcript foci could occupy any radial position. There was no correlation between the apical-basal position of the transcribed locus and the final cytoplasmic site of localization of the RNA along the apical-basal axis of the cell. There was also no relationship between the distance of loci from the nuclear periphery and the amount of nascent mRNA decorating the gene. Our results are consistent with the view that effective transcription can occur without major re-localization of the genes themselves.
| S-EPMC2754251 | biostudies-literature
Project description:SOX9-positive pituitary stem cells differ according to their position in the gland and maintenance of their progeny depends on context.
| PRJNA899885 | ENA
Project description:Acute colon cancer surgery has a poor 90-day mortality of 21.0% compared with only 3% after elective colorectal cancer surgery in Denmark. The high mortality after acute colon cancer surgery compared with elective surgery emphasizes the importance of identifying factors associated with acute onset and poor short-term survival after acute surgery. Socioeconomic position has previously showed to be a risk factor for acute versus elective onset of colorectal cancer. Furthermore, if patients with low socioeconomic position have higher postoperative mortality this could reflect differences in the treatment of patients according to their socioeconomic position.
The aim of the clinical study is:
1. To examine if patients with short education, low income, living alone, or living in rural areas are more likely to undergo acute colorectal cancer surgery than elective surgery compared with patients with longer educations, higher income, living with a partner, or living in urban areas.
2. To examine if there is an association between education, income, cohabitation, or urbanicity and 1-year mortality after acute colorectal cancer surgery.
| 2277284 | ecrin-mdr-crc
Project description:Background: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalised description of nuclear organization. Results: Employing circular chromosome conformation capture (4C), this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we studied the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintained a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. Conclusion: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: (i) heterochromatin and euchromatin represent two distinct interactomes, (ii) interactions between chromosomes correlates with the linear position on the chromosome arm, and (iii) distal chromosome regions have a higher potential to interact with other chromosomes.
2013-11-01 | GSE50181 | GEO