Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA318458 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3382890_1.fastq.gz | Fastqsanger.gz | |||
| SRR3382890_2.fastq.gz | Fastqsanger.gz | |||
| SRR3382883_1.fastq.gz | Fastqsanger.gz | |||
| SRR3382883_2.fastq.gz | Fastqsanger.gz | |||
| SRR3382884_1.fastq.gz | Fastqsanger.gz |
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Project description:Active and inactive enhancers co-operate to exert localized and long-range control of gene regulation
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Project description:Active and inactive enhancers co-operate to exert localized and long-range control of gene regulation [4C-seq]
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Project description:Active and inactive enhancers co-operate to exert localized and long-range control of gene regulation [RNA-seq]
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Project description:3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps of the active and inactive X-chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial re-folding of the inactive X into a conformation resembling the active X, without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X-chromosome independently of transcription. Five or six 4C viewpoints were applied on the mouse female wild type active X-chromosome, the wild type inactive X-chromosome, the conditional Xist X-chromosome and the Xist knock out X-chromosome
2011-06-24 | E-GEOD-29509 | biostudies-arrayexpress
Project description:3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps of the active and inactive X-chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial re-folding of the inactive X into a conformation resembling the active X, without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X-chromosome independently of transcription.
2011-06-24 | GSE29509 | GEO
Project description:Recent epigenomic studies have predicted thousands of potential enhancers in the human genome. However, there has not been systematic characterization of target promoters for these potential enhancers. Using H3K4me2 as a mark for active enhancers, we identified genome-wide enhancer-promoter interactions in human CD4+ T cells. Among the 6,520 long-distance chromatin interactions, we identify 2,067 enhancers that interact with 1,619 promoters and enhance their expression. These enhancers exist in accessible chromatin regions and are associated with various histone modifications and Pol II binding. The promoters with interacting enhancers are expressed at higher levels than those without interacting enhancers and their expression levels are positively correlated with the number of interacting enhancers. Interestingly, interacting promoters are co-expressed in a tissue-specific manner. We also find that chromosomes are organized into multiple levels of interacting domains. Our results define a global view of enhancer-promoter interactions and provide a dataset to further understand mechanisms of enhancer targeting and long-range chromatin organization. Two biological replicates of ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) experiment in CD4+ T cells
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2012-03-29 | E-GEOD-36374 | biostudies-arrayexpress
Project description:Long-range developmental enhancers can regulate cell-type specific target gene expression over distances that exceed hundreds of thousands of base pairs in mammals. Although higher-order chromatin organization provides support for such long-range enhancer—promoter interactions, the genetic factors that regulate these interactions during mammalian development remain largely unexplored. To address this central question, we replaced a limb enhancer, located >800,000 base pairs from its target promoter, with equivalent limb enhancers of similar strength from other genomic loci. We used this replacement strategy to generate six knock-in mouse strains, with enhancers from four distinct genomic loci. All enhancers drove strong expression in developing limb buds when placed adjacent to a reporter gene. However, when transplanted to a distal location, all four enhancers failed to activate remote gene expression and distal limb outgrowth, suggesting that proximally-active enhancers cannot activate transcription remotely. Including a highly conserved, but previously uncharacterized, sequence found adjacent to a long-range limb enhancer rescued gene expression and limb outgrowth. This cis-acting Range EXtender (REX) element does not have classical enhancer activity but is necessary and sufficient for enhancer–promoter communication over very long distances in vivo. The REX element contains highly conserved [C/T]AATTA consensus sequences that match binding preferences of LIM-homeodomain (LHX) transcription factors. We used multiomic single-cell ATAC-seq/RNA-seq profiling to identify [C/T]AATTA homeodomain motifs next to thousands of long-range limb enhancers. The presence of these motifs positively correlates with E–P distance genome-wide. Our data support a model where REX elements facilitate target gene activation by remote enhancers over very long distances in mammalian genomes.
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Project description:The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We have developed 4C technology, or 3C-on-chip, which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active b-globin locus in fetal liver contacts mostly transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, while the inactive locus in fetal brain contacts different, transcriptionally silent, loci. A housekeeping gene in a gene dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture. Keywords: 4C technology
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