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Complex multi-enhancer contacts captured by genome architecture mapping
- Source :
- Nature
- Publication Year :
- 2017
- Publisher :
- Springer Science and Business Media LLC, 2017.
-
Abstract
- The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation). GAM also reveals an abundance of three-way contacts across the genome, especially between regions that are highly transcribed or contain super-enhancers, providing a level of insight into genome architecture that, owing to the technical limitations of current technologies, has previously remained unattainable. Furthermore, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian nuclei.
- Subjects :
- Male
0301 basic medicine
Transcription, Genetic
Sequence analysis
Computational biology
Biology
Genome
Article
DNA sequencing
Epigenesis, Genetic
Mice
03 medical and health sciences
Organ Culture Techniques
Animals
Enhancer
Gene
ChIA-PET
Epigenomics
Genetics
Multidisciplinary
Models, Genetic
Chromosome Mapping
Mouse Embryonic Stem Cells
Sequence Analysis, DNA
Chromatin
Enhancer Elements, Genetic
030104 developmental biology
Subjects
Details
- ISSN :
- 14764687 and 00280836
- Volume :
- 543
- Database :
- OpenAIRE
- Journal :
- Nature
- Accession number :
- edsair.doi.dedup.....0385ebaba259059af4199ee0acc8e374