Unknown,Transcriptomics,Genomics,Proteomics

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Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

ABSTRACT: We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes. The processed heatmap data, showing the number of read pairs corresponding to particular locus pairs in the genome, are linked to the Series record below. The processed eigenvector data used to generate the heatmaps are linked to the Series record below. Additional DNAseI and ChIP-Seq data tracks were used in the paper, and are available at the UCSC browser (http://genome.ucsc.edu/) DNAseI: wgEncodeUwDnaseSeqRawSignalRep2K562 wgEncodeUwDnaseSeqRawSignalRep2Gm06990 ChIP-Seq: wgEncodeBroadChipSeqSignalGm12878H3k36me3 wgEncodeBroadChipSeqSignalGm12878H3k27me3 Interaction maps in 2 different cell types.

ORGANISM(S): Homo sapiens

SUBMITTER: Erez Lieberman-Aiden

PROVIDER: E-GEOD-18199 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Lieberman-Aiden Erez E van Berkum Nynke L NL Williams Louise L Imakaev Maxim M Ragoczy Tobias T Telling Agnes A Amit Ido I Lajoie Bryan R BR Sabo Peter J PJ Dorschner Michael O MO Sandstrom Richard R Bernstein Bradley B Bender M A MA Groudine Mark M Gnirke Andreas A Stamatoyannopoulos John J Mirny Leonid A LA Lander Eric S ES Dekker Job J

Science (New York, N.Y.) 20091001 5950

We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and cl ...[more]

PMID: 19815776

Publication: 1/2

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Project description:The development of the human malaria parasite Plasmodium falciparum is controlled by coordinated changes in gene expression throughout its complex life cycle, but the corresponding regulatory mechanisms are incompletely understood. To study the relation between genome architecture and gene regulation in Plasmodium, we studied the genome structure of P. falciparum at three time points during its erythrocytic (asexual) cycle. Using chromosome conformation capture coupled with next-generation sequencing technology (Hi-C), we obtained high-resolution chromosomal contact maps, which we then used to construct a consensus three-dimensional genome structure for each time point. We observe strong clustering of centromeres, telomeres, ribosomal DNA and virulence genes, resulting in a complex architecture that cannot be explained by a simple volume exclusion model. Internal virulence gene clusters appear to be an important factor in shaping the genome architecture as they exhibit domain-like structures similar to topological domains in mammalian genomes. Midway during the cell cycle, at the highly transcriptionally active trophozoite stage, the genome adopts a more open chromatin structure with increased chromosomal intermingling. In addition, we observed reduced expression of genes located in spatial proximity to the repressive subtelomeric center, and colocalization of distinct groups of parasite-specific genes with coordinated expression profiles. Overall, our results are indicative of a strong association between the P. falciparum spatial genome organization and gene expression. Understanding the molecular processes involved in genome conformation dynamics could contribute to the discovery of novel antimalarial strategies. Analysis of the spatial organization of the P. falciparum genome at three stages of the erythrocytic cycle using chromosome conformation capture coupled with next generation sequencing (Hi-C). As a control, we included one sample for which chromatin contacts were not preserved by crosslinking of DNA and proteins.

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Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Publications

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

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