Title |
The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types
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Published in |
PLOS ONE, March 2013
|
DOI | 10.1371/journal.pone.0058793 |
Pubmed ID | |
Authors |
Zheng Wang, Renzhi Cao, Kristen Taylor, Aaron Briley, Charles Caldwell, Jianlin Cheng |
Abstract |
The spatial conformation of a genome plays an important role in the long-range regulation of genome-wide gene expression and methylation, but has not been extensively studied due to lack of genome conformation data. The recently developed chromosome conformation capturing techniques such as the Hi-C method empowered by next generation sequencing can generate unbiased, large-scale, high-resolution chromosomal interaction (contact) data, providing an unprecedented opportunity to investigate the spatial structure of a genome and its applications in gene regulation, genomics, epigenetics, and cell biology. In this work, we conducted a comprehensive, large-scale computational analysis of this new stream of genome conformation data generated for three different human leukemia cells or cell lines by the Hi-C technique. We developed and applied a set of bioinformatics methods to reliably generate spatial chromosomal contacts from high-throughput sequencing data and to effectively use them to study the properties of the genome structures in one-dimension (1D) and two-dimension (2D). Our analysis demonstrates that Hi-C data can be effectively applied to study tissue-specific genome conformation, chromosome-chromosome interaction, chromosomal translocations, and spatial gene-gene interaction and regulation in a three-dimensional genome of primary tumor cells. Particularly, for the first time, we constructed genome-scale spatial gene-gene interaction network, transcription factor binding site (TFBS) - TFBS interaction network, and TFBS-gene interaction network from chromosomal contact information. Remarkably, all these networks possess the properties of scale-free modular networks. |
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Geographical breakdown
Country | Count | As % |
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United Kingdom | 1 | 1% |
Spain | 1 | 1% |
United States | 1 | 1% |
France | 1 | 1% |
Unknown | 81 | 95% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 24 | 28% |
Researcher | 20 | 24% |
Professor > Associate Professor | 7 | 8% |
Student > Postgraduate | 6 | 7% |
Student > Master | 6 | 7% |
Other | 15 | 18% |
Unknown | 7 | 8% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 43 | 51% |
Biochemistry, Genetics and Molecular Biology | 14 | 16% |
Computer Science | 10 | 12% |
Medicine and Dentistry | 6 | 7% |
Social Sciences | 2 | 2% |
Other | 2 | 2% |
Unknown | 8 | 9% |