Unravelling global genome organization by 3C-seq

The Wistar Institute, Philadelphia, PA, USA.
Seminars in Cell and Developmental Biology (Impact Factor: 6.27). 11/2011; 23(2):213-21. DOI: 10.1016/j.semcdb.2011.11.003
Source: PubMed


Eukaryotic genomes exist in the cell nucleus as an elaborate three-dimensional structure which reflects various nuclear processes such as transcription, DNA replication and repair. Next-generation sequencing (NGS) combined with chromosome conformation capture (3C), referred to as 3C-seq in this article, has recently been applied to the yeast and human genomes, revealing genome-wide views of functional associations among genes and their regulatory elements. Here, we compare the latest genomic approaches such as 3C-seq and ChIA-PET, and provide a condensed overview of how eukaryotic genomes are functionally organized in the nucleus.

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Available from: Hideki Tanizawa, Jan 15, 2014
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    • "Genome organizations have been characterized in terms of several aspects, including chromosomal territories, nuclear bodies and genomic associations involving transcriptional regulatory elements and their target genes (Cremer and Cremer, 2010; Sexton et al., 2009; Tanizawa and Noma, 2012; Williams et al., 2010; Zhao et al., 2009). It is becoming clear that threedimensional (3D) genome organization is connected to various nuclear processes, such as transcription, DNA replication and repair, and chromatin domain formation (Cook, 1999; Labrador and Corces, 2002; Misteli, 2007). "
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    • "The mammalian genome appears to have accommodated widespread repetitive elements by providing each chromosome a specific domain. However, in the more tightly packed yeast nucleus, individual chromosomes are in intimate contact, which could explain why yeast have a limited number of repetititve elements in its genome (Tanizawa and Noma, 2011; Duan et al., 2010; Figure 6A). For mammalian genomes, perhaps the positive functions provided by repetitive sequences (e.g. "
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