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Comment
. 2012 Oct;9(10):961-3.
doi: 10.1038/nmeth.2181.

Zooming in on genome organization

Xianghong Jasmine Zhou, Frank Alber
Comment

Zooming in on genome organization

Xianghong Jasmine Zhou et al. Nat Methods. 2012 Oct.
No abstract available

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Figures

Figure 1
Figure 1
A. Overview of the high-resolution 4C-seq method, . The illustration shows three possible contacts between the viewpoint DNA fragment (red) and other fragments (blue, green, and yellow) mediated by proteins (depicted as grey circles). First, cross-linked chromatin is digested with a 4-base cutting primary restriction enzyme (cutting sites “P” are depicted as solid black lines), followed by proximity ligation. Subsequently, the cross-links are reversed, and DNA fragments are digested with a second, different 4-base cutting restriction enzyme (cutting sites “S” are depicted as dotted grey lines), followed by circularization. Captured fragments containing the viewpoint sequence are then amplified by inverse PCR, followed by high-throughput sequencing. Finally, the “one versus all” contact map is established by computational analysis. B. Illustration of the iterative correction procedure on raw chromosome conformation capture data. The color bar at the bottom represents the magnitude of the row sums. In an iteration, each entry of the matrix is divided by the product of the visibility biases of the two interacting regions, where the bias of a region is calculated as the normalized sum of the corresponding row. After several iterations, the Hi-C map converges to a normalized matrix where each row and column sums to 1.
See this image and copyright information in PMC

Comment on

  • Robust 4C-seq data analysis to screen for regulatory DNA interactions.
    van de Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Valdes-Quezada C, Oz Y, Bouwman BA, Verstegen MJ, de Wit E, Tanay A, de Laat W. van de Werken HJ, et al. Nat Methods. 2012 Oct;9(10):969-72. doi: 10.1038/nmeth.2173. Epub 2012 Sep 9. Nat Methods. 2012. PMID: 22961246

References

    1. van de Werken HJG, et al. 4C-seq for robust identification of physical interactions between genes and regulatory elements. Nature Methods. 2012
    1. Imakaev M, et al. Iterative correction of Hi-C data reveals new features of chromosome organization. Nature Methods. 2012 - PMC - PubMed
    1. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002;295:1306–1311. - PubMed
    1. Hakim O, Misteli T. SnapShot: Chromosome confirmation capture. Cell. 2012;148:1068.e1061–1062. - PMC - PubMed
    1. Simonis M, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C) Nat Genet. 2006;38:1348–1354. - PubMed

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