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Review
. 2013 Sep 26;155(1):39-55.
doi: 10.1016/j.cell.2013.09.011.

Mapping human epigenomes

Chloe M Rivera  1 , Bing Ren
Affiliations
Review

Mapping human epigenomes

Chloe M Rivera et al. Cell. .

Abstract

As the second dimension to the genome, the epigenome contains key information specific to every type of cells. Thousands of human epigenome maps have been produced in recent years thanks to rapid development of high throughput epigenome mapping technologies. In this review, we discuss the current epigenome mapping toolkit and utilities of epigenome maps. We focus particularly on mapping of DNA methylation, chromatin modification state, and chromatin structures, and emphasize the use of epigenome maps to delineate human gene regulatory sequences and developmental programs. We also provide a perspective on the progress of the epigenomics field and challenges ahead.

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Figures

Figure 1
Figure 1
Timeline of Sequencing Based Technologies for Mapping Human Epigenomes
Figure 2
Figure 2
“Epi-nomics” of Human DNA Methylation Technologies
Figure 3
Figure 3
Hierarchical Principles of Nuclear Organization
See this image and copyright information in PMC

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References

    1. Aday AW, Zhu LJ, Lakshmanan A, Wang J, Lawson ND. Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites. Dev Biol. 2011;357:450–462. - PMC - PubMed
    1. Adey A, Shendure J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res. 2012;22:1139–1143. - PMC - PubMed
    1. Adli M, Bernstein BE. Whole-genome chromatin profiling from limitednumbers of cells using nano-ChIP-seq. Nature Protocols. 2011;6:1656–1668. - PMC - PubMed
    1. Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LFA, Van Lohuizen M, van Steensel B. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell. 2013;154:914–927. - PubMed
    1. American Association for Cancer Research Human Epigenome Task Force, European Union, Network of Excellence, Scientific Advisory Board. Moving AHEAD with an international human epigenome project. Nature. 2008;454:711–715. - PMC - PubMed

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