Chromatin modifications distinguish genomic features and physical organization of the nucleus

David A. Wacker, Yoon Jung Kim, Tae Hoon Kim

Research output: Chapter in Book/Report/Conference proceedingChapter


This chapter discusses the fact that chromatin modifications distinguish genomic features and physical organization of the nucleus. The spatial organization of genomic DNA in the nucleus thus represents the next frontier in functional genomics and epigenomics. The specific DNA sequences associated with a particular protein complex are then isolated by immuno-affinity purification using a specific antibody against the protein. The purified DNA fragments are assayed by a variety of molecular techniques, such as Southern blot or polymerase chain reaction (PCR), to determine association of particular DNA sequences with the protein of interest. This genome-wide approach to investigating protein-DNA interactions was extended by the adaptation of the Serial Analysis of Gene Expression (SAGE) technique to analysis of ChIP DNA. The extension of 3C analysis to the entire human genome, coupled with advances in imaging and FISH techniques, promises to provide us with a global understanding of how the entire genome is packaged into the nucleus and how the resulting three-dimensional topology of the genome influences its activity. Combined with detailed genome-wide maps of heterochromatin and euchromatin, an unprecedented molecular view of gene activity, epigenetic structure, and 3D organization of the genome will be possible.

Original languageEnglish (US)
Title of host publicationHandbook of Epigenetics
PublisherElsevier Inc.
Number of pages13
ISBN (Print)9780123757098
StatePublished - 2011
Externally publishedYes

Bibliographical note

Funding Information:
Work in the laboratory is supported by the Rita Allen Foundation, Sidney Kimmel Foundation for Cancer Research, Yale Comprehensive Cancer Center, and Yale University School of Medicine. We thank Spiro Razis for his comments on the manuscript. We apologize to the numerous researchers whose work couldn’t be mentioned in this chapter.

Publisher Copyright:
© 2011 Elsevier Inc. All rights reserved.


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