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

Abstract

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.
Pages159-171
Number of pages13
ISBN (Print)9780123757098
DOIs
StatePublished - Dec 1 2011
Externally publishedYes

Fingerprint

Chromatin
Genes
Genome
DNA
Epigenomics
Proteins
DNA sequences
Euchromatin
Heterochromatin
Human Genome
Genomics
Southern Blotting
Fluorescence In Situ Hybridization
Polymerase chain reaction
Gene expression
Gene Expression
Purification
Polymerase Chain Reaction
Antibodies
Topology

Cite this

Chromatin modifications distinguish genomic features and physical organization of the nucleus. / Wacker, David A; Kim, Yoon Jung; Kim, Tae Hoon.

Handbook of Epigenetics. Elsevier Inc., 2011. p. 159-171.

Research output: Chapter in Book/Report/Conference proceedingChapter

Wacker, David A ; Kim, Yoon Jung ; Kim, Tae Hoon. / Chromatin modifications distinguish genomic features and physical organization of the nucleus. Handbook of Epigenetics. Elsevier Inc., 2011. pp. 159-171
@inbook{c619e6876b7b4094ba2bb9824490c7b0,
title = "Chromatin modifications distinguish genomic features and physical organization of the nucleus",
abstract = "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.",
author = "Wacker, {David A} and Kim, {Yoon Jung} and Kim, {Tae Hoon}",
year = "2011",
month = "12",
day = "1",
doi = "10.1016/B978-0-12-375709-8.00011-3",
language = "English (US)",
isbn = "9780123757098",
pages = "159--171",
booktitle = "Handbook of Epigenetics",
publisher = "Elsevier Inc.",

}

TY - CHAP

T1 - Chromatin modifications distinguish genomic features and physical organization of the nucleus

AU - Wacker, David A

AU - Kim, Yoon Jung

AU - Kim, Tae Hoon

PY - 2011/12/1

Y1 - 2011/12/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84882912098&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84882912098&partnerID=8YFLogxK

U2 - 10.1016/B978-0-12-375709-8.00011-3

DO - 10.1016/B978-0-12-375709-8.00011-3

M3 - Chapter

SN - 9780123757098

SP - 159

EP - 171

BT - Handbook of Epigenetics

PB - Elsevier Inc.

ER -