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Gene Regulatory Elements

  • Nadav Ahituv
Chapter

Abstract

While the annotation and functional characterization of the 2% of our genome that encodes for protein has been extremely successful, the remaining 98% still remains primarily uncharted territory. Within this territory reside gene regulatory sequences that instruct genes when, where, and at what levels to turn on or off. There is abundant evidence, as described in this book, that nucleotide and epigenetic changes in these gene regulatory sequences can lead to human disease. In this chapter, we will define the different types of gene regulatory elements (promoters, enhancers, silencers, and insulators) and how to identify and functionally characterize them.

Keywords

Promoter Enhancer Silencer Insulator Locus control region Transcription factors Nucleosome positioning DNase I hypersensitive sites ChIP 3C 

Abbreviations

BRE

TFIIB recognition element

Inr

Initiator element

DPE

Downstream core promoter element

TBP

TATA-binding protein

TFIID

Transcription factor IID

TFIIB

Transcription factor IIB

TSS

Transcription start site

TFBS

Transcription factor binding sites

SHH

Sonic hedgehog

NIPBL

Nipped-B homolog

CTCF

CCCTC-binding factor

LCR

Locus control region

DHSs

DNase I hypersensitive sites

ChIP

Chromatin immunoprecipitation

3C

Chromatin conformation capture

YAC

Yeast artificial chromosome

BAC

Bacterial artificial chromosome

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Bioengineering and Therapeutic Sciences, Institute for Human GeneticsUniversity of California San FranciscoSan FranciscoUSA

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