Linking Enhancer to Epigenetics: New Way to Think About Human Diseases

Handbook of Nutrition, Diet, and Epigenetics pp 145-163| Cite as

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• Zhuojuan Luo
• Chengqi Lin

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Reference work entry

First Online: 05 January 2019

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Abstract

The spatiotemporal-specific gene expression in different cell types from a common genome of a multicellular organism is the basis of cellular function, tissue development, and homeostasis of the multicellular life. Dysregulation of the spatiotemporal gene expression pattern often leads to disease pathogenesis. Enhancers define distinct cell identities by determining the precise spatiotemporal patterns of gene expression during development. Enhancers can also respond to diverse environmental signals including different nutritional status to fine-tune the cellular functional demands. Thus, unraveling the intricate regulatory process of enhancer in governing gene expression has become a major thrust of the biological field to decipher developmental process and disease pathogenesis.

Keywords

Enhancer Epigenetics Transcription RNA polymerase II Chromatin Histone modification cis-Regulatory element Human diseases Enhancer-promoter communication Topologically associating domain 

List of Abbreviations

3C

Chromosome conformation capture

AF9

ALL1-fused gene from chromosome 9

AFF

AF4/FMR2

AML

Acute myeloid leukemia

BET

Bromodomain and extra-terminal

BRD4

Bromodomain-containing protein 4

Cas9

CRISPR-associated protein-9 nuclease

CBP

CREB-binding protein

CBS

CTCF-binding site

CDK9

Cyclin-dependent kinase 9

CdLS

Cornelia de Lange syndrome

CML

Chronic myelogenous leukemia

COMPASS

Complex proteins associated with set1

CREB

Cyclic AMP-responsive element-binding protein

CRISPR

Clustered regularly interspaced short palindromic repeat

CTCF

CCCTC-binding factor

CTD

C-terminal domain

DHS

DNase I hypersensitive site

DIPG

Diffuse intrinsic pontine glioma

DRB

5,6-Dichloro-1-ß-D-ribofuranosylbenzimidazole

DSIF

DRB-sensitivity-inducing factor

E2

17β-estradiol

EGF

Epidermal growth factor

ELL

Eleven-nineteen Lys-rich leukemia

ENCODE

Encyclopedia of DNA Elements

ENL

Eleven-nineteen leukemia

eRNA

Enhancer RNA

ERα

Estrogen receptor-α

EZH2

Enhancer of zeste homolog 2

Fox

Forkhead box

GTF

General transcription factor

GWAS

Genome-wide association study

H3K27ac

Histone H3 lysine 27 acetylation

H3K27me3

Histone H3 lysine 27 trimethylation

H3K4me1

Histone H3 lysine 4 monomethylation

H3K4me3

Histone H3 lysine 4 trimethylation

HEXIM1

Hexamethylene bisacetamide inducible 1

HEXIM2

Hexamethylene bisacetamide inducible 2

HGP

Human Genome Project

HL

Hodgkin lymphoma

ICGC

International Cancer Genome Consortium

IEG

Immediate early gene

JmjC

Jumonji C

LNA

Locked nucleic acid antisense oligonucleotide

LSD1

Lysine (K)-specific demethylase 1A

MLL

Mixed lineage leukemia

modENCODE

Model Organism Encyclopedia of DNA Elements

mRNA

Messenger RNA

NELF

Negative elongation factor

NFR

Nucleosome-free region

NGS

Next-generation sequencing

NHL

Non-Hodgkin lymphoma

nt

Nucleotide

NuRD

Nucleosome remodeling and histone deacetylation

PcG

Polycomb group

PIC

Pre-initiation complex

PPARγ

Peroxisome proliferator-activated receptor gamma

PRC2

Polycomb repressive complex 2

P-TEFb

Positive transcription elongation factor b

RNA Pol II

RNA polymerase II

RRM

RNA recognition motif

rRNA

Ribosomal RNA

SEC

Super elongation complex

SEC-L2

SEC-like 2

SEC-L3

SEC-like 3

siRNA

Small interfering RNA

SNP

Single nucleotide polymorphism

snRNP

Small nuclear ribonucleoprotein particle

SV40

Simian virus 40

TAD

Topologically associating domain

T-ALL

T-cell acute lymphoblastic leukemia

TCGA

The Cancer Genome Atlas

TPR

Tetratricopeptide-repeats

Trr

Trithorax related

TrxG

Trithorax group

TSS

Transcription start site

TZD

Thiazolidinedione

UTX

Ubiquitously transcribed X chromosome tetratricopeptide repeat protein