Chapter

17
Regulation of Gene
Expression in
Eukaryotes
Lecture Presentation by
Dr. Cindy Malone,
California State University Northridge

© 2017 Pearson Education, Ltd.

Section 17.1: Eukaryotic Gene Regulation

 Eukaryotic gene regulation is more complex

than prokaryotes
– Greater amount of DNA that is associated with
histones and other proteins
– mRNAs must be spliced, capped, and
polyadenylated prior to transport from nucleus
– Genes on numerous chromosomes are enclosed
in a double membrane nucleus

continued

© 2017 Pearson Education, Ltd.

Section 17.1: Eukaryotic
Gene Regulation

 mRNAs have wide range of half-lives (t1/2)

 Modulation of mRNA translation,
protein processing, modification, and degradation
(Figure 17-1)

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 17.2 Eukaryotic Gene Expression Is
Influenced by Chromatin Modifications

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Section 17.2: Gene Expression Influenced by
Chromatin Modifications
 Two structural features of eukaryotes
distinguish them from prokaryotes
– Eukaryotic genes are situated on
chromosomes that occupy a distinct location
– Eukaryotic DNA is combined with histones and
nonhistone proteins to form chromatin

– Compact chromatin structure inhibits

transcription, replication, and DNA repair

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Section 17.2: Chromosome Territory

 Chromosome territory
– In interphase nucleus, each chromosome
occupies discrete domain and stays separate
from other chromosomes
– Interchromosomal domains
 Channels between chromosomes that contain little or
no DNA
 Chromosome structure is continuously
rearranged; transcriptionally active genes are
cycled to edges of chromosome territories

© 2017 Pearson Education, Ltd.

 http://www.nature.com/nbt/journal/v28/n10/fig_tab/nbt.1680_F4.html

Detailed reading on chromosome territories

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829961/

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  Open vs closed chromatin
 Dnase I digests DNA. If nucleosomes present,
no digestion

https://link.springer.com/protocol/10.1007/978-1-62703-284-1_2

© 2017 Pearson Education, Ltd.

Section 17.2: Transcription Factory

 Transcription factories
– Feature within nucleus that may contribute to
gene expression
– Nuclear sites that contain most of the active RNA
polymerase and transcription regulatory
molecules
– Dynamic structures that form rapidly and
disassemble upon stimulation and repression of
transcription

© 2017 Pearson Education, Ltd.

Section 17.2: Nucleosomal Modifications

 Nucleosomes modified via change in

composition
– Important step in gene regulation; involves
changes to either nucleosome or DNA
– Histones contain normal histone H2A
– Variant histones (H2A.Z) affect nucleosome
mobility and positioning on DNA
– Nucleosome position may repress or activate
transcription via gene promoter

© 2017 Pearson Education, Ltd.

 https://www.nature.com/scitable/
topicpage/chromatin-remodeling-
in-eukaryotes-1082/

Figure 1: Dynamic properties of nucleosomes

(A) Remodelling complexes of the SWR1 family can remove the canonical H2A-H2B dimers and replace them with Htz1-H2B dimers (indicated in
green), forming a variant nucleosome with unique tails that might bind unique regulatory proteins (Reg). (B) Nucleosome modification (only
acetylation [Ac] is depicted for simplicity) allows the binding of regulatory factors, which have specialized domains (bromodomains) that recognize
acetylated histone tails. (C) Nucleosome repositioning allows the binding of a regulatory factor to its site on nucleosomal DNA (light-blue segment).
Remodellers are necessary to provide rapid access to nucleosomal DNA by sliding of the octamer along the DNA. Alternatively, the site might be
accessed on the surface through the generation of a DNA wave or through histone-octamer ejection (not shown).
© 2006 Nature Publishing Group Saha, A. et al. Chromatin remodelling: the industrial revolution of DNA around histones. Nature Reveiws Molecular
Cell Biology 7, 437–447 (2006) doi:10.1038/nrm1945.

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Section 17.2: Histone Modification

 Histone modification
– Covalent bonding of functional groups onto N-
terminal tails of histone proteins
 Most common: acetyl, methyl, phosphate
– Acetylation decreases positive charge, which
reduces affinity of histone to DNA
– Histone acetylation of nucleosome is catalyzed by
histone acetyltransferase enzymes (HATs):
associated with increased transcription
(Figure 17-2)

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd. Figure 17-2
Section 17.2: Chromatin Remodeling

 Chromatin remodeling
– Involves repositioning or removal of nucleosomes
on DNA
– Repositioned nucleosomes make chromosome
regions accessible to
 Transcription regulatory proteins
 Transcription activators
 RNAP II (RNA polymerase II)

© 2017 Pearson Education, Ltd.

Section 17.2: SWI/SNF

 SWI/SNF
– One of the best-studied remodeling complexes
– Loosens attachment between histone and DNA
– Loosens DNA strand from nucleosome core
– Causes reorganization of internal nucleosome
components
(Figure 17-2)

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd. Figure 17-2
Section 17.2: DNA Methylation

 DNA methylation
– Associated with decreased gene expression
– Methylation occurs most often on cytosine of CG
doublets in DNA
– Methylation can repress transcription by binding
to transcription factors of DNA

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 17.3 Eukaryotic Transcription Initiation
Requires Specific Cis-Acting Sites

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Section 17.3: Cis-Acting Sequences

 Cis-acting sequence
– Located on same chromosome as gene that it
regulates
– Required for accurate regulated transcription of
genes
 Promoters
 Enhancers
 Silencers

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Section 17.3: Promoters

 Promoters (core and proximal)

– Nucleotide sequences that serve as recognition
sites for transcription machinery
– Located immediately adjacent to regulatory genes
– Critical for transcription initiation
– Core promoter: Determines accurate initiation of
transcription
– Proximal-promoter elements: Modulate
efficiency of basal levels of transcription

© 2017 Pearson Education, Ltd.

Section 17.3: Promoter Diversity

 Great diversity exits in eukaryotic promoters,

in structure and function
 Figure 17-3
– Focused promoters
 Specific transcription initiation at start site
 Major type of initiation for lower eukaryotes
– Dispersed promoters
 Direct initiation from several weak transcriptional start
sites

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 Focused transcription is the predominant mode of
transcription in simpler organisms.

In dispersed transcription, there are several weak

transcription start sites over a broad region of about 50 to
100 nucleotides. Dispersed transcription is the most common
mode of transcription in vertebrates. For instance, dispersed
transcription is observed in about two-thirds of human
genes. In vertebrates, focused transcription tends to be
associated with regulated promoters, whereas dispersed
transcription is typically observed in constitutive promoters
in CpG islands.
https://www.sciencedirect.com/science/article/pii/
S0012160609011166

© 2017 Pearson Education, Ltd. Figure 17-3

Section 17.3: Promoter Structure

 Promoter structure
– Made up of DNA sequence elements including:
 Initiator (Inr)
 TATA box
 TFIIB recognition element (BRE)
 Downstream promoter element (DPE)
 Motif ten element (MTE)

© 2017 Pearson Education, Ltd.

  Fuda NJ, Ardehali MB, Lis JT. Defining mechanisms that regulate RNA polymerase II transcription in
vivo. Nature. 2009 Sep 10;461(7261):186-92. doi: 10.1038/nature08449. PMID: 19741698; PMCID:
PMC2833331.

General transcription factors (GTFs) bind to specific sequence elements in the promoter. These elements (the B recognition element (BRE), the TATA box (TATA), the initiator (Inr), the motif ten element
(MTE) and the downstream promoter element (DPE)) and their approximate locations relative to the transcription start site (TSS, black arrow) are shown 2. Transcriptional regulators (orange oval and
yellow diamond), which are either activators or repressors, bind to specific DNA sequences located near the core promoter of the gene or various distant regions, called enhancers. The regulators can
interact (green arrows) with GTFs, such as TFIID (blue rectangle) and TATA-binding protein (TBP, blue horseshoe), and the Pol II complex (red 'rocket') to enhance or repress transcription. They also
interact (green arrows) with co-regulators (green hexagon) that can interact (blue arrows) with the general ranscription machinery or chromatin-modifying factors, such as histone modifiers or nucleosome
remodellers. The co-regulators can also bind to nucleosomes (green) with various histone modifications, stabilizing the co-regulator binding to the gene.
Activators can recruit, stabilize or stimulate these factors, and repressors can disrupt or inhibit these factors.

© 2017 Pearson Education, Ltd.

Section 17.4: Proximal-Promoter Elements

 Promoters contain proximal-promoter

elements
– Located upstream of TATA and BRE motifs
– Enhance levels of basal transcription
– Examples: CAAT and GC boxes
(Figure 17-5)

© 2017 Pearson Education, Ltd.

 proximal-promoter elements
Beta-globin gene-mutations vs transcription level
© 2017 Pearson Education, Ltd. Figure 17-5
Section 17.3: Enhancers and Silencers

 Enhancers and silencers regulate

transcription of eukaryotic genes
– Cis-acting transcription regulatory elements
 Enhancers: Located on either side of gene,
some distance from gene, or even within gene
– Important in reaching maximum level of
transcription
 Silencers: Repress the level of transcription
initiation

© 2017 Pearson Education, Ltd.

 17.4 Eukaryotic Transcription Initiation Is
Regulated by Transcription Factors That
Bind to Cis-Acting Sites

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Section 17.4: Transcription Factors

 Transcription factors
– Transcription regulatory proteins
– Target cis-acting sites of genes regulating
expression
– Activators increase transcription initiation
– Repressors decrease transcription initiation
 Multiple transcription factors bind to several
different enhancers and promoter elements and
fine-tune the level of transcription initiation

© 2017 Pearson Education, Ltd.

Section 17.4: hMTIIA

 Human metallothionein IIA gene (hMTIIA)

– Example of how a gene can be transcriptionally
regulated due to interplay of:
 Promoters
 Enhancer elements
 Transcription factors that bind to them

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Section 17.4: Protein Product

 Product of hMTIIA
– Protein that binds to heavy metals and protects
cells from toxic effects
– Protects cells from oxidative stress
– Expressed in low levels in all cells
– Transcribed at high levels when exposed to
heavy metals
(Figure 17-6)

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 SP1-stimulates low level expression
BLE: basal element
ARE: AP factor response element
MRE: metal response element
GRE: glucocorticoid res.element

© 2017 Pearson Education, Ltd. Figure 17-6

Section 17.4: Functional Domains

 Transcription factors (proteins)

– Have two functional domains (clusters of amino
acids with a specific function):
– DNA-binding domain
 Binds to specific DNA sequences in the cis-acting
regulatory site
– Trans-activating domain
 Activates or represses transcription by binding to
other transcription factors or RNA polymerase

© 2017 Pearson Education, Ltd.

Section 17.4: Domains

 Characteristic domains of DNA-binding

proteins
– Helix-turn-helix (HTH)
 Present in both eukaryotic and prokaryotic transcription
factors
– Zinc-finger
 Found in wide range of transcription factors that
regulate gene expression
– Basic leucine zipper (bZIP)
 Allows for protein-protein dimerization

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© 2017 Pearson Education, Ltd.
 17.5 Activators and Repressors Interact
with General Transcription Factors and
Affect Chromatin Structure

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Section 17.5: Formation of RNA Pol II
Initiation Complex
Formation of RNA Pol II initiation complex
 General transcription factors (proteins)
– Required at promoter to initiate basal or
enhanced levels of transcription
– Assembly of proteins in specific order forms
pre-initiation complex (PIC)
– PIC provides platform for RNAP II to recognize
transcription start sites

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Core Promoter TFIID

 Core promoter TFIID

– General transcription
factor that assists RNA
Pol II at core promoter
TFIID
– First step in forming
PIC – binding of TFIID
to TATA box via TATA
binding protein (TBP)
(Figure 17-7)

© 2017 Pearson Education, Ltd.

Section 17.5: Mechanism of Transcription
Activation and Repression
 Transcription activators and repressors bring
changes to RNA Pol II transcription
– DNA looping delivers activators, repressors, and
general transcription factors to promoter vicinity

– Recruitment model: enhancers and silencer

elements act as donors; affect regulatory proteins
at gene promoters

© 2017 Pearson Education, Ltd.

Section 17.5: Coactivators and
Enhanceosome
 Coactivators
– Interact with proteins and enable activators to
make contact with promoter-bound factors
– Coactivators form complex “enhanceosome”
 Enhanceosome
– Interacts with transcription complex (Figure 17-8)
 Repressor proteins at silencer elements
decrease rate of PIC assembly and RNA Pol II
release

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd. Figure 17-8
 17.6 Gene Regulation in a Model Organism:
Transcription of the GAL Genes of Yeast

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Section 17.6: GAL Gene System

 GAL gene system in yeast

– 4 structural genes (Gal1, 10, 2, 7)
and 3 regulatory genes (Gal 4, 80, 3)
– Products of structural genes transport galactose
into cell for metabolism
 Positive control: Activator protein must be
present to turn on gene transcription

(Background note: galactose is also a monomeric sugar, when linked with a

glucose, we call the disaccharide lactose)

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Section 17.6: GAL Genes Are Inducible

 GAL genes are inducible

– Transcription is regulated by presence or absence
of substrate (galactose)
– Absence of galactose: GAL structural genes not
transcribed

– Galactose added to medium: Transcription begins

immediately

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Section 17.6: Transcription Is Positively
Regulated
 GAL1 and GAL10 genes (structural..)
– Transcription of both genes is positively regulated

– Controlled by central control region, UASG 170 bp

(upstream activating sequence of GAL genes)
– Contain 4 binding sites for Gal4 protein (Gal4p)
(Figure 17-9)
– UAS is functionally similar to enhancers in
eukaryotes

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Section 17.7: Gal4 Protein

 Gal4 protein
 Encoded by GAL4 gene
– Negatively regulated by
Gal80 protein
 Has DNA-binding
domain that recognizes
and binds to sequences
in UASG
 Binding of
phosphorylated
galactose to Gal80p
and/or Gal4p exposes
activation domain of
Gal4p
(Figure 17-10)
© 2017 Pearson Education, Ltd.
 Deletion mutants
were pivotal to
delineate
functional
regions

© 2017 Pearson Education, Ltd. Figure 17-10

 Gal4 always
bound but
No Gal regulated by
Transactivation Gal 80
domain closed

Gal Gal interacts

Transactivation with Gal3 which
domain of 4 is OPEN together interact
with 4&80

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Transcativation domain activates transcription Figure 17-9
Section 17.6: DNase Hypersensitive

 Chromatin structure of UAS is constitutively

open, or DNase hypersensitive, meaning that
it’s loosely associated with nucleosomes

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Gal4p interacts with other factors
e.g. SAGA-co activator

Then mediator
complex interacts
with Gal4p/SAGA to
recruit RNA pol II

Gal4p also recruits

SWI/SNF to remove
nucleosomes
at the promoter

https://www.sciencedirect.com/science/article/pii/
S1097276517306135
 17.7 Posttranscriptional Gene Regulation
Occurs at Many Steps from RNA
Processing to Protein Modification

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Section 17.7: Posttranscriptional Regulation

 Posttranscriptional regulation plays an equal,

if not more significant, role compared to
transcriptional control (perhaps the major type of
regulation in eukaryotes)
 Mechanisms of posttranscriptional gene
regulation
– Control of alternative splicing
– mRNA stability
– Translation
– RNA silencing

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  Lets remember splicing (go back to Chapter 13 if
you need to)

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 Group I introns

G is the co-factor!

Ribozyme: enzymatic activity

© 2017 Pearson Education, Ltd. Figure 13-13

 Lariat structure!

OH of A attacks
The G, whose OH attacks
The other G (Exon2)

Fungi, protists, bacteria

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 snRNAs (U1, U2 ....)

Not autocatalytic
Needs
SPLICEOSOME

© 2017 Pearson Education, Ltd. Figure 13-14

 Splicing

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© 2017 Pearson Education, Ltd.
Section 17.7: Alternative Splicing

 Alternative splicing
– Generates different forms of mRNA from identical
pre-mRNA (increases number of proteins)
– Expression of one gene gives rise to numerous
proteins with similar and different functions
– Increases number of proteins made from one
gene (Figure 17-11 and Figure 17-12)

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 32 aa peptide to
regulate Ca+2

© 2017 Pearson Education, Ltd. Figure 17-11

© 2017 Pearson Education, Ltd. Figure 17-12
https://www.sciencedirect.com/science/article/pii/S0002929717304548
Section 17.7: Alternative Splicing

 Alternative splicing
– Number of proteins cell can make (proteome) is
not directly related to number of genes in genome
– At least two-thirds of protein-coding genes in
humans undergo alternative splicing

 Spliceopathies: Mutations that affect regulation

of splicing and contribute to several genetic
disorders
– Example: Myotonic dystrophy

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Section 17.7: Sex Determination in Drosophila

 Sex determination in Drosophila – Alternative

splicing
 Three major genes in pathway
– Sex lethal (Sxl)
– Transformer (tra)
– Doublesex (dsx)
 Product of sxl gene selects pathway of sexual
development by controlling splicing
(Figure 17-13)

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd. Figure 17-13
Section 17.7: Control of mRNA Stability

 Steady-state level of mRNA

– Amount of mRNA in cell available for
translation
– Determined by combination of transcription and
mRNA degradation rates
 Half-life (t1/2)
– mRNA is degraded at some point after synthesis
– Lifetime of mRNA varies; regulated by cell need

© 2017 Pearson Education, Ltd.

 t1/2

• Cells 8(8):778DOI:
• 10.3390/cells8080778

© 2017 Pearson Education, Ltd.

Section 17.7: Three Pathways of Degradation

 Pathways of degradation
1) Enzymes shorten length of poly-A tail
• Binding of poly-A binding protein to tail stabilizes
mRNA
2) Decapping enzymes removes 7-methylguanine
cap – mRNA now unstable
3) Endonuclease cleaves mRNA internally

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Section 17.7: p53 Protein and Ubiquitin

Translational and posttranslational regulation

 p53 protein
– p53 levels increase if cell suffers DNA damage or
metabolic stress
– p53 is a transcription factor that induces
transcription of Mdm2 gene (ubiquitin ligase,
blocks transcription)
– Ubiquitin tags proteins for degradation by
enzymes

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© 2017 Pearson Education, Ltd.
 17.8 RNA Silencing Controls Gene
Expression in Several Ways

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Section 17.8: RNA Interference

 RNA interference (RNAi)

– Sequence specific posttranscriptional regulation
– Short RNA molecules regulate gene expression in
cytoplasm of plants, animals, and fungi; repress
translation and trigger mRNA degradation

 Phenomena known as RNA-induced gene

silencing

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Section 17.8: Molecular Mechanisms

 Molecular mechanisms of RNA-induced gene

silencing
 siRNA and microRNAs
– Short, double-stranded ribonucleotides
– siRNAs: Arise in cell due to virus infection –
produce double-stranded RNA, which is
recognized and cleaved by Dicer
– microRNAs: Noncoding RNAs that negatively
regulate gene expression
(Figure 17-14)

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miRNA biogenesis  Biosynthesis of miRNAs. The miRNA
gene is transcribed by RNA polymerase
II as pri-miRNAs which are then
processed by Drosha to produce long
miRNA precursor (pre-miRNA). The pre-
miRNAs are transported to the
cytoplasm where they are further
cleaved by the endoribonuclease Dicer
to mature ∼22 nt long miRNA–miRNA
*duplex. In this process Dicer interacts
with the TRBP, PACT, and Argonaute
proteins, which form the RNA-induced
silencing complex (RISC). Within this
complex, one strand of the miRNA
duplex is removed and the single
stranded miRNA, complementary to the
target mRNA, remains in the complex
and becomes functional. Seven to eight
base pair “seed” sequence in 5′
miRNAs is partially complementary to
the 3 UTR of mRNA targets, and
induces posttranscriptional silencing
through mechanisms such as mRNA
destabilization and translational
repression.
Fine-Tuning Oligodendrocyte Development by microRNA
s
© 2017 Pearson Education, Ltd. Figure 17-14
© 2017 Pearson Education, Ltd.
Also watch this

 https://www.youtube.com/watch?v=5YsTW5i0Xro

 miRNA and siRNA biogenesis

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Section 17.8: RNAi in Biotechnology

 RNAi in biotechnology
– RNAi studied in lab
– Developed as pharmaceutical agent
– Therapeutic RNAi attacks diseases caused by
overexpression of specific gene or normal
expression of abnormal gene product
– Potential use of RNAi in diagnosis of cancers
– RNAi reduces severity of infections by viruses
such as HIV, influenza, and polio

© 2017 Pearson Education, Ltd.

Section 17.8: Animal Models

 Successful RNAi treatment in animal models

– Viral infection
– Eye diseases
– Cancers
– Inflammatory bowel disease
 Science of RNAi holds powerful promise for
molecular medicine; RNAi drugs are expected to
be available within next decade

© 2017 Pearson Education, Ltd.

 17.9 Programmed DNA Rearrangements
Regulate Expression of a Small Number of
Genes

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Section 17.9: Programmed DNA
Rearrangements
 Immunoglobulin system in humans
– Antigen recognition: Immune system binds to
foreign substances (antigens)
– Humoral immunity: Production of
immunoglobins (antibodies) that directly bind to
antigens
– B lymphocytes (B cells): Four variable regions
that recognize specific antigen (Figure 17-15)
 Each B cell synthesizes only one type of
immunoglobulin

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd. Figure 17-15
Section 17.9: Polypeptide Chains

 Immunoglobulin molecules consist of four

poly-peptide chains
– Two identical:
 Light (L) chain and heavy (H) chain form Y-shaped
structure
 DNA regions organized into L (leader) and V (variable)
regions

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Section 17.9: Constant and Variable Regions

 Each L and H chain contains constant and variable regions

– Constant: C-terminus
– Variable: N-terminus

 Antibody diversity occurs in part from random

recombination of different functional LV regions
with any 5 different J (joining) regions
(Figure 17-16)

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© 2017 Pearson Education, Ltd.
 Variable light
chain

© 2017 Pearson Education, Ltd. Figure 17-16

 Further reading:
The Generation of Antibody Diversity
https://www.ncbi.nlm.nih.gov/books/NBK26860/

© 2017 Pearson Education, Ltd.

Section 17.9: Recombination and
Hypermutation
 Two other mechanisms further increase antibody diversity:
1. somatic hypermutation (SHM): random somatic mutation during B cell development
2. class switch recombination (CSR): Joins LV region to J region; not precise, results
in considerable variation
 Both are initiated by the protein activation‐induced deaminase (AID), which
converts cytosine to uracil in the immunoglobulin loci.

© 2017 Pearson Education, Ltd.

 17.10 ENCODE Data Are Transforming Our
Concept of Eukaryotic Gene Regulation

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Section 17.10: ENCODE

 ENCODE: Encyclopedia of DNA Elements

Project
– Goal: Identify all functional DNA sequences and
determine how elements regulate expression
 Discovery by ENCODE
– More than 80% of human genome contains
regulatory elements (once considered “junk
DNA”)

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Section 17.10: Enhancers and Promoter
Elements
 Enhancers and promoter elements
– Promoter elements: 30,000 promoter regions
found within protein-coding genes
– ENCODE data show enhancer elements influence
transcription of several different promoters
– Enhancer elements: Contain promoter elements
that initiate transcription
https://www.encodeproject.org/

© 2017 Pearson Education, Ltd.