Transcription regulatory elements

Transcriptional Regulatory Elements

by: amirhossein heydarian

Introduction

The completion of the human genome sequence led to the

cataloging of∼20,000–25,000 protein-coding genes

And key question is how these genes and their products

function??

introduction

To understand the molecular mechanisms that govern specific expression patterns it is important to identify the transcriptional regulatory elements

Here we review the various classes of transcriptional regulatory elements and the current understanding of how they function.

Transcriptional regulation

One of the mechanisms through which protein levels in the

cell are controlled is through transcriptional regulation.

Certain regions, called cis-regulatory elements, on the

DNA are footprints for the transacting proteins involved in

transcription, either for the positioning of the basic

transcriptional machinery or for the regulation

Basic transcriptional machinery

DNA-dependent RNA polymerase (RNAP) which synthesizes various types of RNA

core promoters on the DNA are used to position the RNAP

other nearby regions will regulate the transcription:

proximal promoter regions, enhancers, silencers, and insulators

Transcriptional Machinery

Factors involved in the accurate transcription of eukaryotic

protein-coding genes by RNA polymerase II can be classified into

three groups:

I. general (or basic) transcription factors (GTFs)

II. promoter-specific activator proteins (activators)

III. coactivators

GTFs

GTFs assemble on the core promoter in order to form a

transcription preinitiation complex (PIC) ,which directs RNA

polymerase II to the transcription start site (TSS).

Activators

In general, activators are sequence-specific DNA-binding proteins whose recognition sites are usually present in sequences upstream of the core promoter

Examples of activator families:

Cysteine rich zinc finger

helix-loop-helix (HLH)

basic leucine zipper (bZIP)

DNA binding domain

The activity of an activator may be modulated by coactivators

Activators

Coactivators

coactivators stimulating PIC assembly or modifying

chromatin.

in a cell can play a major role in determining the

regulatory response, as they can modify an activator’s

ability to positively or negatively regulate transcription

Eukaryotic transcription regulation

The expression of eukaryotic protein-coding genes (also called class II or structural genes) can be regulated at several steps, including:

transcription initiation most regulation

Elongation

mRNA processing

Transport

translation,

Cis-acting transcriptional regulatory

elements

Genes transcribed by RNA polymerase II typically contain two

distinct families of cis-acting transcriptional regulatory elements:

promoter

distal regulatory element

These cis-acting transcriptional regulatory elements contain

recognition sites For trans-acting DNA-binding transcription

factors, which function either to enhance or repress transcription

Transcriptional regulatory elements

promoter:

Core Promoter

Proximal Promoter Elements

distal regulatory elements:

Enhancers

Silencers

Insulators

Locus Control Regions (LCR)

Transcriptional regulatory elements

Transcriptional regulatory elements

Promoter

promoter is a region of DNA that initiates transcription of

a particular gene

Promoters are located near the transcription start sites of

genes.

Promoters can be about 100–1000 base pairs long.

promoter

a promoter, which is composed of a core promoter and nearby

(proximal) regulatory elements

The core promoter is the region at the start of basic transcriptional machinery and PIC assembly, and defines the position of the TSS.

The core promoter usually refers to the region from the transcription start site including the TATA box, which resides approximately 30 bpupstream of the transcriptionn initiation site.

The core promoter is a region around the TSS (+1) of a gene, which contains several DNA elements that facilitate the binding of regulatory proteins.

Core promoter definition

PIC :

Binding of

regulatory proteins is

required formation of

the PIC

(pre-initiation

complex).

Core Promoter

Metazoan core promoters are composed of:

TATA box The first described core promoter element

Initiator element (Inr) the most common element

Downstream Promoter Element (DPE)

Downstream Core Element (DCE)

TFIIB-Recognition Element (BRE)

Motif Ten Element (MTE).

Core Promoter

Core promoter

core promoters are diverse in their content and

organization.

it is clear that PIC assembly does not depend on a single

nucleation point, such as a TATA box; rather, many of the

core promoter elements interact with TFIID and stabilize

PIC assembly

Core Promoter

Proximal Promoter Elements

In Metazon, several other promoter elements exist which

are located upstream of the core promoter:

the proximal promoter elements

The proximal promoter is defined as the region

immediately upstream (up to a few hundred base pairs) from

the core promoter, and typically contains multiple binding

sites for activators.

Proximal Promoter Elements function

An interesting feature of∼60% of human genes is that their promoter falls near a CpG island

DNA methylation is associated with transcriptional silencing.

Methylation at CpG dinucleotides is believed to repress transcription by blocking the ability of transcription factors to bind their recognition sequences

The refractory nature of CpG islands to methylation suggests that a role for proximal promoter elements may be to block the local region from being methylated, and therefore inappropriately silenced.

Distal regulatory elements

Including:

enhancers

silencers

Insulators

locus control regions (LCR)

Distal regulatory elements

Enhancers

enhancer is a short (50-1500 bp) region of DNA that can be

bound with proteins (activators) to activate transcription of a

gene or genes.

These proteins are usually referred to as transcription factors

Enhancers

Enhancers were characterised almost 20 years ago.

Enhancers are typically composed of a cluster of TFBSs

that work cooperatively to enhance transcription and The

transcription factors that bind to enhancers are called

transcriptional activators

Enhancers location

These enhancer regions can be found:

up- and downstream of the TSS

within exons or introns

in the 5 and 3 untranslated (UTR) regions of genes

and even as far as 10,000 bp in Drosophilaor 100,000 bp in

human and mouse away from the gene boundaries

Enhancers

enhancer activation often needs the binding of several

transcription factors to cis-regulatory motifs to the enhancer.

Looping in chromatin plays a role in bringing enhancers

physically close to the proximal or core promoter region of a

target gene.

Once active, the enhancer can bind to the PIC or to

tethering elements in the proximal region of the promoter

and influence (the rate of) transcription by itself.

Enhancers

Silencers

Silencer is a DNA sequence capable of binding

transcription regulation factors, called repressors.

Silencers are sequence-specific elements that confer a

negative effect on the transcription of a target gene

Typically, they function independently of orientation and

distance from the promoter, although some position-

dependent silencers have been encountered.

Silencers location

They can be situated as as part of a proximal promoter, as

part of a distal enhancer and they can be located far from

their target gene, in its intron, or in its 3-untranslated region.

Silencers

Two distinct classes of silencers exist:

position-independent motifs that via their bound TF

(repressors) proteins actively interfere with the PIC assembly

are called silencer elements and are normally found upstream

of the TSS

position-dependent silencers or negative regulatory

elements (NREs) that passively prevent the binding of TFs to

their respective cis-regulatory motifs and can be found both

up- and downstream of the TSS and within introns and exons

Silencers

silencers may cooperate in binding to DNA, and they can act synergistically.

Silencers are binding sites for negative transcription factors called repressors.

Repressor function can require the recruitment of negative cofactors, also called corepressors, and in some cases, an activator can switch to a repressor by differential cofactor Recruitment.

Models for repressor function:

Blocking the binding of a nearby activator, or by directly competing for the same site.

prevent activators and/or GTFs from accessing a promoter by establishing a repressive chromatin structure through the recruitment of histone-modifying activities or chromatin-stabilizing factors.

block transcription activation by inhibiting PIC assembly

Insulators

Insulators function to block genes from being affected by

the transcriptional activity of neighboring genes.

They can block such interactions such as block enhancer-

promoter

It is thought that an insulator must reside between the

enhancer and promoter to inhibit their subsequent

interactions.

Insulators

Two distinct types of insulators have been discovered:

I. barrier insulators

II. enhancer-blocking insulators

Barrier insulators

Barrier insulators safeguard against the spread of

heterochromatin, and thus of chromatin-mediated

silencing, and lie on the border of heterochromatin

domains.

enhancer-blocking insulators

The enhancer-blocking insulators protect against gene

activation by enhancers and interfere with the enhancer–

promoter interaction only if the insulator is located

between the enhancer and the promoter.

Insulators

Insulators

Locus Control Regions

The LCR was identified over 20 years ago in studies of

transgenic mice.

These studies determined that the LCR was required for

normal regulation of beta-globin gene expression

regulation of beta-globin gene

expression

Locus Control Regions

Locus control regions (LCRs) are groups of regulatory

elements involved in regulating an entire locus or gene

cluster.

LCRs are typically composed of multiple cis-acting

elements, including enhancers, silencers, insulators, and

nuclear-matrix or chromosome scaffoldattachment regions.

Locus Control Regions

These elements are bound by transcription factors

coactivators, repressors, and/or chromatin modifiers.

Each of the components differentially affects gene

expression, and it is their collective activity that functionally

defines an LCR and confers proper spatial/temporal gene

expression.

Locus Control Regions

LCRs are often marked by a cluster of nearby DNase I

hypersensitive sites and are thought to provide an open-

chromatin domain for genes to which they are linked.

Locus Control Regions location

Although LCRs are typically located upstream of their

target gene(s), they can also be found within:

intron of the gene they regulate, exemplified by the

human adenosine deaminase LCR

downstream of the gene, as in the case of

the CD2 or Th2 LCR

in the intron of a neighboring gene, as occurs

with the CD4 LCR

Transcriptional regulatory elements

involved in human diseases

Transcriptional regulatory elements

involved in human diseases

Transcriptional machinery components

involved in human diseases