05 the Regulatory Region

Gene Structure
Objectives of the lesson

At the end of this lesson students will be able to
 Analyze the structure of the gene
Define some terminologies associated with gene
structure :
• Genome – entire genetic
material of an individual
• Transcriptome – set of
transcribed sequences
• Proteome – set of proteins
encoded by the genome
Eukaryotic Gene Structure
5’ - Promoter Exon1 Intron1 Exon2 Terminator – 3’

UTR splice splice UTR
transcription
Poly A
translation
protein
Prokaryotic Gene Structure
Promoter CDS Terminator

UTR UTR
Genomic DNA
transcription
mRNA
translation
protein
Promoter
• Promoter determines:
1. Which strand will serve as a template.
2. Transcription starting point.
3. Strength of polymerase binding.
4. Frequency of polymerase binding.

Prokaryotic Promoter
• One type of RNA polymerase.
• Pribnow box located at –10 (6-7bp)
• –35 sequence located at -35 (6bp)
Eukaryote Promoter
• 3 types of RNA polymerases are
employed in transcription of genes:
– RNA polymerase I transcribes rRNA
– RNA polymerase II transcribes all genes
coding for polypeptides
– RNA polymerase III transcribes small
cytoplasmatic RNA, such as tRNA.
Eukaryote Promoter
• Goldberg-Hogness or TATA located at –
30
• Additional regions at –100 and at –200
• Possible distant regions acting as
enhancers or silencers (even more than
50 kb).
Promoter
• Promoters sequences can vary
tremendously.
• RNA polymerase recognizes hundreds of
different promoters
Promoter
• Strong promoter resemble the consensus
sequence.
• Mutations at promoter sites can
influence transcription.
Human gene
Beta globin
• Conclusions:
1. Promoters are very hard to predict.
2. Promoter prediction must be organism-

dependent (and even polymerase-
dependent).
Termination Sites
• The newly synthesized mRNA forms a

stem and loop structure (lollipop).
• A disassociation signal at the end of the

gene that stops elongating and releases
RNA polymerase.
• All terminators (eukaryotes and

prokaryotes) form a secondary structure.
Termination Sites
• The terminator region pauses the polymerase
and causes disassociation.
Splice Sites
• Eukaryotics only
• Removing internal parts of the newly transcribed
RNA.
• Takes place in the cell nucleus (hnRNA)
Splice Sites
• Conserved splice sites are shared by both the

exon and the intron.
• Different signals on the donor site (3’) and on
the acceptor site (5’).
The regulatory region of a gene
A gene consists of a transcriptional region and a
regulatory region.
The transcriptional region is the part of DNA to

be transcribed into a primary transcript (an RNA
molecule complementary to the transcriptional
region).
The regulatory region can be divided into cis-

regulatory (or cis-acting) elements and trans-
regulatory (or trans-acting) elements
The regulatory..
The cis-regulatory elements are the binding

sites of transcription factors which are the
proteins that, upon binding with cis regulatory
elements, can affect (either enhance or
repress) transcription.
The trans-regulatory elements are the DNA

sequences that encode transcription factors.
The regulatory…
The cis-acting elements may be divided into the following four

types:
1. Promoter
The DNA element where the transcription initiation takes
place.
2. Enhancer
The element that, upon binding with transcription factors, can
enhance transcription.
The transcription factors that bind to enhancers are
called transcriptional activators.
3. Silencer
The element that, upon binding with transcription factors, can
repress transcription.
The transcription factors that bind to silencers are
called repressors
4. Response elements
The recognition site of certain transcription factors.
Gene organization
The transcription region consists of exons and

introns.
 The regulatory elements include promoter, response
element, enhancer and silencer.
 Downstream refers to the direction of transcription
and upstream is opposite to the transcription
direction.
 The numbering of base pairs in the promoter region is
as follows.
The number increases along the direction of
transcription, with "+1" assigned for the initiation
site. There is no "0" position. The base pair just
upstream of +1 is numbered "-1", not "0".

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Gene Structure

Objectives of the lesson

5’ - Promoter Exon1 Intron1 Exon2 Terminator – 3’

Promoter CDS Terminator

1. Which strand will serve as a template.

2. Transcription starting point.

3. Strength of polymerase binding.

4. Frequency of polymerase binding.

2. Promoter prediction must be organism-

• The newly synthesized mRNA forms a

• A disassociation signal at the end of the

• All terminators (eukaryotes and

• Conserved splice sites are shared by both the

The transcriptional region is the part of DNA to

The regulatory region can be divided into cis-

The cis-regulatory elements are the binding

The trans-regulatory elements are the DNA

The cis-acting elements may be divided into the following four

The transcription region consists of exons and

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