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Promoters and transcription factors
Context
Transcription -The conversion of DNA information
to RNA information.


Happens before splicing
Mechanism for transcription is RNA polymerase.

Followed by translation - The conversion of RNA
information to amino acid sequence

RNA polymerase
 >10
subunits
 Several
types I-III
 Type
II is involved in "gene" transcription.
 Type
I and III transcribe ribosomal and transfer
RNA
Characteristics of transcription
 Polymerase
does not recognise its promoter
directly, only through use of promoters can
transcription take place.
 TBP (TATA box)
is a common element in
initiation complex but may not bind to a TATA
box in all cases
 TBP binds
 Several
in the minor groove
other transcription factors must also bind
How transcription elements are
discovered
Use of a reporter system


Procedural, makes the enzyme assay routine

Artifacts present, not all factors will be present
Chop off the DNA until you get a change in the
reporter enzyme levels

Mutate a potential site (Single bp changes)

Consensus sequences

Promoters vs Enhancers
Characteristics of each


Promoters <200 bp from start

Enhancers < 'several kb'


May end up closer due to bending
Typically more global regulatory elements, tissue or time
specific

Enhancers several closely packed sites

Promoters more dispersed

Both consist of < 10 bp elements
Example: CAAT Box
"
"
"
Sequence is used by alpha globin, adenovirus,
fibrinogen, two proteins from rat liver
Other sequences around CAAT box probably
influence what actually gets bound to the CAAT
box
A conserved DNA element does not necessarily
imply that the same regulatory element is binding.
Enhancers
"
Can be either upstream or downstream.
"
Could change density of supercoiling.
"
Provide an entry site for the polymerase.
"
Anchor the DNA at a place within the cell for
access.
"
Silencers
"
Insulators
Genomic structure
"
A obvouly recent field
"
Look at the genome anatomy
"
Top down look at the problem
TRANSFAC
"
"
Database of transcription factors
Classifed by a system similar to EC number, but
not directly compairable
"
Open (to non comerical) and updateable
"
Utilized by a variety of tools
Sequence repeats
May have different densities


Called microsatellite DNA

TTAGGG on the ends on chromosome at the telomeres
Transposable elements
35% of human genome is TE


>50% of corn is TE

1.8% of C. elegans is TE

15% of Drosophila is TE
Types of TE's
LTR's (Long terminal repeats)


Retroviruse elements

Short 80-300bp segments SINES

And longer 6-8 kb segments LINES
Psuedogenes
"
A snapshot of evolution
"
New gene functions gained by gene duplication.
"
The duplicated gene is then free to mutate
"
processed psudeogenes, no introns or promoter
regions, thought to be due to RT
Synteny
"
"
"
Fancy word for gene order
The sequence of a gene may change much faster
than the order of the genes
May be a very useful confirmation or hint of the
function of a gene
Operon/clusters
"
"
"
"
It is normal for a prokaryote to transcribe clusters
of genes which are translated toghter as well.
May cluster genes working on the same metabolic
process togther
Eukaryotes there is not the co-transcription and
the clustering is not found
Gene order is still very conserved
ACR
"
Ancient conserved regions
"
20-40% of coding sequences are ACRs
"
Possibly represent proteins present at the time of
prokaryotic/eukaryotic split
Horozontal gene transfer
"
As opposed to vertical transer (inheritance)
"
Mitochondira/Chloroplasts
"
Significant in bacteria 12.8% in E. coli