eukaryotic and prokaryotic promoters

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PROMOTER
SEQUENCEANALYSI
S
Isabella
BS biochemistry
Learning objectives
◦ Introduction
◦ Types of promoter elements
◦ Databases of Promoter elements
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Two languages in our genes
◦ Protein coding information - indirect reading
◦ DNA  transcription  pre-mRNA  splicing  mRNA  translation 
protein
◦ Less than 2% of the human genome
◦ Regulatory information - direct reading
◦ DNA  binding of TF  gene activation
Indirect read-out through
transcription/translationDirect read-out by TFs
Cis 
Trans

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cis-elements = Templates for assembly
The function of cis-elements is being templates for the assembly of
multiprotein complexes 4
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Types of promoter elements
◦ Core Promoter elements
◦ Elements required to initiate the transcription e.g TATA box
◦ Regulatory promoter elements
◦ Responsive elements
◦ CRE, HSE, GRE - mediates response to cAMP, heat shock, glucocorticoids
◦ Cell type specific elements
◦ Location-- mixed with Upstream regulatory elements
(UPEs)
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Three RNA polymerases
- three groups of promoters
◦RNA polymerase I
◦ rRNA (28S, 18S and 5.8S )
◦ RNA polymerase III
◦tRNAs and 5S rRNA
◦RNA polymerase II
◦ Protein-coding genes
80% of total
RNAsynthesis
from these
”Oddpols”
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Transcription factors
Sequence-
specific DNA
binding
Non-DNA
binding
TF1 TF
2
TF
3
TF
4
adapter
HA
T
DNA
Layer I
Layer III
Co-activator
Layer II
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Transcription factors recognition sites
◦ Typically 6-10 positions very selective and several others
show bias
◦ Often selectivity profile summarized by ‘motif’
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Eukaryotic promoter databases
◦ TRANSFAC
◦ JASPAR
◦ PLANT
CARE
◦ PLACE
◦ Consite
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JASPAR (http://jaspar.genereg.net/ )
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Click on it
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PLANT CARE
(http://bioinformatics.psb.ugent.be/
webtools/plantcare/html/ )
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Class work
◦ Scan the following sequence in JASPAR and Plant CARE for identification of putative cis-acting
elements
◦ Save the results as pdf and email me today
◦ CTGGTCTACTTGGCATTGTAGAAACCATTGAAACTTAACCTGCCAACCTATGTGACCTCTTCCTTTTAG
AAACTTGGCTTACGATGCTACATCCCTAGTGGATGCTGATGCATACCTCTTACCCTTCTGGTCAGACT
GGTTATCCTTCAACATGTTAGCTGAAAAAAGTACTATGTTGCATGCCATCAATCTCAATAAAAGTTTTGA
TGACTTCCACCGACCCGGCAAAAAAAAAAAACAGATATATAGAATTGGCCTTATTAATAACAAGCC
TTATTAAGCTAATCGATCGACAGGACTAGCGTTCGGGACAGCCTGCATAAGTGTCCGTACCAGTA
CGGTCAGAGTGACATATGGGAAAACCAGTACAGTTAAACTGTATTTATTCTCCAGAAAAAAAAATTG
TAGTCTTTGTTACGCCTGTAATATTGCCAGTGAAAGTAATTAACCACTCCCCAGAAAAATGCATGGC
GTGTGACCAAGTAAATTTTTGACTAGTCTGCAGAGTGATCAGTGACAAAATTAATGATATGCTAAAAG
GTAGCAAAAGCTGCTCGTAATGTCCTTCTCATAATCCTTAATTACCGGCCGGTTCGAAACAATTTGATT
TGATCCCAAGATAATGGCGACCAAGTAAATGAAAAAGGTTGGAAACAATAGTTCTTTCGATCGATG
ACTTAGCATGCAGGTCATTGATTGATGATGCACGCTCGTTGGCCCTTTCTGCAGATCCGAACATAAC
TACTGCTATCCTTAATTTCCTTCAAAAAGAGATAAAAGATAACTACTCTATGCCATCGTCAAAATGTGT
GAAAACACAATCGACCACGTCAGGTTAGTTAGTAGTGCCGATACATATATTTTTAAGCTGAAAAGTTC
AACCTGCAGGCAGCAAATTGCAGACCATTTCAGTCTACTAGCTGACATCAGTTCAGATTAATTGACT
TGTTCAGTTGTTCACAAGTTCACGCTGCCGCGCCCCTGCGGCTATATAAGCACATTAATCCTCCAC
AGCCAAAGCATCACCCAACGATAACACAAGCAGTTAGCTAGCAGCTAGCTAGCTTCTCAGCCA
CCAGAGAAACAGCAAATAATTCAGCAGAGAAG 23
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