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Promoters. Oriane Broustal BIO 535. Promoters. About promoters ( structure, function,…) Two types of human promoters based on CG content Bidirectional promoters in human genome. Questions:. What are the differences between eukaryotic and prokaryotic promoters?

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Promoters

Promoters

Oriane Broustal

BIO 535


Promoters1

Promoters

  • About promoters ( structure, function,…)

  • Two types of human promoters based on CG content

  • Bidirectional promoters in human genome


Questions

Questions:

  • What are the differences between eukaryotic and prokaryotic promoters?

  • Explain what you know about bidirectional promoters in human genome.


Function of promoter

Function of promoter

  • ARN polymerase binding site

  • Initiation of transcription

  • control by regulatory sequences => control the expression of genes


Prokaryotic promoters

Prokaryotic promoters

  • - 35 box and – 10 box ( also called Pribnow box) are consensus sequences

  • The two boxes are far appart from a specific distance, so they are located on the same face of the double helix.


Prokaryotic promoters1

Prokaryotic promoters

  • Possible to have variations in the consensus sequences

  • There is often a correlation between level of expression of a gene and degree to which the –35 and –10 region agree with their consensus sequence


Eukaryotic promoters

Eukaryotic promoters

  • There are two parts:

    - The core promoter or basal promoter

    - Upstream promoter element ( one or more)

  • Core promoter is constituted by the TATA box and the transcriptional start site (TSS)

  • Initation complexe bind to the core promoter

  • Upstream elements are responsable of the regulation of the transcription


Eukaryotic promoters1

Eukaryotic promoters


Regulation of transcription

Regulation of transcription

  • Two categories of regulatory sequences:

    - Activating sequences= Enhancers

    - Repressing sequences = Silencers

  • In Prokaryotes, regulatory sequences are located around the promoter

  • In Eukaryotes, regulatory sequences are often upstream the promoter at about 100 bp away, but sometime they are far away (several thousand nucleotides) or they can also be dowstream from the promoter


Two types of promoter based on cpg content in human genome

Two types of promoter based on CpG content in human genome

  • CpG = Cytosine followed by a Guanine ( linked together by a phosphate)

  • CpG island = regions of the DNA which have a high concentration of CpG

  • Based on CpG content, there are two types of promoters:

    - with high CpG content ( called HCG) = 72%

    - CpG content characteristic of averall genome = 28%

  • In HCG, the CpG region is symetric and peaks aroud the core promoter (specially around the TSS).


Dna methylation

DNA methylation

  • Occurs on Cytosine in 5’ position

  • inhibits transcription if methylated region is close to a promoter, which is the case for CpG islands.

  • CpG island associated with HCG are often hypomthylated =>more expressed . It is often associted with House-keeping gene.

  • Whereas, in promoter with lower CpG, CpG are often methylated => inhibit the expression. This often finds in tissue-specific genes.

  • With CpG islands around promoter, posibility to have methylation mediated regulation


Dna methylation1

DNA methylation


Cytosine methylation and mutation

Cytosine methylation and mutation


Bidirectional promoters in human genome

Bidirectional promoters in human genome

  • Pairs of genes control by same promoter but located on opposite strand and opposite direction. Their TSS are separated by less than 1,000 bp.

  • In general, they are rich in CpG content

  • Function of genes represented in bidirectinal class are often: DNA repair genes, chaperone protein, and mitochondrial genes.

  • Seem to be conserved in evolution


Bidirectional promoters in human genome1

Bidirectional promoters in human genome

  • Genes control by bidirectional promoters are oftne coexpress, but a minority of bidirectional genes have a mutual exclusive expression.

  • No correlation between lenght of promoter and degree of expression

  • Cell type seems to affect the activity of the promoter. Indeed, scientist made an experiment with different cell lines.


Bidirectional promoters in human genome2

Bidirectional promoters in human genome

  • Genes of bidirectional promoters shared some element of the promoter

  • If there is deletion of TSS of one transcript, the transcription of the gene on the opposite direction is increased.

  • Conclusion: bidirectional promoter acts as an inseparable functional units which reglate the transcription of both genes.


Promoters conclusion

Promoters ( conclusion)

  • About promoters ( structure, function,…)

  • Two types of human promoters based on CG content

  • Bidirectional promoters in human genome


Promoters

References:Robert J. Brooker. Genetics, Analysis & Principle (second edition)T.A. Brown. Genomes (second edition)Wikipedia web siteSerge Saxonov, Paul Berg, and Douglas L. Brutlag. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two classes of promoters. PNAS (January, 23, 2006)Nathan D. Trinklein, Shelley Force Aldred, Sara J. Hartman, Diane I. Schroeder, Robert P. Otillar and Richard M.Myers. An Abundance of Bidirectional Promoters in the Human Genome. Genome Research (2004)


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