Promoters Oriane Broustal BIO 535 Promoters About promoters

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

Function of promoter • ARN polymerase binding site • Initiation of transcription • control by regulatory sequences => control the expression of genes

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 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 • • 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 promoters

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 Cp. G content in human genome • Cp. G = Cytosine followed by a Guanine ( linked together by a phosphate) • Cp. G island = regions of the DNA which have a high concentration of Cp. G • Based on Cp. G content, there are two types of promoters: - with high Cp. G content ( called HCG) = 72% - Cp. G content characteristic of averall genome = 28% • In HCG, the Cp. G region is symetric and peaks aroud the core promoter (specially around the TSS).

DNA methylation • Occurs on Cytosine in 5’ position • inhibits transcription if methylated region is close to a promoter, which is the case for Cp. G islands. • Cp. G island associated with HCG are often hypomthylated =>more expressed. It is often associted with House-keeping gene. • Whereas, in promoter with lower Cp. G, Cp. G are often methylated => inhibit the expression. This often finds in tissue-specific genes. • With Cp. G islands around promoter, posibility to have methylation mediated regulation

DNA methylation

Cytosine methylation and mutation

Bidirectional promoters in human genome • Pairs of genes control by same promoter but located on opposite strand opposite direction. Their TSS are separated by less than 1, 000 bp. • In general, they are rich in Cp. G 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 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 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) • About promoters ( structure, function, …) • Two types of human promoters based on CG content • Bidirectional promoters in human genome

References: Robert J. Brooker. Genetics, Analysis & Principle (second edition) T. A. Brown. Genomes (second edition) Wikipedia web site Serge Saxonov, Paul Berg, and Douglas L. Brutlag. A genome-wide analysis of Cp. G 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 Research (2004)