Fawad KaleemFA14-R02-007

General description of promoters ( structure, function)

types of promoters based on CG content

Bidirectional promoters

General types of Promoters

a promoter is a region of DNA that initiates transcription of a particular gene.

Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5' region of the sense strand).

Promoters can be about 100–1000 base pairs long

Conserved eukaryotic promoter elements

Consensus sequence

CAAT box GGCCAATCT

TATA box TATAA

GC box GGGCGG

CAP site TAC

• RNA polymerase binding site

• Initiation of transcription

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

• - 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.

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

• 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

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).

• 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

• 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 bidirectional class are often: DNA repair genes, chaperone protein, and mitochondrial genes.

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

• No correlation between lenght of promoter and degree of expression

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.

bidirectional promoter acts as an inseparable functional units which regulate the transcription of both genes.

Constitutive promoters

Inducible Promoters

Tissue Specific Promoters

Synthetic Promoters

Induce the expression of the downstream-located coding region in all tissues irrespective of environmental or developmental factors.

e.g: plant pathogen promoters(CaMV 35S promoter)

the activity of these promoters is induced by the presence or absence of biotic or abiotic factors.

inducible promoters are grouped as:

1. Chemically-regulated promoters2. Physically-regulated promoters

Operate in particular tissues and at certain developmental stages

may be induced by endogenous and exogenous factors.

e.g: tomato pz7 and pz130 gene promoters (for ovary gene expression)

comprise consensus DNA sequences of common elements of natural promoter regions.

maize ubiquitin 1 gene (Ubi-1) core promoter. cytomegalovirus (CMV) promoter. CAG promoter(cmv,actin,globin)