What proteins modulate the expression of genes?

Answer 1

well good examples of proteins regulating gene expression can be seen in most prokaryotic operons. Such as the trp operon or lac operon. These both contain sites upstream from the multiple cistrons, which code for repressor proteins (trpR and lacI - is says I but its still a repressor protein being produced). The trp operon is under negative repressible control which means transcription is turned of by the repressor binding to the operator gene (and also switched of by presence of an effector - in this case tryptophan). The same for the lac operon (except its under inducible negative control so is switched of until an effector is present - lactose).

Also i the lac operon it is under positive control by the catabolite activator protein (CAP) - When glucose is in low levels the levels of CAMP (cyclic adenosine mono-phosphate) tend to be high. CAMP binds to CAP allowing CAP to bind to a region upstream from the Lac operons promoter (Approx 16 base pairs up). This assists in allowing RNA polymerase to bind to the DNA upregulating he gene expression for the cistrons downstream).

In eukaryotes (I.e. us) however it is not a simple as a well organised length of DNA like the operons. They use a complex mix of control mechanisms. Such as enhancers, silencers etc..

The 2 types of regulation can be categorised into 2 groups:

Cis- acting elements and trans -acting.

Cis acting - these are regions of DNA that happen to be within the close proximity of the gene they wish to (excuse the anthropomorphism) regulate. These regions of DNA do not encode proteins but are acted on by trans-acting factors.

Trans elements - these are genes which encode proteins, they are usually found quite some distance away from the target length of DNA for regulation.

Probably a bit long winded, but its best to be thorough(ish) ;)

Answer 2

both eukaryotes and prokaryotes.