Transcription factor proteins, as well as the DNA-dependent, RNA polymerases that synthesize RNAs, are themselves the products of genes.

The set of transcription factors present within a cell, together with transcription factor activity (remember, since transcription factors are proteins their activities can be regulated) is a major determinant of which genes are active (i.e. transcribed) and the number of transcripts are synthesized.

Inside the cell, DNA exists in association with various proteins.  This DNA-protein complex is known as chromatin.

A kilobase (e.g. 10³ base pairs) of DNA is about 0.25 µm in length.   A bacterium, like E. coli, has about about 3 x 10⁶ base pairs of DNA; the cell itself is only about 0.8 µm in diameter and about 2 µm in length.

To fit a 750 µm long DNA molecule into a 2 µm long cell takes some packing. 

The way the DNA is assembled into chromatin, particularly in eukaryotic cells, can dramatically influence the ability of transcription factors to bind to regulatory sequences. 

Regions of chromatin that are packaged so as to be essentially inaccessible to regulatory proteins are known as heterochromatin.

Chromatin that is accessible and transcriptionally active is known as euchromatin.

Some regions of chromatin are folded away more or less permanently; they are unfolded only during DNA replication; these are known as constitutive heterochromatin.

Other regions can be unpacked in different cell types and are known as facultative heterochromatin.

A particularly dramatic example of this process occurs in female mammals.  One of the two X chromosomes is packed into a heterochromatic state, known as a Barr body.

Most of the genes on this chromosome are not expressed.

Transcription factors also influence the proteins that act on chromatin to make the DNA within it accessible or inaccessible.   This regulation of chromatin packing can act on blocks of DNA, regulating the genes within affected region. 

In the end, the gene regulatory elements compete with one for the binding of RNA polymerases. Genes that assemble the most efficient promoters are the most effective at loading RNA polymerase.

These genes will produce more copies of the RNA that they encode.

• How would you activate a gene that is within a heterochromatic region?
• Why, do you think, that one of the two female X chromosomes is packed into heterochromatin?  What is the point of that?  

A cell's behavior will be determined in large part by which of its genes are actively expressed. 

How can the cell determine that the "right" set of genes is activated for a particular situation?

Genes that need to be expressed together to perform a function can be co-regulated by using similar sets of regulatory sequences.

Multicomponent loops: Transcription factors act on regulatory sequences in a close loop arrangement.

Regulator chains: In this arrangement, a transcription factor binds to regulatory sequences in another gene and induces expression of a second transcription factor, which in turns binds to regulatory sequences in a third gene, etc. 

The chain ends with the production of some non-transcription factor product (if not, it is probably a multicomponent loop). 

Single and Multiple (roll over) input modules: A transcription factor binds to sequences in a number of genes, regulating their coordinated expression.  

In most cases (roll over), sets of target genes are regulated by sets of transcription factors binding together to target genes. 

Regulation of regulatory networks:  Transcription factors are proteins, and so their activity can be regulated by the interactions with other proteins, allosteric factors and post-translational modifications.  

It is through such interactions that signals from outside the cell can alter the patterns of gene expression.

At the same time, internal signals, generated by metabolic processes, can also feedback to the gene regulatory system in order to maintain the homeostatic state. 

If fact, such feedback is critical to maintaining the regulatory network – inhibiting it from spiraling out of control – which would lead to death.

• How would you design a multicomponent loop to produce a steady level of products?
• Why might single input modules be rare?
• How would the presence of a repressor factor influence the various modules described above?
• How is the gene regulatory network of a bacterium 1 µm in diameter like evolutionary genetic drift?  
• How can transcription factors be regulated?
• How does regulating the intracellular localization of a transcription factor alter gene expression?