what factors affect gene expression?

alleles. whether each allele (gene) in each parent is dominant or recessive. for example; johns mother had brown eyes and his father had blue, john therefore inherited brown as it is more dominant than blue, however he also carries the recessive gene of blue eyes. it's all to do with genotypes (which characteristics inherited are actually visible)

That is a question that science is STILL trying to answer, and there are SOOOO many answers.

To list some of the better understood ones:

1. Whether or not the proteins around which the DNA is coiled are methylated or acetylated; this can cause the DNA to uncoil or coil more tightly (see #3)

2. Whether or not the DNA encoding the gene has methyl groups attached to it (if it does, the gene can't be expressed)

3. How tightly coiled the region of DNA containing the gene is (RNA polymerase can't read tightly packed DNA, and if RNA polymerase can't read it, it can't be expressed)

4. The transcription and translation of many genes is regulated by various regulatory proteins. The proteins can either stimulate or inhibit expression depending on whether or not certain chemical are present in the cell.

I'm pretty sure there are a bunch more, but like I said, it's a very complex system.

Codon Usage: there is little tRNA made for rare codons. In E. coli these are mainly AGA and AGG (Arg codons). The genes encoding the tRNAs can be co-overexpressed.

Promoters used should be very tight. Tight promoters are for example arabinose (BAD), rhamnose and lactose (provided that lacIQ is co-overexpressed). Note that tryptone contains sugars such as lactose that will induce expression and thus counteract your efforts to keep expression levels down under non-inducing conditions. Replacing tryptone by NZ amine A will solve this problem.

Translation initiation signal (Shine-Delgarno Sequence - serves to align the ribosome on the message in the proper reading frame.) Optimal: AGG AGG, the last G should be 9 bases upstream from the A of the AUG (start of translation) Start codons on mRNA are: AUG (90%, codon for Met), GUG (9%), UUG (1%) and CUG (0.1%) Avoid secondary structure involving SD sequence and the initiator AUG In polycistronic mRNAs, the initiation site should be close to the termination codon of the upstream gene.

Regulation of translation: is sometimes (not often) affected by sequences in the coding region: +5 and +10 should be A or T

RNA Stability can be increased if stem-loop structures are cloned at the 3' end of the coding region