Except for simple organisms, the number of genes in a given species is somewhat a matter of speculation, even when the complete DNA sequence is known. This is partly because of the multiple splicing of mRNA and overlapping transcription that are sometimes found.The definition of a "gene" also changes as we continue to learn of ways new functions are encoded in the genome. Even with the simplest classical definition of genes as protein codes, a complex organism typically has tens of thousands of genes.
This raises an important biological question. Why, if essentially all cells in an organism contain the entire genome, whatever the number of genes that includes, do individual cells differ in their structure and behavior? The answer is that this is mainly because, in any given cell or cellular context, only a subset of these genes are used. Genes are turned "on" or "off" (are expressed or repressed) in a highly controlled active way that is affected by circumstances. This control is mediated through DNA sequences, another form of information in the genome—information that controls the use of coding information. How is this done?
The key is cis-regulation, whose information signals are found in sequence on the same chromosome (hence, cis) as the protein-coding gene (Figure 4-7) (Davidson 2001; Davidson et al. 2002). Usually the regulatory signals are in the nearby 5' flanking region. Gene expression is also regulated by the local state of the DNA in terms of its packaging or chemical modification. Typically, a gene is expressed when a complex of specific regulatory proteins including an appropriate polymerase is bound to promoter sequences just upstream (5') of the transcription start site.
This is a generic signal found in corresponding places in most genes, but specific gene expression is affected by other sequence elements flanking (and sometimes within) a gene; these are known as enhancers, repressors, or other response, or regulatory, elements (REs), which are bound in the appropriate cellular context by a variety of regulatory or DNA-processing proteins to make the DNA accessible to the polymerase. "Binding" means that the chemical structure of DNA with a particular nucleotide sequence—the RE—fits the charge and shape of a binding domain of the regulatory protein.
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