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In molecular terms, a gene is commonly defined as the entire nucleic acid sequence that is necessary for the synthesis of a functional gene product (polypeptide or RNA). According to this definition, a gene includes more than the nucleotides encoding an amino acid sequence or a functional RNA, referred to as the coding region. A gene also includes all the DNA sequences required for synthesis of a particular RNA transcript, no matter where those sequences are located in relation to the coding region. For example, in eukaryotic genes, transcription-control regions known as enhancers can lie 50 kb or more from the coding region. As we learned in Chapter 5, other critical noncoding regions in eukaryotic genes include not only the promoter, but also sequences that specify 3′ cleavage and polyadenylation, known as poly(A) sites, and splicing of primary RNA transcripts, known as splice sites (see Figure 5-15). Mutations in these sequences, which control transcription initiation and RNA processing, affect the normal expression and function of RNAs, producing distinct phenotypes in mutant organisms. We examine these various control elements of genes in greater detail in Chapters 9 and 10.

Although most genes are transcribed into mRNAs, which encode proteins, some DNA sequences are transcribed into RNAs that do not encode proteins [e.g., tRNAs and rRNAs, described in Chapters 5 and 10; miRNAs and siRNAs that regulate mRNA translation and stability, discussed in Chapter 10; and long noncoding RNAs (lncRNAs) that regulate transcription, discussed in Chapter 9]. Because the DNA sequences that encode tRNAs, rRNAs, miRNAs, siRNAs, and lncRNAs can cause specific phenotypes when they are mutated, these DNA regions are generally referred to as tRNA, rRNA, miRNA, siRNA, and lncRNA genes, even though the final products of these genes are RNA molecules and not proteins.

In this section, we will examine the structure of genes in bacteria and eukaryotes and discuss how their respective gene structures influence their gene expression and evolution.