Transcription refers to the process of synthesizing RNA from a DNA template. This involves the unwinding of double-stranded DNA to allow DNA sequence information to be transcribed from the template DNA strand into complementary RNA molecules (primary transcripts) by RNA polymerase: the linear sequence (5' to 3') of the RNA molecule will be the same sequence and direction as the non-template DNA strand (Fig. 1.10). The non-template strand is also referred to as the 'sense strand', and is the sequence usually shown; the template strand is referred to as the 'antisense strand'. Orientation of regions relative to the gene sequence is with respect to the sense strand, for example the 5' untranslated region is at the 5' end of the sense strand. Genes are found in both orientations throughout the genome such that genes may be transcribed in opposite orientations. Sets of three DNA nucleotides ('base triplets', for example 'ATG') are decoded to RNA where the sequence of three nucleotides (a codon) define a particular amino acid (for the codon sequence 'AUG' the amino acid is methionine). The primary
RNA transcript is 'spliced' to remove internal sequences (introns) with rejoining of protein coding exonic sequences: this complex process generates increased protein diversity for most genes by having a number of possible alternatively spliced transcripts (Fig. 1.10). The 5' end of the primary RNA transcript is capped by linkage of a methylated nucleoside to the first 5' nucleotide of the transcript, a process which protects against degradation and facilitates transport and splicing. Other RNA processing events include polyade-nylation in which a poly(A) tail (approximately 200 adenylate residues) is added at the 3' cleavage site at the end of the transcript, about 15-30 nucleotides (nt) downstream of the AAUAAA poly-adenylation signal sequence. The poly(A) tail is also involved in RNA transport, stability, and facilitating translation. Although traditionally viewed as occurring in a stepwise manner, transcription and RNA processing are highly dynamic and interactive processes such that there is a complex and extensively coupled network of gene expression factories (Maniatis and Reed 2002).
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