Chapter 11: Transcription & RNA Processing

Transcription, the synthesis of a complementary RNA molecule from a DNA template strand, is catalyzed by highly complex RNA polymerases that synthesize chains in the 5 ′ to 3 ′direction. In prokaryotes, a single RNA polymerase holoenzyme recognizes promoters, such as the conserved −10 (TATAAT) and −35 (TTGACA) sequences, using a sigma (σ) factor for initiation, followed by elongation and termination that is either rho-dependent or rho-independent. Due to the lack of a nuclear membrane, prokaryotes often exhibit coupled transcription and translation. Conversely, eukaryotes rely on five specialized RNA polymerases (I, II, III, IV, V) to synthesize distinct RNA types, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and micro RNA (miRNA). Eukaryotic pre-mRNAs, transcribed by RNA Polymerase II, undergo extensive posttranscriptional modification in the nucleus before translation in the cytoplasm. These modifications include the co-transcriptional addition of a 5 ′7-methyl guanosine cap and the cleavage-dependent addition of a 3′poly(A) tail at sequences like the AAUAAA polyadenylation signal. Furthermore, most eukaryotic genes are "split," containing coding sequences called exons interrupted by noncoding sequences called introns. These introns must be precisely removed via splicing, a process evidenced by R-loop hybridization experiments. While some introns, like those in rRNA precursors, are self-splicing (autocatalytic), introns in nuclear pre-mRNAs are excised by a large ribonucleoprotein machinery known as the spliceosome, which utilizes small nuclear RNAs (snRNAs: U1, U2, U4, U5, U6) to execute the intricate two-step removal process. The chapter also highlights rare exceptions to the Central Dogma, such as reverse transcription and RNA editing, where the nucleotide sequence of the transcript is chemically altered post-transcriptionally, changing the resulting protein product, as seen in the apolipoprotein-B C-to-U conversion.