Transcription (biology)

Transcription is synthesis of RNA using one DNA strand as a template by an RNA polymerase. During elongation the RNA polymerase reads that template $3^{\prime }\to 5^{\prime }$ while extending RNA $5^{\prime }\to 3^{\prime }$. Only the selected region is transcribed; other regions need not be active, and the template strand can differ between genes. See Alberts et al.: RNA polymerase and selection of transcribed DNA regions.

For the displayed example, align these three nucleotide sequences in the same left-to-right positions:The first template triplet TAC selects AUG: T pairs with A, A with U, and C with G. The next CGA selects GCU, and ATT selects UAA. The coding strand therefore matches the RNA lettering except for T versus U, whereas the template is complementary. Reading that template in its own $5^{\prime }\to 3^{\prime }$ direction gives $5^{\prime }\text{-}\mathrm{TTAAGCCAT}\text{-}{3}^{\prime }$; orientation cannot be discarded. The gene expression diagram keeps all three rows aligned. See Clark, Douglas and Choi, Biology 2e: template and coding strands in transcription.

This correspondence makes nucleotide sequences interpretable, but replacing T by U is valid only after identifying the coding strand. Moreover, RNA may be processed after transcription, so the initial product and mature messenger RNA need not have identical uninterrupted nucleotide sequences. Transcription also makes functional RNA that will not undergo biological translation. See Alberts et al.: RNA processing and RNA as the final gene product.

The locally opened region of DNA in which RNA polymerase exposes a template for RNA synthesis. Its stability depends on base pairing, stacking and interactions with the enzyme; dye separation in a FRET reporter depends on the labelling geometry and need not change with the same sign for every reporter.

The initial stage of transcription, including RNA polymerase association with a promoter, local DNA opening, and the first RNA synthesis events before productive elongation. Open-complex formation, abortive synthesis and promoter escape are distinct transitions; an unwound bubble need not disappear when escape occurs.

An open promoter complex is a promoter-bound RNA polymerase assembly in which a short region of DNA is unwound and the template strand is accessible to the active site. This distinguishes it from the initially bound closed complex; it need not yet have escaped into productive elongation.

Consider unbound U, bound closed C and open O in a continuous-time Markov chain, with rates $U\to C=a$, $C\to U=b$, $C\to O=c$, and O absorbing over the observation interval. The mean first-opening times satisfy $T_U=1/a+T_C$ and $T_C=1/(b+c)+b{T}_U/(b+c)$, hence $T_U=(a+b+c)/(ac)$. Repeated unsuccessful binding attempts make this different from $1/c$. A FRET trace that cannot distinguish U from C does not by itself identify the individual binding and opening rates.

The transition from initiation at a promoter to productive elongation by RNA polymerase. Initial short RNA products may be released before escape; retention or loss of a sigma factor is not by itself a universal marker of escape.

A state of reduced transcriptional activity, potentially broad or gene-selective. In germ cells, repression of somatic programmes must be distinguished from complete polymerase shutdown.

An RNA polymerase used in transcription is an enzyme that synthesizes RNA from a DNA template. Unlike a replicating DNA polymerase, it can start a new strand without a pre-existing paired strand end; initiation still requires the appropriate DNA signals and associated machinery. See Alberts et al.: RNA polymerase and transcription initiation.

A protein that confers promoter-recognition specificity on a bacterial-type RNA polymerase. Plastid sigma factors can be nuclear encoded and imported.

A nuclear-encoded plastid sigma factor involved in activation of the psbD gene promoter in Arabidopsis thaliana.^[ref]

An RNA polymerase that uses RNA as its template. In some RNA interference pathways it helps generate substrates for small-RNA production.

An RNA-dependent RNA polymerase contributing to double-stranded precursors for canonical RdDM small RNAs.

The eukaryotic polymerase responsible for transcription of protein-coding genes and several noncoding transcripts. Its C-terminal-domain phosphorylation state helps regulate elongation.

The Mediator complex is a multiprotein coactivator involved in coupling regulatory proteins to RNA-polymerase-II transcription. A requirement for mediator activity can be tested by removal and restoration in a reconstituted transcription system.

For a specified transcription unit, the coding strand is the DNA strand matching the initial RNA product in the $5^{\prime }\to 3^{\prime }$ direction, with T in place of U. The opposite DNA strand is the template. The name does not imply that every transcribed gene encodes a protein. See Clark, Douglas and Choi: coding and template strands.