Regulation of gene expression

Control over when, where and how much a gene is expressed. Evolutionary changes in expression domains can alter developmental identity without requiring movement of a formed organ.

Gene silencing is reduction or suppression of a gene's functional expression. It can occur at transcription through chromatin regulation or after transcription through RNA destruction or inhibition of biological translation. The common outcome does not imply that every silencing mechanism removes the DNA sequence. ^[ref]

In the classic Caenorhabditis elegans experiment, double-stranded RNA produced strong, sequence-specific interference with the corresponding gene's activity. Comparing double-stranded and single-stranded inputs helped identify the effective trigger. ^[ref] A reduced protein readout alone still does not locate the step affected: transcript abundance, translation and protein turnover can each change it.

Post-transcriptional regulation controls gene expression after RNA synthesis through processes such as RNA splicing, export, localization, biological translation and degradation. Two cells can produce the same initial transcript yet accumulate different mature products if processing or stability differs. Nonsense-mediated decay illustrates selective removal based partly on the context of biological translation termination. Transcript abundance alone therefore cannot distinguish altered transcription from altered lifetime. ^[ref]

Movement of RNA from the nucleus to the cytoplasm in the relevant eukaryotic pathway. Processing, recognition and quality control can be coupled to export; export is distinct from transcription or subsequent biological translation.

The spatial distribution and targeting of messenger RNA within a biological cell. concentration enrichment, total fraction recruited, residence time and transport are different observables.

The ratio of RNA concentration inside an assembly to that outside, with accessible volumes and molecule detection specified. A high concentration ratio does not mean a large fraction of all cellular molecules is recruited.

Degradation of RNA molecules. RNA abundance reflects both production and decay, so a steady-state abundance difference alone does not establish a change in stability.

An RNA sequence element enriched in adenine and uracil that can recruit regulatory proteins affecting RNA stability.

The time for half of an RNA molecular population to disappear under specified conditions. For a homogeneous first-order decay process it equals $\ln 2/k_{\mathrm{d}}$; ongoing synthesis and changing biological cell states complicate abundance measurements.

Artificial recruitment of a candidate effector to a chosen RNA through a separate recognition module. It tests activity after recruitment while bypassing native recognition; physiological targeting and necessity require independent evidence.

Control of the rate or pattern of biological translation. ribosome occupancy depends on initiation and passage, so more occupied ribosomes need not mean more completed protein.

An operational measure often estimated from normalized ribosome footprints relative to RNA abundance. It reflects occupancy per transcript and is not automatically a direct rate of completed protein production.

Imaging newly emerging peptide chains at individual RNA molecules. Release and run-off controls help distinguish translation-dependent signals from aggregates or completed proteins.

Inhibition of uptake of an inducing substrate by a preferred-carbon-source regulatory system. Glucose-dependent inhibition of lactose permease reduces formation of allolactose and reinforces lac operon repression.

An Escherichia coli transcription unit encoding lactose-use proteins. Expression integrates LacI-dependent repression, allolactose induction, catabolite activator protein activation and inducer exclusion.

IPTG is a nonmetabolizable lactose analogue used as an inducer of the lac operon. Binding changes LacI's affinity for the lac operator; it supplies a way to change repressor availability without assuming that cytoplasmic transport is instantaneous.

A DNA recognition sequence bound by LacI. Repeated copies are used in fluorescent operator-repressor chromosome labelling.