Regulation of Gene Expression

Operon

Entire stretch of DNA with promoter, operator, and the genes they control; enables coordinated control of related genes.

Operator

DNA switch segment (usually within the promoter) where a repressor can bind to block transcription.

Promoter

DNA site where RNA polymerase binds to start transcription.

Repressor

Regulatory protein that binds the operator and prevents transcription by blocking RNA polymerase.

Regulatory gene

Separate gene whose product (often a repressor) controls an operon.

Corepressor

Small molecule that activates a repressor so it can bind the operator and switch an operon off (example: tryptophan for trp).

Repressible operon

Operon usually ON; binding of an active repressor to the operator shuts off transcription (example: trp operon).

Inducible operon

Operon usually OFF; an inducer inactivates the repressor and turns on transcription (example: lac operon).

Inducer

Small molecule that inactivates a repressor, allowing transcription (example: allolactose).

trp operon

Repressible operon for tryptophan synthesis; ON when tryptophan is low, OFF when tryptophan (corepressor) is high.

lac operon

Inducible operon for lactose metabolism; OFF when lactose absent, ON when lactose present (inducer inactivates repressor).

Negative gene regulation

Regulation where a repressor protein decreases transcription (common in operons).

Differential gene expression

Cells with the same genome express different sets of genes, producing different cell types.

Gene regulation

Control of when genes are expressed and how much product is made.

Chromatin

DNA plus associated proteins (histones); packaging affects gene accessibility.

Heterochromatin

Highly condensed chromatin; genes within it are usually not expressed.

Chromatin modification

Chemical changes to histones and/or DNA that change chromatin packing and influence transcription.

Histone tails

Protruding histone regions that can be chemically modified to affect chromatin structure.

Histone acetylation

Addition of acetyl groups to histone tails; loosens chromatin and promotes transcription initiation.

DNA methylation

Addition of methyl groups to DNA bases; often associated with reduced transcription and long-term gene silencing.

Cellular differentiation (via methylation)

Long-term inactivation of genes can help lock in cell identity during development.

Genomic imprinting

DNA methylation causes expression of only the maternal or paternal allele of certain genes early in development.

Epigenetic inheritance

Heritable changes in gene expression not caused by changes in DNA sequence (often via chromatin modifications).

Transcription initiation regulation

Control of whether transcription begins, often via chromatin accessibility and transcription factor binding.

Chromatin-modifying enzymes

Enzymes that alter chromatin structure to make DNA more or less accessible to transcription machinery.

Control elements

Noncoding DNA segments that serve as binding sites for transcription factors that regulate transcription.

Transcription factors

Proteins that help RNA polymerase initiate transcription and control transcription levels.

General transcription factors

Transcription factors required for transcription of essentially all protein-coding genes.

Specific transcription factors

Transcription factors that regulate particular genes by binding specific control elements.

Proximal control elements

Control elements located close to a gene’s promoter.

Distal control elements

Control elements located far from a gene; can still regulate transcription.

Enhancer

Group of distal control elements that increases transcription when bound by activators.

Activator

Transcription factor that binds an enhancer and stimulates transcription.

Repressor (transcription factor)

Transcription factor that inhibits expression of a gene by various mechanisms.

Mediator proteins

Proteins that help activators communicate with the transcription initiation complex.

DNA-bending protein

Protein that helps loop DNA so distant enhancers can interact with promoter-bound machinery.

TATA box

A common promoter sequence important for forming the transcription initiation complex in many eukaryotic genes.

RNA polymerase II

Eukaryotic RNA polymerase that transcribes protein-coding genes into pre-mRNA.

Transcription initiation complex

Assembly of RNA polymerase II, general transcription factors, and other proteins needed to start transcription.

Combinatorial control

A gene is activated only when the right combination of control elements and activators is present.

Coordinately controlled genes (eukaryotes)

Genes can be co-expressed even if scattered across chromosomes, because they share control elements recognized by the same activators.

RNA processing

Steps that convert primary transcript into mature mRNA (includes splicing and other modifications).

Primary transcript (pre-mRNA)

Initial RNA copy made from DNA in eukaryotes before processing.

Exon

Expressed sequence retained in mature mRNA (usually coding or UTR).

Intron

Intervening sequence removed from pre-mRNA during splicing.

Alternative RNA splicing

Producing different mRNAs from the same primary transcript by including/excluding different exons.

Noncoding RNA (ncRNA)

RNA that does not code for protein but has regulatory/structural roles.

microRNA (miRNA)

Small single-stranded RNA that binds target mRNA and can block translation or promote degradation.

miRNA–protein complex

Protein-associated miRNA complex that guides binding to complementary mRNA targets.

Small interfering RNA (siRNA)

Small RNA that guides mRNA degradation or silencing; similar to miRNA.

RNA interference (RNAi)

Gene silencing mechanism using small RNAs (often siRNAs) to block gene expression.

mRNA degradation (via small RNAs)

If small RNA pairs well with target mRNA, the mRNA can be cut/degraded.

Translation blocking (via small RNAs)

If pairing is imperfect, translation of the mRNA can be inhibited.

Signal pathway → gene expression

Cell signaling can alter gene expression by changing chromatin state or transcription factor activity, affecting protein production.