Bacterial Operons, Eukaryotic Transcription, Splicing, and Chromatin Regulation

Comprehensive vocabulary flashcards covering bacterial gene regulation (lac and ara operons), eukaryotic RNA processing (capping, splicing, 3' polyadenylation), mRNP export, translational control, and chromatin accessibility.

lacZ

A structural gene in the lactose operon encoding $\beta$-galactosidase ($\beta\text{gal}$), an enzyme that cleaves lactose into glucose and galactose and isomerizes lactose into allolactose.

lacY

A structural gene in the lactose operon encoding lactose permease, a membrane transport protein responsible for importing lactose and related galactosides into the bacterial cell.

lacI

A gene transcribed from its own promoter ($\text{lacP}_i$) that encodes the lactose repressor protein (LacR).

Allolactose

The true physiological inducer of the lac operon, produced from lactose by $\beta$-galactosidase via a $\beta\text{-1,6}$ linkage rather than a $\beta\text{-1,4}$ linkage, which binds LacR to reduce its affinity for operator DNA.

LacR Repression Loop

A DNA loop formed when a V-shaped LacR tetramer (dimer of dimers) simultaneously binds operator $lacO_1$ ($+11$) and $lacO_3$ ($-82$), physically blocking RNA polymerase access to the promoter.

Catabolite Repression Protein (CRP)

A transcriptional regulatory dimer (also called CAP) that binds $\text{cAMP}$ under low glucose conditions, binds the consensus sequence $5'\text{-AANTGTGAnnnnTAnnTCACAnTT-3'}$, bends DNA by $\sim 90^\circ$, and contacts the $\alpha$-subunit of RNAP to activate transcription across $\sim 500$ regulon genes.

lacP2

An alternative promoter for the lac operon with a transcription start site at $-22$ and an RNAP affinity $\sim 200\times$ lower than $lacP_1$, serving to raise baseline LacY and $\beta\text{gal}$ expression $\sim 5\text{-fold}$ above background when glucose levels are high.

IPTG

A gratuitous synthetic inducer of the lac operon that is transported by LacY and binds to LacR to release repression, achieving $50\%$ induction of the operon at a concentration of $2 \times 10^{-4}\,\text{M}$.

ONPG

A colorimetric substrate cleaved by $\beta$-galactosidase into an orange-colored product, used exclusively in spectrophotometric liquid assays or screens, but never in genetic selections.

TONPG

A toxic galactoside transported by LacY that kills bacterial cells when the lac operon is constitutively ON, utilized as a counter-selection agent against constitutive mutants like $lacI^-$ and $lacO^c$.

Equilibrium Dialysis

An experimental technique used to detect LacR binding to radioactive $[^3\text{H}]\text{-IPTG}$ across a dialysis membrane whose pores exclude the protein while allowing the small ligand to equilibrate.

AraC

The dimeric dual-function regulatory protein of the L-arabinose operon that acts as a repressor in the absence of arabinose (forming a DNA loop between $araO_2$ and $araI_1$) and as an activator in its presence (binding $araI_1$ and $araI_2$).

Helical Phasing (Ara Operon)

A property of DNA loops under $500\,\text{bp}$ where inserting or deleting half-turns of the double helix ($\pm 5\,\text{bp}$, $\pm 15\,\text{bp}$, $+25\,\text{bp}$) rotates operators out of alignment and disrupts AraC repression looping, whereas full turns ($+10\,\text{bp}$, $+31\,\text{bp}$) maintain loop formation.

Rpb1 CTD

The carboxy-terminal domain of the largest subunit of RNA polymerase II, functioning as a scaffold that recruits and orchestrates the enzymes responsible for $5'$-capping, splicing, and $3'$-cleavage/polyadenylation.

5'-Cap

A modified guanine nucleotide structure added to eukaryotic pre-mRNAs consisting of $7^{\text{me}}\text{Gppp}$ ($\text{cap } 0$), with additional $2'\text{-O-methyl}$ groups on ribose 1 ($\text{cap } 1$) and ribose 2 ($\text{cap } 2$) in multicellular eukaryotes.

Sm Ring

A conserved spliceosomal heptameric protein complex composed of seven peptides ($\text{D1}$, $\text{D2}$, $\text{F}$, $\text{E}$, $\text{G}$, $\text{D3}$, and $\text{B/B'}$) that assembles onto snRNAs such as U1, U2, U4, and U5.

Branch Point Sequence (BPS)

A conserved intronic cis-element ($\text{CURAC}$ in humans, $\text{UACUAAC}$ in yeast) containing an invariant adenosine whose $2'\text{-OH}$ group attacks the $5'$-splice site during the first transesterification step of splicing.

Spliceosome Ribozyme Core

The catalytically active RNA core formed by U6 and U2 snRNAs paired with two $\text{Mg}^{2+}$ ions, specifically containing the catalytic active site within nucleotides $59\text{--}82$ of U6 snRNA.

Exonic Splicing Enhancers (ESEs)

Exonic cis-regulatory RNA sequences that bind positive splicing regulatory factor proteins (such as the Ser-Arg rich SRSF family) to promote the inclusion of alternative exons.

RON Pre-mRNA Alternative Splicing

The alternative processing of the RON receptor tyrosine kinase pre-mRNA, in which epithelial cells include exon 11 via SRSF2 to yield a regulated receptor, whereas mesenchymal cells exclude exon 11 via back-splicing to generate constitutively active $\Delta\text{RON}$ and an exonic circular RNA (ecRNA).

Microexons

Very short vertebrate exons ($3\text{--}51\,\text{nts}$) predominantly expressed in nervous, heart, and muscle cells that modulate protein surface interactions (such as switching TENM2 synapse specificity from excitatory to inhibitory) without changing overall protein abundance.

CPSF

Cleavage and Polyadenylation Specificity Factor; a multiprotein processing complex that recognizes the polyadenylation signal ($\text{AAUAAA}$) and employs its CPSF73 subunit as an endonuclease to cleave the pre-mRNA at the $5'\text{-CA-3'}$ cleavage site.

CSTF2 Alternative Polyadenylation

A regulatory mechanism during T-cell activation where low CSTF2 levels in naive cells favor the downstream polyadenylation site ($\text{PA2}$), while high CSTF2 levels in mature effector cells recognize the weak upstream site ($\text{PA1}$), skipping the final exon of NFATc1.

Torpedo Model of Termination

A mechanism of transcription termination where endonucleolytic pre-mRNA cleavage creates an unprotected $5'$ end on the nascent RNA, allowing a $5' \rightarrow 3'$ exonuclease to degrade the remaining transcript and disrupt RNAPII upon collision.

Exon Junction Complex (EJC)

A multiprotein core deposited on mRNA transcripts approximately $20\,\text{bp}$ upstream of each exon-exon junction during splicing, functioning in nuclear export and downstream mRNP surveillance.

FG-Nups

Nucleoporins within the nuclear pore complex containing hydrophobic phenylalanine-glycine repeats ($\text{FxFG}$ and $\text{GLFG}$) that form a selective central meshwork and interact with transport receptors like NXF1/NXT1.

eIF4F

A eukaryotic translation initiation factor complex comprising the cap-binding protein eIF4E ($24\,\text{kDa}$), the DEAD-box RNA helicase eIF4A ($46\,\text{kDa}$), and the scaffold protein eIF4G ($176\,\text{kDa}$) that connects the $5'$-cap to PABPC1 and eIF3.

Kozak Sequence

A conserved eukaryotic sequence surrounding the initiator codon with the consensus $5'\text{-GCC GCC GCC AUG G-3'}$, functioning to direct the ribosomal pre-initiation complex to the authentic start codon.

Internal Ribosome Entry Site (IRES)

A specialized RNA structure that bypasses the requirement for a $5'$-cap and Kozak sequence by directly recruiting ribosomal subunits to initiate translation at internal open reading frames.

Terminal Nucleotide Transferases (TENTs)

A family of template-independent RNA polymerases (comprising $11$ members in mammals) that catalyze $3'$-polyuridylation to accelerate the degradation of deadenylated transcripts by $3' \rightarrow 5'$ exonucleases.

6-Methyladenine (6mA / m6A)

The most common internal covalent mRNA modification in eukaryotes (occurring at $\sim 3$ residues per transcript) that influences translation rate, degradation kinetics, export efficiency, and alternative splicing.

DNase I Hypersensitive Sites (DHS)

Chromatin regions devoid of regular nucleosome arrays where transcription factors bind to naked DNA, rendering the underlying sequence exceptionally susceptible to preferential cleavage by DNase I.

ATAC-seq

Assay for Transposase-Accessible Chromatin using sequencing; a genome-wide profiling technique that utilizes hyperactive Tn5 transposase to insert sequencing adapters into accessible, nucleosome-free chromatin regions.