Lecture 5 (Part II) – Eukaryotic Transcription & Gene Expression

A vocabulary set covering the essential enzymes, DNA elements, protein factors, and mechanistic terms involved in eukaryotic transcription initiation and promoter architecture.

RNA Polymerase I (RNAP I)

14-subunit nuclear polymerase that synthesizes most ribosomal RNAs (rRNAs) in the nucleolus.

RNA Polymerase II (RNAP II)

12-subunit nuclear polymerase that produces mRNAs, most snRNAs, and microRNAs in the nucleoplasm.

RNA Polymerase III (RNAP III)

17-subunit nuclear polymerase that transcribes tRNAs, 5S rRNA, U6 snRNA, 7SK RNA and other small RNAs.

α-Amanitin

Mushroom toxin that strongly inhibits RNAP II (≤ 1 µg mL⁻¹) and, at higher doses, RNAP III, but spares RNAP I.

CTD (C-terminal domain)

Heptad-repeat tail (YSPTSPS) on RNAP II’s largest subunit (Rpb1); platform for phosphorylation-dependent regulation.

RNAP IIo

Form of RNAP II in which the CTD is highly phosphorylated.

RNAP IIa

Form of RNAP II whose CTD is unphosphorylated; promoter-bound state.

RNAP IIb

Proteolytic fragment of RNAP II lacking the CTD; not found in intact cells.

General Transcription Factors (GTFs)

Six protein factors (TFIIA, ‑B, ‑D, ‑E, ‑F, ‑H) that assemble with RNAP II at core promoters to form the PIC.

Pre-Initiation Complex (PIC)

Full complement of RNAP II plus GTFs positioned on a promoter before transcription begins.

TFIID

Multisubunit GTF containing TBP and TAFs; first binds core promoters and nucleates PIC assembly.

TBP (TATA-Binding Protein)

Subunit of TFIID that recognizes the TATA box, binds the DNA minor groove, and bends DNA ~80–90°.

TAFs (TBP-Associated Factors)

Proteins within TFIID that contact Inr/DPE elements and interact with activators to aid PIC formation.

TFIIA

Heterodimeric GTF that stabilizes TBP–DNA interactions and enhances basal transcription.

TFIIB

GTF that binds TBP/BRE, sets PIC orientation, and recruits the RNAP II–TFIIF complex.

TFIIF

Heterodimer that escorts RNAP II to promoters and stays bound during early elongation.

TFIIE

Heterodimer that recruits and regulates TFIIH within the PIC.

TFIIH

10-subunit GTF with XPB helicase for promoter melting and CDK7/Kin28 kinase for CTD Ser5 phosphorylation.

XPB

ATP-dependent helicase/ATPase subunit of TFIIH that opens the DNA duplex at promoters.

CDK7/Kin28

CTD kinase in the TFIIH kinase module that phosphorylates Ser5 (and Ser7) during initiation.

Core Promoter

Minimal DNA region (≈ -40 to +40) that directs basal transcription and PIC assembly.

Proximal Promoter

Nearby upstream sequences (< ≈200 bp) bound by sequence-specific activators to boost transcription.

TATA Box

Consensus TATAAA element ~25–30 bp upstream of TSS; present in ~10 % of human promoters.

Initiator (Inr)

Core promoter element spanning the TSS; present in ~50 % of promoters; contacted by TAF1/TAF2.

BRE (TFIIB Recognition Element)

Sequence immediately upstream or downstream of TATA that strengthens TFIIB binding.

DPE (Downstream Promoter Element)

Core element at +28 to +32 contacted by TAF6/TAF9; important in TATA-less promoters.

DCE (Downstream Core Element)

Tripartite downstream motif that works with Inr in some promoters.

MTE (Motif Ten Element)

Downstream promoter motif synergizing with Inr/DPE for transcription initiation.

Enhancer

Orientation- and position-independent DNA element bound by activators to increase transcription via looping.

Silencer

DNA element that recruits repressors or chromatin modifiers to diminish transcription.

Sequence-Specific Transcription Factor (SSTF)

DNA-binding protein (activator or repressor) that modulates particular genes, unlike general factors.

Activator

SSTF that binds enhancers or proximal elements and stimulates transcription, often via coactivators.

Repressor

SSTF that inhibits transcription, sometimes by recruiting corepressors or chromatin remodelers.

Coactivator

Protein complex that connects activators to the general transcription machinery but lacks DNA-binding ability.

Corepressor

Protein complex that partners with repressors to inhibit transcription, typically without binding DNA directly.

Basal Transcription

Minimal level of RNA synthesis driven by RNAP + GTFs in the absence of activators or repressors.

Promoter Clearance

Transition of RNAP II from initiation to elongation, requiring CTD phosphorylation and TFIIH helicase action.

Open Promoter Complex

PIC state in which TFIIH has unwound promoter DNA, allowing template entry into RNAP II.

Class I Promoter

RNAP I promoter that drives rDNA transcription; repeated in tandem arrays.

Class II Promoter

RNAP II promoter comprising core and proximal regions; subject to regulation by enhancers and GTFs.

Class III Promoter

RNAP III promoter; classic forms contain internal elements Box A, Box B, and/or Box C.

Box A / Box B / Box C

Internal promoter sequences within RNAP III genes that recruit TFIIIC and TFIIIB.

Upstream Activation Sequence (UAS)

Yeast enhancer-like element bound by activators to stimulate class II promoters.

GC Box

G-C-rich proximal element bound by Sp1 activator; common in TATA-less promoters.

Sp1

Zinc-finger activator that binds GC boxes and recruits TFIID via interaction with TAF4.

PSE (Proximal Sequence Element)

Upstream element in snRNA promoters; together with DSE controls RNAP II or III transcription.

DSE (Distal Sequence Element)

Enhancer-like sequence upstream of snRNA genes collaborating with the PSE.

Ion-Exchange Chromatography

Technique that separates proteins by charge; used by Roeder & Rutter to discover three RNAPs.

Anion-Exchange Chromatography

Form of ion-exchange using a positively charged matrix (e.g., DEAE) to retain negatively charged proteins.

Epitope Tagging

Genetic fusion of a short antigenic peptide to a protein to enable immunopurification or detection.

Immunopurification (Immunoprecipitation)

Isolation of a protein or complex from cell lysate using a specific antibody.

Heptad Repeat (YSPTSPS)

Seven-residue motif repeated 26× in yeast and 52× in mammals within RNAP II CTD.

Ser5 Phosphorylation

Modification by TFIIH kinase on CTD repeats that marks early transcription initiation.

Ser2 Phosphorylation

CTD modification associated with productive elongation (added mainly by P-TEFb, not TFIIH).

Template Melting

ATP-dependent separation of DNA strands at the promoter by TFIIH to create a transcription bubble.

7SK RNA

Small RNA produced by RNAP III that regulates RNAP II elongation by controlling P-TEFb.

Housekeeping Gene

Gene expressed constitutively in most cells, often driven by TATA-less promoters.

Inducible/Tissue-Specific Gene

Gene activated in response to signals or in limited cell types; frequently has a TATA box.

Mitochondrial RNA Polymerase

Distinct single-subunit polymerase that transcribes the mitochondrial genome.

Promoter Orientation

Direction of transcription determined by TFIIB binding to TBP and BREs.

Template-Directed RNA Synthesis

Catalytic activity of RNAPs that extends RNA in the 5′→3′ direction using NTPs.

Closed Promoter Complex

PIC state prior to DNA unwinding; RNAP II engaged but strands still annealed.