Chapter 17 | Transcriptional Regulation in Eukaryotes

Eukaryotic vs. Prokaryotic Transcription

Eukaryotes perform transcription in the nucleus and translation in the cytoplasm, preventing co-transcription and co-translation. Prokaryotes perform both simultaneously in the nucleoid region

Chromatin Remodeling Requirement

Eukaryotic DNA is wrapped around histones, so histones must be removed, modified, or repositioned for RNA polymerase to access the DNA during transcription

Eukaryotic RNA Polymerases

Eukaryotes have three primary RNA polymerases—RNA pol I (rRNA), RNA pol II (mRNA), and RNA pol III (tRNA and other small RNAs). Prokaryotes use a single RNA polymerase for all RNA types

Complexity of Eukaryotic Promoters

Eukaryotic transcription involves core promoters and cis-acting elements with extensive regulatory sequences, unlike the simpler prokaryotic promoter structure

Eukaryotic Transcription Factors

Eukaryotes use many complex transcription factors, whereas prokaryotes rely primarily on the sigma factor (e.g., σ⁷⁰) as a general transcription factor

Transcription Factories

Localized nuclear regions where clusters of RNA polymerase II and nucleotides (UTP) concentrate. These punctate regions mark sites of active mRNA transcription

Chromosome Looping in Transcription

Chromosomal loops bring together regions of euchromatin and heterochromatin within transcription factories, aiding regulated access to transcriptional machinery

Nucleolus Function in RNA Transcription

Dense nuclear area where rRNA is transcribed; similar factory-like organization also occurs for mRNA transcription

Histone Tail Modifications

Chemical modifications to histone tails signal chromatin to condense (heterochromatin) or decondense (euchromatin), regulating access for transcription

HAT (Histone Acetyltransferase)

Adds acetyl groups to histones, promoting chromatin de-condensation, allowing RNA pol II access, and facilitating transcription

HDAC (Histone Deacetylase)

Removes acetyl groups from histones, promoting chromatin condensation and reducing transcription

Focused Promoters (Eukaryotic Context)

Promoters with a single, specific +1 transcription start site. Produce one major transcript. Similar to prokaryotic promoter organization

Dispersed Promoters

Promoters with multiple possible transcription start sites. Common in higher eukaryotes (~60%), often in housekeeping genes. Produce transcripts of varying lengths

Core Promoter Elements

DNA sequences located near the transcription start site that recruit RNA polymerase II. Includes BRE (TFIIB response element), TATA box, initiator (+1), and motif ten elements. Serve the same function as σ⁷⁰ in prokaryotes

TATA Box

A conserved sequence located around –30 that binds TFIID and helps position RNA polymerase II for transcription initiation

Initiation Sequence (+1 Region)

A loosely conserved sequence spanning –2 to +4 that helps define the transcription start site

Consensus Sequence Variability

Imperfect promoter consensus sequences reduce RNA polymerase binding strength and can lower transcription levels

Enhancers

DNA elements that activate transcription from long distances—upstream, downstream, or within genes. They bind specific proteins and loop DNA to interact with promoters, even from different chromosomes

Silencers

DNA elements located potentially far from the gene that bind regulatory proteins to repress transcription

GC Box

A proximal promoter element that binds general transcription factors and modulates transcription levels

CCAAT Box

A proximal promoter element located up to ~100 nucleotides upstream that helps recruit transcription machinery

Pre-Initiation Complex (PIC)

A massive multiprotein complex, similar in size to a ribosome, containing general transcription factors, RNA polymerase II, and enhancer-binding proteins necessary for transcription initiation

Mediator Complex

A large protein complex that interacts with the PIC to regulate RNA polymerase II activity and integrate enhancer and promoter signals

Proximal Promoter Elements

Nearby promoter sequences that bind transcription factors to modulate transcription levels

Response Element (RE)

A promoter segment capable of binding specific regulatory proteins to fine-tune promoter activity

TFIID

General transcription factor that recognizes and binds the TATA box to initiate assembly of the transcription machinery

Metallothionein IIA Gene Regulation

A gene that detoxifies heavy metals; regulatory proteins bound by metals attach to response elements to recruit transcription machinery

SP1 Binding to GC Box

SP1 transcription factor binds GC boxes to maintain basal expression of the metallothionein gene

Glucocorticoid Receptor (GR) and GRE

Hormone-activated glucocorticoid receptor binds the glucocorticoid response element (GRE) to enhance transcription

Enhancer Distance in Eukaryotes

Eukaryotic enhancers can act from ≥1000 nucleotides away from the promoter

RNA Polymerase II Docking Function

The general transcription machinery assembles at the TATA box to dock RNA polymerase II, analogous to σ⁷⁰ in prokaryotes but more complex

Pre-Initiation Complex (PIC)

A ~45-protein complex forming around the TATA box to position and activate RNA polymerase II

TBP (TATA-Binding Protein)

A TFIID subunit that binds the TATA box, bends DNA ~90°, and recruits additional transcription factors

TBP Saddle Structure

The C-terminal region of TBP forms a saddle shape that binds the minor groove of DNA

TFIIA

A heterodimer that stabilizes TBP binding to the promoter

TFIIB

A monomeric factor that contacts DNA on both sides of TBP via BRE sites and helps position RNA polymerase II

TFIIF

A heterodimer that binds RNA polymerase II prior to PIC assembly, blocks the exit channel to prevent premature transcription, and helps melt DNA

TFIIE

A tetramer that creates the docking platform for TFIIH

TFIIH

A 10-subunit complex with helicase activity to enlarge the transcription bubble and kinase activity to phosphorylate the CTD of RNA polymerase II

CTD (C-Terminal Domain) of RNA Pol II

A flexible repeat-rich tail whose phosphorylation by TFIIH acts as the “ON” switch for transcription initiation

Release of TFIIB

After assembly is complete, TFIIB leaves the exit channel to allow RNA polymerase II to begin transcription

In Vitro Reconstitution

The described assembly order of the PIC is based on in-vitro studies and may not occur identically in vivo