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