Regulation of Gene Expression in Eukaryotes

What are the main stages at which gene expression can be controlled in eukaryotes?

Activation/repression of chromatin structure, initiation of transcription, transcription processing, transport to cytoplasm, and translation (see page 5 diagram).

What are cis-regulatory elements?

Non-coding DNA sequences (like promoters and enhancers) that regulate the transcription of nearby genes (see page 3).

What is the function of enhancers?

DNA elements that increase transcription by binding activator proteins; they can act from a distance through DNA looping (page 6).

What do insulators do?

Insulators or boundary elements block communication between enhancers and promoters, preventing inappropriate activation (page 7 diagram).

How do activators recruit transcriptional machinery in eukaryotes?

They recruit transcription factors (like TFIID and Mediator) that then help recruit RNA polymerase II to the promoter — usually via DNA looping (page 14 diagram).

How do bacterial and eukaryotic activators differ?

In bacteria, activators directly contact RNA polymerase; in eukaryotes, activators recruit it indirectly via cofactors (page 14).

What is the function of the Gal4 activator in yeast?

It binds to UAS sites upstream of the GAL1 gene and activates transcription 1000-fold in presence of galactose (page 8).

What are the two main functional domains of activators?

A DNA-binding domain and an activating domain connected by a flexible linker (page 8).

What motif do most bacterial transcription regulators use?

The helix-turn-helix motif, where each monomer inserts an α-helix into the major groove of DNA (page 9).

How do eukaryotic transcription regulators expand DNA-binding specificity?

By forming heterodimers — different monomers combine to recognize new DNA sequences (page 9).

Describe the structure of a homeodomain protein.

It contains a helix(2)-turn-helix(3) motif; helix 3 is the recognition helix that contacts DNA (page 10 diagram).

How does a zinc finger protein bind DNA?

It uses a Zn²⁺ ion coordinated by Cys and His residues to stabilize its structure; α-helices insert into the major groove (page 11).

What is the function of zinc cluster domains (like Gal4)?

They use multiple zinc-binding motifs linked end-to-end to increase DNA-binding affinity and sequence recognition (page 11).

What is the leucine zipper motif?

A dimerization and DNA-binding structure where two α-helices form a coiled coil held by hydrophobic leucines; it grips DNA like a pincer (page 12 diagram).

What is the helix-loop-helix (HLH) motif?

A dimerization motif made of two helices separated by a flexible loop; DNA binding occurs via basic residues in the α-helix (page 13).

What determines whether transcription factors can bind to DNA in nucleosomes?

Binding is reduced when DNA is packaged into nucleosomes; accessibility depends on the site’s location (edges easier) and type of binding domain (Zn fingers > HLH) (page 15).

What proteins do activators recruit to modify nucleosomes?

Nucleosome-modifying proteins like histone acetyltransferases and chromatin remodeling complexes (page 16 diagrams).

What are the two main types of chromatin structure control?

Covalent modifications (acetylation, methylation, ubiquitination, phosphorylation, sumoylation, DNA methylation) and structural modifications (ATP-dependent remodeling, protein factor binding) (page 17).

What is the histone code hypothesis?

Specific combinations of histone modifications act as a code that regulates gene expression by altering chromatin accessibility (page 19).

How does histone acetylation affect gene activity?

Acetylation loosens chromatin packing, making DNA accessible and genes active (page 19).

How does histone methylation affect gene activity?

Methylation tightens chromatin packing, making DNA inaccessible and genes inactive (page 19).

Where do most histone modifications occur?

On the N-terminal tails of histones, through specific enzymes that can be recognized by regulatory proteins (page 20).

What are ATP-dependent chromatin remodeling complexes?

Protein complexes that use ATP to slide, evict, or restructure nucleosomes, exposing DNA for transcription (pages 28–30).

What is cis vs trans histone transfer?

Cis transfer moves a histone octamer along the same DNA strand; trans transfer relocates it to a different DNA molecule (page 28).

What is the role of transcriptional repressors in eukaryotes?

They inhibit transcription by hiding activating regions or recruiting histone modifiers that condense chromatin (page 24).

How does DNA methylation silence genes?

Methylated cytosines prevent transcription factor binding and recruit MeCP2, which brings histone deacetylases and methylases to condense chromatin (page 25 diagram).

What is the difference between promoter structure in prokaryotes and eukaryotes?

Prokaryotic promoters are simple and located close to start sites; eukaryotic promoters have complex enhancers and regulatory elements far from start sites (page 6).

What is chromatin remodeling?

The process by which ATP-dependent complexes transiently expose DNA sequences by disrupting histone-DNA contacts (pages 28–30).

Name some types of histone covalent modifications.

Acetylation, methylation, ubiquitination, phosphorylation, sumoylation (page 17).

What are structural chromatin modifications?

ATP-dependent remodeling, histone H1 binding, and heterochromatin factor interactions (page 17).

What happens when DNA is methylated?

It becomes tightly packed with nucleosomes, making DNA inaccessible — gene inactive (page 19).

What happens when histones are acetylated?

Chromatin loosens; DNA accessible — gene active (page 19).

What is the function of TFIID in transcription initiation?

Part of the general transcription machinery; binds to TATA box and recruits other factors and RNA polymerase II (page 14 diagram).

What is the role of Mediator complex?

Bridges activator proteins bound to enhancers with RNA polymerase II at the promoter (page 14 diagram).

How does nucleosome position affect transcription factor binding?

Binding sites near the edge of nucleosomes are more accessible than those near the center (page 15).

What are examples of chromatin-modifying enzymes?

Histone acetyltransferases (HATs) and histone deacetylases (HDACs) (page 27 diagram).

What is the energy source for chromatin remodeling complexes?

ATP hydrolysis (page 30).

What effect does promoter DNA methylation have on transcription?

It represses transcription by preventing activator binding and recruiting repressor complexes (page 25).

What role do chromatin remodelers play in transcription?

They reposition or remove nucleosomes to allow transcription factors and RNA polymerase II to bind (pages 28–30).