D8 Eukaryotic transcription contd.

What must happen before transcription can begin in eukaryotes?

Chromatin must be opened so DNA is accessible for protein binding.

Where do transcriptional activators bind?

Promoter-proximal elements or enhancers (cis-acting elements).

What type of receptor is the glucocorticoid receptor (GR)?

A nuclear hormone receptor that acts as a transcription factor when activated.

What hormone activates the GR?

Cortisol.

What structural motif does GR use to bind DNA?

Zinc finger DNA-binding domain.\

What happens when cortisol binds GR?

GR dimerizes, becomes active, and binds a hormone response element (cis-acting element).

What does GR recruit after binding DNA?

Co-activators such as HIC5 and HAT complexes (e.g., p300/CBP).

How does a HAT promote transcription?

Acetylates histone tails → reduces nucleosome interaction → opens chromatin.

What role does Mediator play?

Acts as a bridge that connects activators with RNA polymerase II at the promoter.

Why do athletes receive hydrocortisone injections?

Hydrocortisone activates GR → upregulates genes that suppress immune activity → reduces inflammation.

What does RNA polymerase I transcribe?

rRNA genes.

What does RNA polymerase III transcribe?

tRNAs and some non-coding RNAs.

What does RNA polymerase II transcribe?

mRNA-coding genes and some noncoding RNAs.

Why can’t RNA polymerase II find promoters on its own?

It lacks a sigma-like DNA-binding subunit.

What is the CTD of RNA Pol II, and why is it important?

C-terminal domain; contains serines that are phosphorylated to trigger transcription initiation and later help RNA processing.

How can you identify a general transcription factor?

It is named “TFIIX” (TF = transcription factor, II = RNA Pol II).

What is the role of TFIID?

Locates and binds promoter elements.

What major subunit is inside TFIID?

TBP (TATA-binding protein).

What do TAFs do?

Recognize promoter elements when no TATA box is present.

What is the job of TFIIF?

Escorts RNA Pol II to the promoter complex.

What does TFIIH do?

Acts as a helicase to open DNA AND as a kinase to phosphorylate Pol II CTD

What is the “green light” for transcription to begin?

TFIIH phosphorylating serines in the CTD after Mediator has bridged activators to Pol II.

What is the default state of most eukaryotic genes?

Off—need activation to be transcribed.

One way a repressor blocks transcription?

Competes with activators for binding sites.

Another way repressors inhibit transcription?

Recruit co-repressors that block co-activators.

How can repressors alter chromatin structure?

Recruit histone deacetylases (HDACs).

What effect does histone acetylation (e.g., H4K16ac) have on chromatin?

Opens chromatin → promotes transcription.

How does removing acetyl groups affect chromatin?

Restores positive charge to lysines → nucleosomes interact tightly → chromatin condenses.

What modification marks heterochromatin?

H3K9 trimethylation.

What protein binds H3K9-me3 to help form heterochromatin?

HP1 (Heterochromatin Protein 1).

How does HP1 promote heterochromatin spreading?

HP1 molecules interact and recruit more histone methyltransferases.

Example of large-scale heterochromatin formation?

X-chromosome inactivation in biological females.

What is combinatorial control?

Mixing/matching different transcription factors and cis-acting elements to produce cell-specific gene expression.

How can two cell types with identical genomes express genes differently?

They express different sets of transcription factors → bind different regulatory sites → yield different transcription outputs.

Why can one gene be regulated 36 different ways in the example?

Because transcription factors form dimers with mix-and-match subunits.