Transcription

RNA Polymerases

RNA Polymerase I

Synthesizes pre-ribosomal RNA.

RNA Polymerase II

Synthesizes mRNA and regulatory RNAs. Similar to DNA Polymerase, will read in the 3' → 5' direction, and therefore synthesize in the 5' → 3' direction.

Inhibited by alpha-amanitin (mushroom toxin)

RNA Polymerase III

Synthesizes tRNAs and smaller RNAs

Transcription Regions

The template strand (3' → 5') is read by RNA pol II to form the non-template strand (5' → 3') which is identical to the template, only with Thymine replaced with Uracil.

Promoter: UPSTREAM of coding sequence. Where Transcription Factors (TFs) will bind.
Terminator: DOWNSTREAM of coding sequence. Where Transcription Factors (TFs) will pop off the gene.

Promotion

Upstream of coding sequence. Site of PIC assembly. DNA Looping allows for activators and enhancers to influence transcription despite being far from base pair.

Initiator Element: Found at start point (Base pair 1)
Core Promoter: TATA box (TA rich), found around base pair 25-30. Many genes do not have this element and will instead have a downstream promoter element (DPE).

Pre-initiation complex (PIC)

Facilitates binding of RNA pol II.

Assembly of PIC

1. TATA box present: TF-II D will bind (bending the DNA)
2. TATA box not present: Inr and DPE are recognized by Transcription Activating Factors (TAFs)
3. TF-II A binds upstream of TF-II D, stabilizing TF-II D & TF-II B interaction
4. TF-II B binds TF-II F which is attached to RNA Pol II
5. TF-II E and TF-II H bind to the B/F complex, unwinding the DNA

TL;DR
TF-II D → TF-II A → TF-II B → TF-II F (binds RNA Pol II) → TF-II E/H (helicase)

Once PIC is assembled, a 3' → 5' phosphodiester bond is formed between RNA Pol II and DNA.

Elongation

After around 60-70 nucleotides are transcribed, TF-II E and TF-II H are released. These elongation factors assist RNA Pol II in transcription.

Elongation factors may also contribute to post-translational modifications by attaching to the C-Terminal of RNA Pol II. For example, TF-II H is required for adding the cap to mRNA.

pTEFb: Phosphorylates the C-Terminal (required for promoter clearance)

Promoter-Proximal Pausing

Regulates elongation. After synthesis of the first 20-100 nucleotides, transcription machinery will be paused. P-TEFb (recruited by TFs like c-Myc) will unpause the transcription.

Modifiers

Enhancer: Binds transcription factors which recruit coactivators/RNA pol II to specific genes, increasing their transcription.
Silencer: Binds transcription factors which decrease transcriptions. Repressors will bind here.

Repressors

Stable repression results in methylation via DNA Methyltransferase. The methyl group is added to cytosines found in CpG dinucleotides. Transient repression results in a repressor protein binding silencers which decrease transcription or reduce presence of activators.

Hormone Receptors

Monomeric Type 1

Sex hormones (estrogen, progesterone, androgens) and glucocorticoids.

Found in cytoplasm. Upon binding, the hormone/receptor complex will bind Hormone-Response-Element (HRE) to recruit coactivators and activate transcription.

Monomeric Type 2

Thyroid Hormone Receptor (TR).

Found in nucleus bound to the corepressor Retinoid X Receptor (RXR). Will form a heterodimer with RXR and the corepressor will pop off, activating transcription.

Chromatin Remodeling Complexes

These modify how tightly DNA is wound, affecting its ability to be transcribed. The tighter the winding around nucleosomes, the harder it is for transcriptional machinery to attach. Chromatin can either exist as heterochromatin (tightly wound, inactive), or as euchromatin (loosely wound, active).

Histones: Small proteins rich in amino acids who's Lysine's interact with DNA
Nucleosomes: Groups of 8 histones

Types of Complexes
Histone acetyltransferase (HAT): Adds an acetyl group to histone, heterochromatin → euchromatin
Histone deacetylase complex (HDAC): Removes an acetyl group from histone, euchromatin → heterochromatin
Histone methyltransferase: Can create either heterochromatin or euchromatin depending on methylation site.
Histone Kinase: Adds a phosphate to histone, heterochromatin → euchromatin