-Makes heterogeneous nuclear RNA (hnRNA) that is processed to mRNA

-Makes snRNA (involved in splicing and other RNA processing events)

-Micro RNAs, telomerase RNA, etc.

-Pol II RNAs have a 5' end cap

-Makes tRNA and 5S rRNA

-tRNA and 5S rRNA do not have caps (PPP instead)

-Only one type

This is not covered in his transcription lecture and is actually pretty complicated

http://en.wikipedia.org/wiki/RNA_polymerase#RNA_polymerase_in_bacteria

Pol I and III-Structural

Pol II-Protein Encoding

RNA Pol I

Actinomycin D: anti-cancer drug, intercalating agent

RNA Pol II

Aplha-amantin: mushroom toxin

RNA Pol III

Sensitive to both (more so Actinomycin D)

Regulatory DNA Elements: Promoters

Role in transcription?

Features?

Core DNA elements required for all transcription

-Near start site of mRNA transcription

-"TATA Box" @ 25-30nt (can be TATA-less)

-"CCAAT box" @ ~40-110 nt

"Housekeeping genes" @ ~40-110nt (essential genes expressed in nearly every cell)

DNA Regulatory Elements: Enhancers

Role in Transcription?

Features?

Required for tissue-specific positive control (increase) of expression

Orientation and Distance independent

DNA Regulatory Elements: Silencers/Repressors

Role in Transcription?

Features?

Required for tissue-specific negative control (decrease) of expression

Orientation and Distance independent

Promoter Binding Proteins

What RNA Pol is focused on? What is created when this RNAP is combined with accessory proteins?

What is TATA Binding Protein? What is its function? When is it required?

-RNA Pol II plus accessory proteins are called "RNA polymerase holoenzyme" or "pol II complex"

(Transcription Factor II A, B, C, etc.)

-TATA Binding Protein is a subunit of TFIID and binds DNA at TATA Box

-TBP is required for RNA Pol I, II, and III (even in TATA-less Pol II promoters)

Enhancer/Repressor Binding Proteins

What are they? Function? Which ones must be activated before binding DNA?

-Recruit basal transcription factors and promoter-binding factors to transcriptional start site

-Usually bind DNA as Dimers (2 similar proteins interact w/ each other before binding DNA)

Homodimer: same protein

Heterodimer: another member of same protein family

Hormone responsive TFs must bind ligand (e.g.-estrogen and testosterone)

Many must be phosphorylated (kinase) or dephosphorylated (phosphatase)

Histones

What are they? Function? What happens when they are modified? How are they removed?

-Concentrated in "closed" regions of chromatin that are transcriptionally inactive

-Bind DNA and keep it coiled

-Presence around promoter inhibits transcription

-Acetylation of histones increases trasncription (can be remembered through generations-epigenetics)

-Promoter/Enhancer BPs displace histones

Heterochromatin: darker staining, more tightly packed, less transcriptionally active

Euchromatin: lighter staining, less tightly packed, more transcriptionally active