Transcription

DNA to RNA World started with RNA We have RNA because we need a regulatory intermediate (make more or less of something) RNA different because of hydroxyl group on bottom right ribose sugar nucleotide

RNA

1. RNA Polymerization: Open transcription bubble DNA coding strand = sense strand DNA template strand = antisense strand (Pairs with nascent RNA) RNAP = RNA polymerase RNAP DNA comes in at a very sharp angle into the enzyme, then split into template and coding strands inside. Unwinds DNA Active site uses two MG2+

![[Pasted image 20260303085233.png]]

	Replication	Transcription
Direction	5'- 3'	5'-3'
Substrate	dNTPs	NTPs
Primer	Yes (RNA primer)	no, RNAP initiates without primer
Speed	Fast	Slow
Sliding clamp	Yes	No
Error rate	Low (proofreading)	High (less proofreading)

Cis-acting DNA sequences called Promoters tell the transcription machinery where to initiate

Bacteria transcription sigma factor proteins direct RNAP to the promoter recognize specific upstream sequences (-35 TTGACA) and (-10 TATAAT) regions

Eukaryotic DNA dependent RNA polymerases RNAP 1: makes most rRNA RNAP 2: most mRNA RNAP 3: tRNA, 5S rRNA, and others

RNAP 2 +GTFS = Pre-initiation complex (PIC) GTFs and RNAP 2 assemble at eukaryotic promoter TBP (TATA-binding protein): crucial subunit of TFIID. Introduces a massive 45 degree bend into double helix to locally untwist DNA Enhancer Sets of enhancer sequences bind combinations of activator proteins, change the genes expressed (diff in cardiac vs skeletal muscle, etc. )

Mediator huge complex of proteins, required for efficient transcription from all RNAP 2 promoters ![[Pasted image 20260303090330.png]]

Regulation by accessibility to chromatin

Chromatin can take heterochromatin (dense) or euchromatin (unwinded) forms

Motors that use ATP, shove nucleosomes back and forth on DNA. Resemble Helicases but can't unwind DNA

Writer enzymes add marks to chromatin DNMTs HATs HMTs Eraser enzymes remove them HDACs LSDs Marks can be made on Histones OR DNA

Most common type of mark on DNA is methylation Cytosine C-5 in CpG dinucleotides enzymes: DNA methyltransferases substrates: DNA (CpG) and SAM 60-90% of CpGs are methylated in mammals

Covalent modification of histones. N-terminal tails of Histones are sites of regulation Phosphorylation (Ser, Thr) adds - charge Acetylation (Lys) neutralizes + charge Methylation (Arg, Lys) Ubiquitination ![[Pasted image 20260303091845.png]]

In general Active genes = heavily acetylated Primed genes = less heavily acetylated histones Heterochromatin = silenced genes are not heavily acetylated, heavily methylated on DNA AND on histones

Transcription initiation is regulated by DNA accessibility through chromatin structure

Transcription elongation

Phosphorylation of the RNAP 2 CTD allow the polymerase to leave the promoter

Elongator complex contains histone acetyltransferase that helps displace nucleosomes CTD tail: C-terminal domain of RNAP 2 is a disordered tail, consisting of 52 repeats of YSPTSPS. Phosphorylation of CTD allows the polymerase to leave promoter and being elongation Elongator complex binds once the CTD is phosphorylated. Has a histone acetyltransferase (HAT) that helps to displace nucleosomes out of the polymerase's way