BCH 507 RNA II: Transcription

gene

basic unit of heredity

gene function

encoded info for protein peptide or RNA

genes have 2 regions

regulatory regions and transcribes region

genes found on

DNA usually located on genome

gene expression

process by which information from a gene is used in the synthesis of a gene product

Cis-acting element

non coding DNA involved in regulation of transcription of nearby genes

Trans-acting element

Gene (DNA) that encodes regulatory molecule

• Encoded molecule acts on cis-acting element

RMA polymerase function

Catalyzes all RNA polymerization (mRNA, tRNA, rRNA, etc.

core enzyme parts

two α-units, one β, one β’, and one ω unit.

holoenzyme parts

contains an additional σ unit (called sigma factor)

sigma promoter function

recognizes DNA element called promoter (-10 and -35 sites)

Prokaryotes have multiple sigma (σ) factors because they

recognize different promoters

and are expressed under different conditions

Most common promoter in E. coli is

the sigma 70 recognition site

consensus sequence

sequences of DNA or proteins with similar structure and function

Pribnow box

-10 site (AT rich region allows separation of DNA)

initiation of transcription in Prokaryotes

Activators enhance binding of RNAP to DNA

Repressors decreases binding of RNAP to promoter

Initiation in prokaryotes requires a ___ to recognize the promoter

sigma factor (part of RNA polymerase) to recognize the promoter.

Once bound to the promoter, RNA polymerase will

locally unwind DNA to form an open complex

After a few failed attempts (abortive initiation), the RNA polymerase will

escape the promoter and elongation will begin

Three major RNA polymerases (I, II, III)

cant initiate transcription by themselves

best studied POL

POL 2

RNAP 1 subnits

14

RNAP 2 subnits

12

RNAP 3 subnits

17

RNAP 1 location

nucleolus

RNAP 2 location

nucleus

RNAP 3 location

nucleus

RNAP 1 product

Pre-RNA (except 5S)

RNAP 2 product

Pre-mRNA, snRNAs, siRNA, miRNA, lncRNA

RNAP 3 products

Pre-tRNA, 5S rRNA, other small RNAs

Cis-Acting Elements in Eukaryotic Promoters

TATA box

Initiator element

CpG island

binding sites of general transcription factors

TATA box & initiator (INR) element

binding sites of specific transcription factors

CpG island

TATA box

best studied

~24% of human genes contain TATA box

Initiator element (Inr)

~49% of human genes contain initiator element

CpG island

Found in ~70% of human genes

• Proximal regulatory sequence

• Epigenetic relevance

General transcription factors function

help recruit and sctivate RNA polymerase

Specific transcription factors function

Regulatory transcription factor

• Bind only to specific genes and help regulate them

• Allows expression of different genes in different tissues or in response to different signals

general transcription factors required but

not sufficient, for initiation( Required to load RNA polymerase onto DNA)

TFIID

Coordinates pre-initiation complex formation; scaffold

TFIIB:

Stabilizes DNA-TBP interaction; Recruits RNAP and other TF

TFIIA

Stabilizes pre-initiation complex

TFIIE

Recruits TFIIH; may help melt promoter DNA

TFIIH

Helicase (melts promoter), Kinase

TFIIF

Prevents non-specific binding of RNAP to DNA

• Only TF to continue to elongation

specific transcripton factors required for

activation of RNA polymerase II

ranscription – Initiation in Eukaryotes

(Specific Transcription Factors)

Activators required for initiation in humans

Must be bound to both proximal regulatory regions and distal regulatory

region (enhancers)

• Activators may also be required to loosen chromatin (LECTURE 508)

• Directly or indirectly interact with RNAP II or general transcription factors

Initiation of RNA polymerase II in eukaryotes requires

general transcription factors, the correct activators bound to both the proximal regulatory region and the enhancer region, DNA looped so that the activator-bound enhancer region can interact with the promoter region, and a mediator so that activators bound to the enhancers can interact with the RNA polymerase.

what steps of transcriptional initiation can be repressed?

almost every step

During elongation, RNA is polymerized by ___ in what direction?

RNA polymerase in the 5’ to

3’ direction.

RNA polymerase reads the

antisense strand of DNA via Watson - Crik Base pairing

The synthesized strand of DNA will

look very similar to the sense strand of DNA

Transcription - Prokaryotic Termination

transcription complex is very stable

factor (rho) dependent

factor (rho) independent

• Prokaryotic termination primarily occurs via

factor independent termination

prokaryotic termination mechanism

RNA polymerase synthesizes a termination signal (complementary CG-rich

sequences followed by a string of adenines on DNA)

• The complementary CG-rich regions on RNA form a hair pin loop that

destabilizes A-U interactions between DNA and RNA, which results in

destabilization of the transcriptional complex.

Factor dependent uses an RNA helicase to

destabilize DNA-RNA interaction