BIOL 4320-18 Transcription

Transcriptome

Full complement of RNA transcripts present in a given cell or tissue under specific conditions

How is the transcriptome analyzed?

Using microarrays and RNA-seq[uencing]

What is transcription catalyzed by?

DNA-dependent RNA polymerases

What do RNA polymerases build?

RNA complementary to the template strand of duplex DNA

What do RNA polymerases use to build complementary RNA?

ribonucleoside 5’-triphosphates [rNTPs]

What are the steps of transcription?

1 binding of RNA polymerase core to DNA promoter

2 Formation of transcription bubble

3 Initiation

4 Elongation

5 termination and recycling

What do bacteriophage RNA polymerases consist of?

One polypeptide chain

What do all cellular RNA polymerases consist of?

multiple polypeptides

What do Bacterial RNA polymerase holoenzymes vary based on?

sigma subunits

How many types of RNA polymerases do eukaryotes have?

3

What are the 3 types of RNA polymerases in eukaryotes?

RNA Polymerase I

RNA Polymerase II

RNA Polymerase III

What does RNA Polymerase I account for?

80% of all transcription

What does RNA Polymerase I do?

Transcribes precursor rRNA [pre-rRNA] and processes it into the mature 5.8S, 18S, and 28S rRNAs

What does RNA Polymerase require?

Transcription factors

What factors are required for Low transcription [In RNA Polymerase I]?

Selectivity factor 1 [SL1]: The TATA box binding protein [TBP] and transcription-associated factors [TAFs]

What factors are required for higher transcription [in RNA Polymerase I]?

Selectivity factor 1 [SL1] and upstream binding factor [UBF]

What does RNA Polymerase II do?

Transcribes mRNAs, microRNAs, and some other non-coding RNAs, and recognizes thousands of promoters

How many subunits does RNA Polymerase II have

12

What are required transcription factors of RNA Polymerase II?

General transcription factors bind to the core promoter and special transcription factors bind to regulatory elements

What does RNA Polymerase III do?

Transcribes short, untranslated RNAs [tRNAs, 5S rRNA, small RNAs involved in RNA processing] most that are less than 300 nucleotides long

What is notable about RNA Polymerase III?

Largest RNA polymerase with the most subunits

What are the required transcription factors for RNA Polymerase III?

tRNA genes: TFIIIB [Including TBP] and TFIIIC

5S rRNA genes: TFIIIB [Including TBP], TFIIIC, and TFIIIA

How can RNA transcription be inhibited?

Some small molecules inhibit transcription by binding to RNA polymerases

What can inhibitors of RNA transcription be used for?

To detect which polymerase produces specific types of RNA

How can specific inhibition of RNA Polymerases be useful?

Antibiotics and research

What do bacterial sigma factors do?

binds to the polymerase and recruits it to a particular type of promoter and converts the closed complex to an open complex

What is notable about initiation?

It is primer independent and produces short, abortive, transcripts

What does RNA Polymerase do in Elongation?

Continues along DNA template until it reaches a termination signal

How does RNA Polymerase correct errors in elongation?

corrects errors in newly synthesized transcripts through kinetic proofreading or nucleolytic proofreading

How often is an error made in elongation

about one error for every 10^4-10^5 ribonucleotides

What occurs in bacterial termination?

Transcription stops when the RNA polymerase transcribes through termination sequences in the DNA template

What are the different types of bacterial termination?

rho dependent and rho independent

What do eukaryotic polymerases need?

transcription factors to begin efficient transcription at promoter sequences

What does TFIIIC recognize with tRNA promoter?

Box A and box B

What does TFIIIC recognize with 5S rRNA promoter?

Box A and Box C

What do eukaryotic transcription factors do?

help RNA polymerases find and access promoter in the cell nucleus and help assemble transcription complexes on chromatin and recruit the polymerase to the promoter

What are the different regions of the promoter

-35 region, -10 region, and the spacer

What does sigma 70 do?

makes it so closed complex can spontaneously convert to a transcription-competent open complex

What does sigma 54 do?

Requires an AAA+ protein to form the open complex at a promoter

What is a difference between DNA and RNA transcription?

RNA transcription does not need a primer while DNA transcription does

What happens if the promoter is not cleared in initiation?

Abortive initiation

Kinetic Proofreading

RNA Polymerase pauses, does a de-pyro phosphorylation reaction, and snips incorrect nucleotide

What occurs in rho independent termination

mRNA is able to dissociate by itself [make hairpin sturcture]