Lecture 11: Transcription

What is the core promoter?

Sequence of DNA that is recognized and binded by RNA pol.

What is the CRM?

Cis regulatory module which is recognized and bound by transcription factors

True or False: CRM are always located upstream

False

What is the coding region made up of?

Introns which are spliced out and exons which are expressed in mRNA

Downstream sequences can determine

Stability of mRNA and the transcription stop site

Bacteria core promoter vs Eukaryote core promoter

In bacteria, the core promoter is a TATA box located from -10 to -35

In eukaryotes, the core promoter is a TATA box located from -25 to -80

Transcription is completed by RNA polymerases (RNAPs), what are the 3 classes of RNAPs in animals and what are they responsible for?

RNAP 1- Ribosomal RNA

RNAP 2-mRNA, microRNA, lncRNA

RNAP 3-tRNA

What are the three stages of transcription?

Initiation, Elongation, Termination

What is initiation?

When RNAP binds to the core promoter

In bacteria, what binds to the core promoter?

Sigma factor which recruits 2 alpha and 2 beta subunits to form a Holoenzyme

There are many sigma factors and each recognize a sequence in which each nucleotide is the one that occurs most frequently at the site also which is also known as a

Consensus sequence

-35 and -10 consensus sequence, why?

None of the sequence is incorporated into the RNA

In eukaryotes, which sites are recognized by binding proteins?

A-T rich sites

A binding proteins bonds to an … which is a sequence necessary for general transcription factor recruitment

Initiator element

What is the TATA box?

TATAAA initiator element recognized by TBP (TATA-Binding Protein)

TBP is a subunit of what enzyme?

TFIID which is a general transcription factor that recruits other general transcription factors to from the pre initiation complex with RNAP

TFIIB function

Promotes binding of RNA pol 2 to the core promoter

function of TFIIH

Acts as helicase to form an open complex

General transcription factors vs Sequence specific transcription factors

GTF are necessary for transcription, do not regulate transcription, recognize the same general consensus initiator elements

Sequence specific TF bind to elements in the CRM or TRM for transcriptional regulation

What two parts make up a transcription factor?

DNA binding domain and protein interaction domain

a mutation of the CRM of which gene can lead to legs growing on the head of a fly?

Antp

One major mechanism for chromatin remodeling is

Acetylation and deacetylation

What enzyme aids in acetylation and what enzyme aids in deacetylation

Acetyltransferases and deacetylases

Acetyltransferase makes chromatin into …. And deacetylases makes chromatin into….

Euchromatin (loose) and Heterochromatin (tight)

What is another mechanisms for gene expression regulation?

CG islands

CG islands are methylated by

DNA methyltransferases

DNA methyltransferases add a methyl group to

Cytosines

Hemimethylated vs Fully Methylated

What is the mediator?

The mediator is essential for transcription in nearly all genes transcribed by RNAP 2

Transcription takes how many nucleotides per second in prokaryotes vs eukaryotes

50-60 nucleotides per second in prokaryotes

15-20 nucleotides per second in eukaryotes

Splicing in bacteria vs eukaryotes

Bacteria: Very rare;self splicing

Eukaryotes: occurs in protein encoding pre-mRNA via spliceosome (protein and RNA complex)

Splicing involves 3 consensus sequences

1. 5’ splice site

2. 3’ splice site

3. Branch point adenine

Most mature mRNAs have a … attached at their 5’ end in an event known as capping

7-methylguanosine

Most mature mRNAs have a string of adenine nucleotides at their 3’ ends known as

The poly-A tail

What is RNA editing?

Exon sequence is alter after transcription