Lecture 2: Transcriptional regulation in eukaryotes

What is gene/ transcriptional regulation and why is it necessary

The process of turning genes off and on, allows cells to adapt to their environment and differentiate for specific functions

Why must chromatin be remodelled for gene expression

As in it’s natural, coiled state, DNA isn’t accessible as it is too closely packed, so it needs to be relaxed for transcription to take place

Where does chromatin remodelling take place

The DNA and histone levels

What is densely packed chromatin also called

Heterochromatin

And loosely packed?

Euchromatin

What do chromatin-remodelling complexes reposition

The nucleosomes

What does this then allow

transcription factors and RNA polymerase to bind to promotors and initiate transcription

What are the 2 types of chemical modification of histone proteins

Methylation and acetylation

Overall, what does acetylation of histones cause

Relaxation of chromatin (heterochromatin to euchromatin)

How does it do this

Different enzymes neutralise the positive charge of the histone attracting the DNA to the nucleosome, which then causes a structural change in the chromatin, opening recognition sites for transcription factors

Overall, what does DNA methylation do to chromatin

Stabilises it (repressing gene transcription)

Where does methylation of DNA usually occur

CpG island

What is the CpG island, why do yo not find a lot of them in vertebrate genomes

Clusters of CG nucleotides

The methylated cytosine is very likely to mutate into a thymine so genomes are depleted for CpGs

Where are the CpG island usually found

In the promotors of genes

What are the methyl groups added to

Cytosines, forming 5-Methyl cytosine

What does the methylation recruit, what does this do to the chromatin

Histone modifying proteins, stabilising chromatin and repressing gene transcription

What is genomic imprinting

A form of sex-specific gene expression where only 1 allele (maternal/paternal) is expressed, while the other is silenced

What causes this silencing

DNA methylation

Why is pregnancy an example of genomic imprinting

Balance of expression between paternal gene (promoting fetal growth) and maternal gene (limiting excessive growth)

What is dosage compensation in sex chromosomes

The differential regulation of genes in the X chromosome between male and females (females have double, so one has to be silenced - X inactivation - as expression of X is equal in males and females)

What region of the X chromosome is associated with X inactivation, what gene does this hold

The X-chromosomal inactivation centre, hols the Xist gene

How does this gene lead to the repression of transcription

On detecting a X chromosome that is about to become inactive, the transcription of Xist increases (it is non-coding so isn’t translated), but instead coats the X chromosome which promotes DNA methylation and histone deacetylation

How can histone modification both increase and decrease transcription

Histone acetylation = increases

Histone deacetylation = decreases

How many binding sites do regulatory transcription factors have

2 - one for binding to a particular DNA sequence (called the enhancer), the other recruits general transcription factors

Where doe these general transcription factors assemble

Near the TATA box (upstream of where transcription begins)

What is the role of the general transcription factors

Attract the RNA polymerase complex for transcription

What are silencers

A type of DNA sequence that the regulatory transcription factors called repressors can bind to which represses transcription

What are enhancers

The opposite of silencers, TFs called activators

What is the difference between regulatory and general transcription factors

Regulatory - Highly diverse, regulate one gene or a group of genes

General - All the same

What is combinatorial control

The overall effect of all the enhancer/silencer regions of the DNA (balance of activator transcription factors and repressor transcription factors)

What is a DNA insulator

Blocks the action of an enhancer on a promotor when the insulator lies between the enhancer and promotor

What does this create

Regulatory neighbourhoods

What are topologically associated domains

Due to the nature of the DNA coil, some areas are more likely to interact with themselves than other regions, these are called TADs

What do insulators do in TADS

Create neighbourhoods of gene regulation inside the different TADS, by enhancers interacting with promotors within a TAD but not interacting with promotors in other TADs

What is the pre-initiation complex

Large complex of proteins which begins transcription process

What is the fist step of assembly of the PIC

TFIID binds to the TATA box on the DNA (upstream of the transcription start site)

What does this then cause to bind

Other transcription factors like TFIIH

And lastly this recruits

RNA polymerase to form complete PIC

What does TFIIH do to RNA Polymerase II to initiate transcription

Phosphorylates it, and also unwinds the DNA double helix to allow RNA polymerase II to access the template strand