Class notes

Lecture notes BIOL3015 Epigenetics

0 purchase

Course

Institution
University Of Southampton (UOS)

Lecture notes from a series of lectures in BIOL3015 Regulation of Gene Expression, epigenetics. Covering: DNA methylation, chromatin structure, epigenetic modifiers, non-coding RNAs, Epigenetics and disease, social environment, cancer and tumour supression

[Show more]

Preview 2 out of 13 pages

View example

Uploaded on December 11, 2023
Number of pages 13
Written in 2021/2022
Type Class notes
Professor(s) Karen lillycrop
Contains Biol3015 epigenetics

regulation
gene expression
gene
epigenetics
methylation
chromatin
rna
disease
environment
zoology
biology
chemistry
cancer
tumour

Institution
University of Southampton (UOS)
Education Unknown
Course Unknown

$7.12

Add to cart

Add to wishlist

100% satisfaction guarantee
Immediately available after payment
Both online and in PDF
No strings attached

Epigenetics
Epigenetics
 Literally means ‘on top of genetics ‘
 Definition – Processes that include long-term stable changes in gene activity without
a change in gene sequence
 Main 3 processes are: DNA methylation, Histone modification and non-coding RNAs

DNA methylation
 Cytosine is methylated to 5-methyl Cytosine
 90% of methylated cytosine is found as a dinucleotide CpG
 Hemi methylated – one strand methylated
Mapping methylation status of genes
 Two restriction enzymes used:
 MspI – recgonises and cuts CCGG, will also cut CCMeGG
 HpaII – only cuts CCGG is second C is not methylated
 If 3 unmethylated CCGG both enzymes will cut all of them
 If a site is methylated, Msp1 will cut all sites, Hpa2 will only cut non methylated
CCGG
 Hence, different size bands are left
 Can show if methylation is present
Analysis of methylation status of the globin gene
 Erythroid cells produced the same number of bands of the same size hence no
methylation
 Liver cells Msp1 got two bands whereas Hpa2 only had one band
 If the gene transcriptionally active then the cells were unmethylated (Erythroid), but
if the gene transcriptionally inactive then the cells are methylated (Liver cells)
Methylation and transcription
 If low levels of methylation in the promotor region – the gene active
 high levels of methylation in promotor regions – gene inactive
Model for DNA methylation inhibition of gene expression
 Transcription factor binding is blocked by DNA methylation
 MeCP2 (Methyl CpG binding protein) Binds to methylated CpG and coats it to block
RNA polymerase
DNA methyl transferases (DNMTs)
 DNMT 1:
 Copies methylation marks from original strand of DNA onto new DNA
 DNMT3a and 3b: de novo DNMT’s:
 Responsible for establishing methylation marks
 If removed in mice – they are lethal
 DNMT2 not lethal in mice – unknown function
Search for DNA demethylase
 Could not be found
 Suggested that passive process could remove methylation
 Dnmt1 does not replicate methylation marks, leaving hemimethylated DNA which in
the next round of replication will produce DNA without methylation
Active demethylation

,  Hydroxy methyl cytosine (hmC)
 Found in 1972
 2009 Tet1 (ten-eleven translocase 1) found to convert 5mC to 5hmC)
 Hydroxy form is thought to be intermediate in demethylation of DNA
 Oxidation or deamination can then remove methylation
5hmC an intermediate in removal of 5mC
 Low levels in the genome (less than 105 of 5mC i.e., short-lived entity)
 Over expression of tet1 leads to decrease in 5mC, increase in unmethylated Cytosine
 Tet 1 depletion leads to an increase in 5mC

Chromatin structure
 Nucleosome structure
 DNA loop wrapped around a core of histones
 Histones are positively charged proteins – 8 histones
 Nucleosome is then folded upon itself to make a solenoid structure/ 30nm fibre
 Further looped and compacted to form 200 nm fibre which forms DNA in cells
DNase 1
 Endonuclease that cleaves double-stranded DNA
 Chromatin from erythroid cells added to increasing concentration of DNase 1
 Run on gel, blot and hybridized with probes from gene of interest
 Ovelbumin – transcriptionally inactive in cells – little or no digestion of gene –
condensed form so difficult for DNase 1 or RNA polymerase to access
 globin gene – Active in cells – complete digestion of gene even in low
concentrations – easy for DNase 1 and RNA pol to gain access
Chromatin structure
 Loose or tight
 Transcriptionally active gene – unmethylated – relaxed structure – accessible to RNA
pol
 Transcriptionally inactive – methylated – condensed structure – not accessible to
RNA pol
DNase 1 hypersensitive sites
 Erythroid cells –

 Located at the 5 prime ends of genes
 Are nucleosome free
 Initiation is reduced on DNA that is associated with nucleosomes
Transcription factors can recruit co-activators
 Modify histone structure

The benefits of buying summaries with Stuvia:

Guaranteed quality through customer reviews

Stuvia customers have reviewed more than 700,000 summaries. This how you know that you are buying the best documents.

Quick and easy check-out

You can quickly pay through credit card or Stuvia-credit for the summaries. There is no membership needed.

Focus on what matters

Your fellow students write the study notes themselves, which is why the documents are always reliable and up-to-date. This ensures you quickly get to the core!

Frequently asked questions

What do I get when I buy this document?

You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.

Satisfaction guarantee: how does it work?

Our satisfaction guarantee ensures that you always find a study document that suits you well. You fill out a form, and our customer service team takes care of the rest.

Who am I buying these notes from?

Stuvia is a marketplace, so you are not buying this document from us, but from seller olivereames. Stuvia facilitates payment to the seller.

Will I be stuck with a subscription?

No, you only buy these notes for $7.12. You're not tied to anything after your purchase.

Can Stuvia be trusted?

4.6 stars on Google & Trustpilot (+1000 reviews)

69252 documents were sold in the last 30 days

Founded in 2010, the go-to place to buy study notes for 15 years now

Start selling