Lecture 3: Chromosomes & Epigenetics Flashcards
What is epigenetics?
the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself
What is cellular epigenetic memory?
Process that ensures cells are locked in to a specific cell type through differentiation
What does histone code hypothesis state?
Gene regulation is partly dependent on histone modifications
What’s the difference between gene expression in closed and open chromatin?
Closed: inaccessible, gene is silenced and highly packages with nucleosomes
Open: accessible, active gene is loosely packed with chromosomes
What characteristics does constitutive heterochromatin have?
- constitutes 10% of nuclear DNA
- highly compacted
- gene poor
- transcriptionally inert
- replicates late in S phase
What characteristics does euchromatin have?
- 90% of nuclear DNA
- less condensed
- gene rich
- transcriptionally active
- replicates early in S phase
What is facultative heterochromatin?
Inactive regions of euchromatin
What is a nucleosome and what is its structure?
Nucleosome is the basic packaging unit of chromatin, consisting of 146bp DNA wrapped around a histone octamer
What is a chromatosome?
A nucleosome bound to a linker histone H1, which packages DNA further
How do histone tails influence gene expression?
- N and C terminal tails are targets for post translational modifications
- modifications act as signals to switch genes on and off
What are the types of modifications that can happen to histone tails?
- acetylation or lysine residues
- methylation of argenine or lysine
- phosphorylation of serine
- ubiquitination of lysine
How do histone writer, readers and erasers influence histone code?
Don’t bind directly to DNA and are instead recruited by transcription factors/machinery to specific locations of the genome
How is histone acetylation regulated?
By opposing actions from 2 families of enzymes
- histone acetyltransferases (HATs, writers)
- histone deacetylases (HDACs, erasers)
What is histone acetylation?
Additional of acetyl groups (CH3CO) to specific lysine residues in histones
How does histone acetylation trigger transcription?
Acetylation neutralises the lysines positive charge, which weakens interactions between histones and the negatively charged DNA, leading to loosened chromatin
What is histone methylation?
Additional of methyl groups (CH3) to histone tails
What residues are commonly methylated?
Lysine or argenine residues on H3/H4
What residues are commonly methylated?
Lysine or argenine residues on H3/H4
How is histone methylation regulated?
Catalysed by methyltransferase (writer)
Removed by demethylase (eraser)
What are the different marks of activity and inactivity (heterochromatin)?
Activity mark = H3K4me3
Inactivity mark = H3K9me3 which is recognised by heterochromatin protein 1
What is ChIP?
Chromatin immunoprecipitation, used to detect DNA sequences associated with specific chromatin modicifations
What are the steps involved in ChIP?
- chromatin is fragmented either physically or by nucleases
- fragments remain in nucleosome structure
- specific antibodies are used to recognise marks
- antibody conjugated to a bead can pull down via centrifuge or magnet
- antibody binds to histone, which is bound to DNA, so enriches DNA fragments containing mark of interest
- purify DNA out of the histone so DNA can be identified
What are the 3 types of histone changes associated with Ganges in gene activity?
- histone post-translational modifications
- histone remodelling
- variant histones
What is CENPA?
Variant histone of H3 found in centromeres
What can different copy numbers of Su(var) genes result in?
One copy: less heterochromatin formation, more expression from white gene = red eye
Three copies: drive more extensive heterochromatin formation, and enhancement of reported gene silencing = white eye
How does position effect variagation happen?
Results from heterochromatin spreading out with centromere region and silencing nearby translocated gene
What is DNA methylation?
Addition of methyl group to a cytosine residue, specifically a cytosine preceding guanine in invertebrates
How much of mammalian DNA is methylated?
70-80%, methylation is a repressive mark
What’s the difference in methylation between areas with high GpC content compared to low CpG content?
High CpG: low methylation, open chromatin
Low CpG: highly methylated, examples include heterochromatin and repeat elements
What is MecP2?
Methyl binding domain found in readers, which only binds to methylated CpG and condenses chromatin by recruiting other complexes
How do female mammals achieve sex chromosome dosage compensation?
By x inactivation which occurs by heterochromatin formation
What is XIC?
X inactivation center, which is necessary and sufficient for x inactivation
What is XIC?
X inactivation center, which is necessary and sufficient for x inactivation
What is the Xist gene and what does it produce?
X inactivation specific transcripts, which is transcribed from the inactive X to produce a non-coding RNA
How does Xist silence a chromosome
XIST RNA coats the chromosome and recruits silencing chromatin modifications and DNA methylation specifically to that chromosome
Xi CpG islands are methylated all along the chromosome except at Xist, which is methylated on the active chromosome
