Epigenetics, TEs, Sex Chromosomes Flashcards
What is the function of DNA methylation?
prevent gene expression!
- Hypermethylation in cis regulatory regions can prevent gene expression
- DNA methylation is a way to control retrotransposons
How is DNA methylation detected?
You can detect DNA methylation using southern blots with methylation sensitive and insensitive enzymes
You can detect DNA methylation by bisulfite sequencing: conversion of unmethylated cytosines to uracils with bisulfite & then sequencing
What are the patterns of DNA methylation?
Methylation patterns vary during development and in different cell types
Where does DNA cytosine methylation typically occur?
Typically occurs in a CG dinucleotide context
also can occur in CHG or CHH (H=A, T, or C)
Functions of histone methylation and acetylation
Cause changes in chromatin structure
- Affect gene expression either positively or negatively
What are the patterns of histone methylation and acetylation?
Patterns vary during development and in different cell types
Where does histone methylation typically occur?
H3 & amp; H4 – H3K4me2
Where does Histone acetylation and deacetylation typically occur?
Typically occur on lysines (K) on tails of H3 & H4
What is the mechanism of histone acetylation?
Histone acetyltransferases adds acetyl groups on lysines (K) on tails of H3 & H4
What is the mechanism of histone deacetylation?
Histone deacetylases (HDAC) removes acetyl groups on lysines (K) on tails of H3 & H4
Histone methylation is often part of ________ chromatin and ________ gene expression
Histone methylation is often part of condensed chromatin and helps prevent gene expression
How to go from euchromatin to heterochromatin?
Histone methylation
Histone deacetylation
Corepressor complexes
How to go from heterochromatin to euchromatin?
Histone acetylation
Coactivator complexes
What is the effect of histone acetylation?
DNA unravels from heterochromatin –> euchromatin as histone modifications are added
What is the effect of histone deacetylation?
DNA condenses from euchromatin –> heterochromatin
How do DNA methylation and histone modifications interact?
Methyl C binding protein MECP2 binds methylated DNA & recruits histone deacetylases
What are histone modifications?
A combination of different molecules can attach to the ‘tails’ of proteins called histones. This alters the activity of the DNA around them.
i.e. Acetylation and deacetylation
How can histone acetylation be altered and studied?
Acetylation can be altered with trichostatin A: it induces acetylation & allows you to study effects of acetylation
What is the mechanism of DNA cytosine methylation
Methyl group is added to fifth of cytosine by DNA methyltransferase
What are the two main components of the epigenetic code?
DNA methylation and Histone modifications
What is DNA methylation?
Methyl marks added to certain bases that repress gene activity
What are the mechanisms of transcriptional silencing?
1) Methylation of promoter regions
2) Chromatin remodeling: euchromatin to heterochromatin
Human X size
Medium sized chromosome, about 1000 genes
Human X gene traits
- Genes biased towards those involved in sex-specific characteristics & reproduction, as well as in brain function
- Gene set mostly conserved in placental mammals.
Human X and Y interactions
Most of the X & Y do not recombine, except for pseudoautosomal region
Human Y size
Small chromosome, ~45 genes plus a few pseudogenes
- mostly satellite repeats
Human Y gene traits
- SRY gene: testis determining factor
- Most genes have homologs on X
- Genes mostly involved in sex determination and spermatogenesis
Differentiation of the X & Y from an ancient autosome
Autosome - acquired sex determining locus Proto-X,Y (Y has TDF) - accumulate male advantage genes X specific (MSY - Male specific region) - recombination suppressed PAR - Y mutation and deletion X and Y
Mammalian X and Y evolution
Thought to have evolved from autosomes
- One of ancestral chromosomes acquired a sex determining gene SRY
- Recombination was GRADUALLY suppressed
- Massive gene deletion and pseudogene formation on the Y
Xist and X chromosome inactivation
Xist RNA spreads out to chromosome arms
Xist RNA coats chromosome
Ancient and added regions on the human X and Y
PAR – pseudoautosomal region
YAR – added region
YCR – ancient conserved region
Mammalian Y chromosome degradation
- Few genes remain on Y; chromosome shrunk
- Forces thought to cause degradation:
- Higher mutation on Y than on X: point mutations, indels
- Less selection on non-recombining chrosmosome
Which of the following is NOT true about the human Y chromosome?
A) It contains ancient and added regions
B) There are many satellite repeat regions
C) Most genes do not have homologs on the X
D) It has a pseudoautosomal region at the tip
C) Most genes do not have homologs on the X
X chromosome inactivation – imprinting
Occurs by heterochromatin formation:
- Silenced X is highly methylated and deacetylated
- Initiated at X inactivation centre and spreads along the X chromosome
What does Xist stand for?
Xist – X inactive specific transcript
Long non-coding RNA – 17Kb
Xist vs TsiX
Both are long non-coding RNA
- Xist is expressed only on inactive X chromosome
- TsiX is expressed on active X
What is TsiX?
TsiX – long non-coding RNA
- antisense to Xist
- expressed on active X
How does Xist function?
- Accumulates along X chromosome to be inactivated & facilitates heterochromatin formation;
- helps recruit other factors involved
- Starts at X activation centre & spreads outwards
What is the function of Tsix?
binds to Xist & represses it
What is the ZW system?
Sex chromosome systems in some vertebrate groups
How to determine sex in ZW system
ZW – female, ZZ – male
kinda the reverse
Who has ZW system?
ZZ/ZW: snakes, birds turtles,
ZZ/ZW multi: lizards, amphibians,
fish - (XY or ZW, temperature dependent)
XY vs ZW
Y and W – highly heterochromatic and few genes, smaller
- Mammalian XY and bird ZW have different sets of genes and no sequence homology
Autonomous TEs
contains protein(s) involved in transposition
Non-Autonomous TEs
Does not contain protein(s) involved in transposition
- must get them from a closely related auto. TE
Which of the following types of TEs do not have terminal repeats? A) DNA transposons B) LTR retrotransposons C) Non-LTR retrotransposons D) All of them have terminal repeats
C) Non-LTR retrotransposons
LTR retrotransposons — long terminal repeats
2 coding regions:
Reverse transcriptase, protease, RNAase, integrase
DNA transposons — class 2
TE excise & insert elsewhere in genome: cut & paste Transposase recognizes terminal repeats
Non-LTR retrotransposons — no terminal repeats
Contains Endonuclease, reverse transcriptase
- no terminal repeats
LINEs – long interspersed nuclear elements
SINEs – short interspersed nuclear elements
RNA Elements - Class 1
mRNA transposition intermediate Often present in high copy numbers
Transposon dynamics and effects on genome structure:
• Nested retrotransposons: Nested TEs that inserted into other TEs
- Can lead to greatly increased distance between genes and increased genome size
TE Transposition Mechanisms
- Transposition (cut and paste)
- Replicative retrotransposition
- Target site primed reverse transcription
Non-LTR RetroTransposition Mechanism
Target site primed reverse transcription
Target site primed reverse transcription mechanism
Transcription
Priming and reverse transcription
Second strand synthesis
Completion of integration
LTR Retrotransposon mechanism
Replicative retrotransposition
Replicative retrotransposition mechanism
“Copy paste” Transcription Reverse transcription Transport of cDNA to nucleus Integrase enzymes integrate into target
DNA Transposons mechanism
Transposition (cut and paste)
Transposition (cut and paste) mechanism
“Cut and paste”
Transposase binding
Transposase Excision
Integration to target
