W11 L2 Thurs epigenetic 1

Question 1

What is epigenetic

Answer 1

-modification of the DNA by changing the structure instead of the code itself

Question 2

Why is epigenetic important

Answer 2

• Key to cell differentiation, stem cell maintenance, cloning, totipotency, Pluripotency
  *involve in Many different disease states including cancer
• Long-term transgenerational effects of exposures during development

Question 3

packaging of DNA

Answer 3

• Histones package DNA by forming a nucleosome
• Modifications of histone/ nucleosome alter DNA accessibility
  -histone tail modification
• Heritable changes across cell lineage

Question 4

methylation

Answer 4

• Cytosine residues methylated
• DNA is silenced
• Chromatin structure altered
• Heritable
• Altered in disease/ cancer

Question 5

Inheritance of methylation

Answer 5

• In DNA methylation, one strand of the daughter DNA would lack methyl group
  -regconised by DMNTs and add methyl group to it
  -inheritance of DNA methylation

Question 6

lnc RNA

Answer 6

lncRNAs bind chromatin modifying proteins
* Target specific regions of the genome
* lncRNAs also affect mRNA stability / splicing / translation

Question 7

Epigenetic Diseases

Answer 7

• Typically mutation in genes that affect ,Demethylases, ICRs
• Environmental factors biggest effectors

Question 8

What is X-inactivation

Answer 8

• Chromosome wide phenomena – silences single* X-chromosome in female cells
• Regulate balance in gene expression between male and female cells

Question 9

Epigenetic mechanism of X-inactivation

Answer 9

• Long non-coding RNA (LncRNA)
• Histone modification
• DNA methylation

Question 10

Step in X-inactivation inheritance

Answer 10

-inactivation and condensation of a randomly selected X chromosome
-Direct inheritance of the pattern of chromosome condesation

Question 11

X chromosome inactivation : XIC and Xist

Answer 11

XIC – X chromosome Inactivation Center
* XIC controls expression of the XIST gene
* XIST: X-inactive-specific transcript
* XIST produces a non-coding 17 kb RNA molecule
* Xist “Coats” the entire local X chromosome – cis-acting

Question 12

X-inactivation mechanism

Answer 12

– Initial XIST RNA expression and coating
– Association of chromatin modifying proteins
– DNA methylation 5’ of X- chromosome genes
– Modification of histones by methyltransferases (HMTase)
– recruit other chromatin modifying proteins

Question 13

How can mutation affect X inactivation

Answer 13

• Deletion of the A-loop prevents the chromatin modifier PRC2 binding
• trimethylates histone H3 on lysine 27; H3K27me3
• More active gene state

Question 14

Control of XIST expression

Answer 14

• Tsix promotes Xist promoter CpG methylation
• Active expression of Tsix on active X-chromosome inactivates any Xist
  -Knock-down of TSIX Causes Skewed X- Chromosome Inactivation

Question 15

X-inactivation evolution

Answer 15

• Variable mechanisms in mammals
• Marsupials (next closest group of mammals) don’t have XIST or XACT (mice XIST) and have a different lncRNA altogether with no homology

Question 16

X-inactivation & disease

Answer 16

• Skewed X-inactivation with deleterious alleles
• ATRX patients
• Incontinentia pigmenti IKBKG mutations
• Fragile X (marker of skewed inactivation)

Question 17

background of Genomic Imprinting

Answer 17

• The genomes we inherit from our mothers and fathers are not functionally equivalent
• Certain genes are expressed in a parent-of-origin-specific manner. If the allele inherited from the father is imprinted, it is silenced and only the allele from the mother is expressed.

Question 18

Result of genomic impriting

Answer 18

• Results in monosomy for ~100 genes (almost) all
  essential for normal fitness
• Must be faithfully reproduced during cell divisions and erased in germ line
  -Paternal and maternal genomes are both required for normal development.

Question 19

Epigenetic mechanism for genomic imprinting

Answer 19

• DNA (CpG) methylation
• Long non-coding RNA (LncRNA)
• Histone modification

Question 20

Genomic Imprinting Cycle

Answer 20

• After fertilization, active demethylation of parental inherited genome
• after blastocyst formation, denovo methylation occur
  -the imprint is heritably maintained in somatic cell, erased in PGC
  -Sex specific methylation of PGC