Trigger 8: Interrogating the epigenome

Question 1

Name a way of interrogating DNA methylation in the genome

Answer 1

Sodium Bisulfite Conversion

Question 2

Sodium Bisulphiite Conversion

Answer 2

1) Sodium bisulphite convers all unmethylated cytosines to uracil
2) then DNA is amplified with PCR- converting all Uracil to thymine
3) The DNA sequenced
4) everything cytosine present is methylated

Question 3

name a sodium bisulphite kit

Answer 3

EZ DNA methylation-Direct

EZ DNA methylation-Gold

Question 4

target sequencing methods

Answer 4

Bisulphite based

• direct sequencing
• clones bisulphite PCR
• Bisulphite- pyrosequencing

Question 5

NGS: Genome wide method

Answer 5

Bisulphite based

• Affinity Based
• SMrt

Question 6

direct bisulphide sequencing

Answer 6

do not provide information about methylation patterns of individual alleles

Question 7

pyroseqeucnign

Answer 7

fasta dn relaibel realtime sequencing method for the analysis of short to medium length DNA sequence

Question 8

pyrosequencing emtho

Answer 8

nucleotides ar added sequentially to the reaction and pyrophosphate released during nucleotide incorporation, is detected as light produced by an enzyme substrate cascade

Question 9

pros of bisulfites pyrosequencing

Answer 9

• quick
• cost effective
• target specific regionss of genome
• reproducible

Question 10

cons of bisulite pyroseuqencing

Answer 10

• low throughoutput

- small fragments

Question 11

whole genome bisulfites sequencing (WGBS)

Answer 11

• whole genome coverage
• costly ad the consuming
• requires extensive bioinformatics
• limited scalability per run