Epigenetics - Nelson

Question 1

4 categories of epigenetic DNA modification

Answer 1

DNA methylation
Histone modifications by methylation, acetylation, and phosphorylation
DNA reprogramming
Gene regulation by small, double-stranded RNAs

Question 2

Generally, what does DNA methylation do?

Answer 2

Turns genes off

Question 3

Maintenance DNA methyltransferase

Answer 3

Enzyme that will act to match the methylation of a copy strand from its original methylated strand of DNA

Question 4

What happens if DNA methyltransferase is over expressed?

Answer 4

Too much DNA methylation can occur and the gene will be undesirably silenced. Prevalent in cancer

Question 5

de novo DNA methyltransferase

Answer 5

Enzyme that methylates new cytosines. Occurs much in embryology
It also works in conjunction with maintenance DNA methyltransferase to methylate DNA. (ex. knockout of DNMT3A alone, reduced methylation only 3%…knockout of DNMT1+DNMT3A = 95% reduced methylation, so gene stays on in colorectal cancer)

Question 6

What nucleotide is usually methylated?

Answer 6

Cytosine

Question 7

How can histones be modified?

Answer 7

Methylation/de, phosphorylation/de, acetylation/de

Question 8

What do histone modifications do?

Answer 8

Affect the binding of DNA to other histones and proteins to other chromatin

Question 9

What is bisulfite sequencing used for?

Answer 9

Method used to determine 5 methyl cytosine (5mC) bases in DNA. Can ultimately sequence entire epigenome

Question 10

What are two methods of gene silencing by RNA?

Answer 10

RNA-mediated destruction of mRNAs in the cytoplasm or RNA interference (RNAi)

RNA directed DNA methylation (RdDM)

Question 11

RISC

Answer 11

RNA induced silencing complex

Question 12

Argonaute protein

Answer 12

Main protein component of the RISC. Slices the siRNA after dicer extracts it from dsRNA and slices it. Passenger strand is cleaved

Question 13

Dicer

Answer 13

Takes miRNA strand from long dsRNA