Lecture 3 final

Question 1

What is the goal of bisulfide sequencing

Answer 1

chemical modification of cytosine to uracil in order to study DNA methylation

Question 2

During Bisulfide sequencing, __________________________________ but those that are methylated are resistant to this modification and remain

Answer 2

cytosine to uracil

cytosine

Question 3

What are the steps of bisulfide sequencing

Answer 3

1. bisulfate treatment
2. PCR amplification
3. sequencing of genome

Question 4

What are the analysis steps

Answer 4

1. Align reads to known DNA

2. Determine methylated cytosine

Question 5

What are the 4 steps of bisulfide analysis

Answer 5

1. convert all genomic Cs to Ts in the reference genome
2. Convert all Cs to Ts in the read was well (only As, Gs, and Ts in all sequencing)
3. Align with regular aligners- C/T discrepancy is gone! Alignment is more accurant
4. Compare sequence of the original reference genome and reads

Question 6

Based on graph,

DNA methylation has a ________________ bias

Answer 6

3’ bias

Question 7

_______________ are uniformly methylated

Answer 7

pseudogenes and non expressed genes

Question 8

Expression of methylated Genes:
Body methylated genes tend to have higher than average expression. Promotor methylated genes tend to have __________________

Answer 8

lower expression

Question 9

Promotor methylated genes tend to have _____________

Answer 9

tissue specific expression

Question 10

What are the two types of Chromatin?

Answer 10

• Euchromatin

- Heterochromatin

Question 11

What are the qualities of euchromatin?

Answer 11

• Less dense appearance in EM
• enriched with acetylated histones and there positive chromatin modifications
• permissive transcription

Question 12

What are the qualities of heterochromatin?

Answer 12

• Dense appearance in EM
• Enrichment in hypoacetylated histones and negative chromatin modification
• non permissive for transcription
• formation of chromosomal structures
• chrommers and temoers

Question 13

What is the function of Histones

Answer 13

Compacting DNA strands and regulation of gene expression

Question 14

Histones are highly basic proteins abundant in ____________________ residues that are found in eukaryotic cell nuclei

Answer 14

Lysine and arginine

Question 15

What are the 5 classes of histones

Answer 15

• Core: H2A, H2B, H3, H4

- Linkage: H1/4

Question 16

What are the functional units of chromatin

Answer 16

nucleosomes

Question 17

Histones are positively charged which allowed them to associate with DNA which is ______________

Answer 17

negatively charged

Question 18

Histones undergo post translational modification which alter their _____________

Answer 18

interaction with DNA and nuclear proteins

Question 19

How do you name a histone

Answer 19

1. Name of histone
2. Single letter abbreviation of amino acid and position
3. Type of modification

Question 20

Euchromatin is accurate with ____________

Answer 20

activation

Question 21

How does histone activation promotes transcription?

Answer 21

A bromodomain (BD) is protein domain that recognizes acylated lysine residues such was this on the N terminal tail of histones

Question 22

Coding in histones may be ____________

Answer 22

heritable

Question 23

Generally:

Histone activation is associated with ________________

Answer 23

transcriptionally active genes

Question 24

Generally:

Histone deaccetylation is associated with

Answer 24

deactivation

Question 25

How to study histone medications: development and usage of _______________

Answer 25

histone modification specific antibodies | Ex: Western blot; immunoflourescnce, chromatin immunoprecipation (CHIP) assays

Question 26

______________ is useful for extraneous the enrichment of specific histone modification or binding of specific factors to the gene of intrest in vivo

Answer 26

CHIP assay

Question 27

What are the steps of CHIP assay

Answer 27

1. DNA protein crosslinking 2. Chromatin isolation 3. Immunoprecipation (IP) 4. Find out what these sequences are

Question 28

After the DNA associated with the complex is purified to find out what DNA sequences are associated with the modification histone:

Answer 28

- PCR - Microarrays - CHiip seq **Chiip seq discussed later

Question 29

______________ shows the absolute fragment counts shown. Isolated peaks show where the protein has bound in the data

Answer 29

chip-seq

Question 30

________________ in embryonic stem cells.

Answer 30

Distinct histone modification pattern

Question 31

Differential cells contain either __________________ but not both

Answer 31

repressive or active markers

Question 32

Hypothesis bivalent domain silence developmental genes in ________ them posed for activation later

Answer 32

ES cells

Question 33

Epigenetic changes are common in ____________

Answer 33

epigenetic diseases

Question 34

Turning the clock back on epigenetic diseases. ______________

Answer 34

epigenetic therapies are effective because

Question 35

Epigenetic changes are ____________

Answer 35

reversible

Question 36

Epigenetic changes do not normally associate with __________

Answer 36

genetic mutations

Question 37

_____________ can be used to turn genes on or off

Answer 37

epigenetic therapies