Epigenetics

Question 1

DNA methylation: where it occurs

Answer 1

Usually at CpG dinucleotides (C’s next to G’s)

Question 2

Can DNA methylation be inherited across cell division?

Answer 2

Yes- DNA methyltransferases methylate daughter strand in replication

Question 3

Consequences of DNA methylation

Answer 3

DNA methylation is associated with repressed genes

Methylation acts with other factors that result in “repressive” chromatin

Question 4

Removing methyl groups from DNA

Answer 4

DNA demethylases remove methylation marks

Especially important in CpG islands (located in promoters of housekeeping genes)

Question 5

Chromatin: what is it?

Answer 5

DNA and its associated proteins

Question 6

Two functions of chromatin

Answer 6

Packaging DNA into nucleus

Regulating DNA expression

Question 7

Proteins that DNA is tightly bound to in order to form chromatin

Answer 7

Histones: positively charged proteins (DNA is negatively charged)

Question 8

Histone marks

Answer 8

Usually occurs on histone tails
Large number of covalent marks that can be added to histones and large number of enzymes that can make, read, and erase marks
Correlate with gene activity

Question 9

Histone mark naming rules

Answer 9

1. H for histone
2. Histone #
3. Which amino acid affected
4. Amino acid # in histone
5. Me for methylation or Ac for acetylation
6. How many groups

Question 10

Effects of histone acetylation

Answer 10

Loosening chromatin structure (decreasing positive charge, lessening affinity to DNA)
Increased transcription of DNA

Question 11

Effects of histone methylation

Answer 11

Can increase or decrease transcription, depending on which amino acids in histone are methylated and how many methyl groups are added

Question 12

Indirect effects of histone marks

Answer 12

Some histone marks can attract other factors (ex- some me3 can attract HP1, protein involved in establishing and spreading heterochromatin)

Question 13

ENCODE project

Answer 13

Encyclopedia of DNA Elements
Comprehensive parts list of functional elements in human genome (transcription, chromatin structure, histone modification, etc.)
Used to show relationship between gene regulation and disease
Growing resource

Question 14

RNA sequencing

Answer 14

Used in ENCODE project

1. Isolate RNAs from samples of interest
2. Reverse transcribe RNA into cDNA
3. Sequence cDNA
4. Map to genome

Question 15

What RNA sequencing reveals

Answer 15

Expression levels 
Alternative splicing
Gene structure
Discovery of new genes 
Chimeric genes (made from parts from different sources) in cancer or translocations

Question 16

Chromatin immunoprecipitation (ChIP-seq)

Answer 16

Used in ENCODE project

1. Bind protein to DNA
2. Fragment DNA
3. Immunopreciptation pulls out DNA bound to protein
4. Release DNA
5. Sequence DNA
6. Map to genome

Question 17

What ChIP seq can reveal

Answer 17

Transcription factors

Histone marks

Question 18

DNAse I hypersensitive sites

Answer 18

Used in ENCODE project
Using DNAse I to cleave active sites of DNA (not tightly bound to histones)
Cleaved active sites can be sequenced and reveal transcription factor binding

Question 19

Chromosome conformation capture

Answer 19

Used in ENCODE project
Maps molecular interactions between genomic regions
Enables determination of which enhancer is touching which promoter through digestion of cross-linking sequences