Exam 2 - Chromatin Structure and Histone Modification

Question 1

Chromatin

Answer 1

Nicely Organized DNA with lots of proteins

Question 2

Nucleosome

Answer 2

147 bp wrapped around 8 histones

Question 3

Increasing levels of condensation

Answer 3

Nucleosome to higher order chromatin folding

Question 4

How to identify what is in a nucleosome?

Answer 4

Nuclease can digest linker DNA

Question 5

Why are histones used in wrapping DNA?

Answer 5

Rich in positively charged, basic aa.

Interact with negative charges DNA

Question 6

Evidence of increasing levels of condensation

Answer 6

X-ray structures of 2 nucleosomes

Evidence at the tetra-nucleosomal level

X-rays of much thicker fibers than beads on a string

Question 7

Heterochromatin

Answer 7

more dense

Question 8

Euchromatin

Answer 8

less dense

Question 9

How can you test if a region is heterochromatin or euchromatin?

Answer 9

Southern blotting

Question 10

Southern blotting

Answer 10

Separates DNA fragments by size

Electrophoresis, transfer to membrane

Hybridization with labeled sequence-specific probe

Detection of labeled DNA

Question 11

How can cells loosen up nucleosomes to enable transcription?

Answer 11

Alter ionic interaction between histone and DNA (change charge on histone tail)

Question 12

Hyperacetylation

Answer 12

De-condensed chromosome
Adds acetyl group on aa K

HAC = Histone acetyltransferase

Alters Histone tail charge making it neutral

Question 13

Hypoacetylation

Answer 13

Condensed chromatin
HDAC = removes acetyl group

Question 14

acetylCoA

Answer 14

source of acetyl

Important intermediate covalently linked to coenzyme A

Question 15

Methylation

Answer 15

Prevent acetylation
Maintain positive charge

HMT = Histone methyltransferase
HDM = Histone demethylases

Question 16

Trimethyl

Answer 16

Recruits reader heterochromatin 1 (HP1)

Question 17

HP1

Answer 17

Binds to H3k9 trimethyl as a reader

Oligomerize

Recruits writer H3Kp methyltransferase

Spread Heterochromatin until boundary element.

Question 18

Boundary element

Answer 18

Protein

Enzyme

activated region

Question 19

Histone code

Answer 19

specific post-translational modification combinations in different chromatin regions

Question 20

Epigenetic memory

Answer 20

set of mods to a cells DNA that don’t alter the sequence

Question 21

Epigenetic memory preserved during cell division

Answer 21

Chromatin modifications are preserved

Histone and chromatin split along with modifications

Reader-writer complex marks new nucleosomes –> modification return to daughter cell form.

Question 22

X-Chromosome inactivation

Answer 22

Inheritance of epigenetic memory

Females acquire one more X

Creates mosaic of active/inactive copies throughout cells

Question 23

ATAC-seq

Answer 23

Finds regions that are accessible via sequencing

Amplify and sequence open region

Results shown as peaks mapped to genome browser

Larger peaks = open chromatin

Question 24

Chromatin Immunoprecipitation (ChIP

Answer 24

Identify epigenetic marks in entire genome and map them

Antibodies used to recognize histone modifications and bind

Sequence the DNA