Midterm Review

Question 1

core particle

Answer 1

146bp

nucleosome with directly interacting DNA

Question 2

chromatosome

Answer 2

166

nucleosome with H1

Question 3

nucleosome

Answer 3

180-200, repeating unit of chromatin; histone and dna

Question 4

translational position

Answer 4

positioning of histone relative to DNA; check with MNase, which breaks down linker DNa

Question 5

rotational positioning

Answer 5

position of DNA relative to histone– flexibility, AT

Question 6

core histones

Answer 6

lack poly A tails

made in s phase

Question 7

variant histones

Answer 7

synthesized throughout cell cycle
have poly a tails
more evolutionarily conserved
affect transcription, regulation, DNA repair, chromatin organization/compation

Question 8

HMGB

Answer 8

HMB1box

affinity to 4 way junction structures, stim. binding of other DNA binding protiens

Question 9

HMGN

Answer 9

nucleosome binding domain

specifically binds to nucleosomes, gene activation

Question 10

HMGA

Answer 10

AT hook

binds minor groove of DNA using AT hook, bends DNA

Question 11

H5

Answer 11

variant of H1

chromatin compaction and repression; avians and amphibians

Question 12

H2Az

Answer 12

H2A

transcriptional regulation, chromatin segregation

Question 13

H2Ax

Answer 13

H2a

DNA repair, phosphorylated– gamma form, marker for DNA damage

Question 14

H3.3

Answer 14

H3

transcription, active genes

Question 15

CENP-A

Answer 15

h3 variant

centromere function

Question 16

H4

Answer 16

no sequence variant, S phase independent version

Question 17

H3K4me3

Answer 17

observed at active promoters

Question 18

H3K36me3

Answer 18

seen in downstream transcribed region of active genes

Question 19

H3K4me1 and H3K27ac–

Answer 19

seen at active transcriptional enhancers

Question 20

H3K9me3

Answer 20

heterochromatin

Question 21

H3K27me3

Answer 21

associated with polycomb-mediated repression

Question 22

histone acetylases

Answer 22

use AcCoa

Question 23

rpd/HDAC

Answer 23

use nothing

Question 24

Sir2/SirT/HST deacetylase

Answer 24

NAD+

Question 25

methylases

Answer 25

s-adenosyl methionine

Question 26

LSD-1/JHDM demethylase

Answer 26

FAD/Fe(II)

Question 27

heterochromatin

Answer 27

doesnt condense in interphase, repetitive DNA, condensed throughout cell cycle, replicates late s-phase

Question 28

euchromatin

Answer 28

most single copy of DNA, decondenses interphase, replicates throughout S

Question 29

HP1

Answer 29

heterochromatin protein, binds H3K9met

Question 30

HMGA with heterochromatin

Answer 30

localized predominantly to heterochromatin

Question 31

PEV- position effect variegation

Answer 31

-euchromatic genes repressed by spreading heterochromatin

Question 32

Su(var)

Answer 32

suppressor of PEV; promotes heterochromatin

Question 33

E(var)

Answer 33

enhancer of PEV; enhances when mutated. decreases heterochromatin, activates euchromatic genes

Question 34

Su(var)2-5

Answer 34

encodes HP1

Question 35

Su)var)3-9

Answer 35

H3K9 methylase, HP1 binds to chrome with methylated H3K9

Question 36

RNA-seq

Answer 36

genome-wide sequence of steady state RNA 1. poly_A selection, fragmentation 2. cDNA strand synth 3. end-repair, phosphorylate, A-tailing 4. adapter ligation

Question 37

RPKM

Answer 37

reads per kb exon per million reads, normalizes number of reads

Question 38

GRO-seq

Answer 38

global run on sequencing, total level of nascent RNA, ongoing transcription

Question 39

ChIP-seq

Answer 39

antibodies; fixation, fornication, immunoprecipation, hydrolysis, analysis

Question 40

ICE chip

Answer 40

chip followed by illumina sequencing

Question 41

MNase-seq

Answer 41

reveals canonical nucleosomes, primarily cleaves AT

Question 42

MPE-seq

Answer 42

little sequence specificity, but locates non-canonical chromatin particles reveals pre-nucleosome like particles

Question 43

DNase-seq

Answer 43

genome-wide DNase 1; recognizes 1 sequence, cleaves 20bp away

Question 44

ATAC-seq

Answer 44

genome-wide chromatin accessibility analysis; nextera - tagmentation, DNA fragmentation and ligation - alternative to MNase/DNase - less cells

Question 45

3C

Answer 45

Chromosome-conformation capture | -crosslink--> digest--> ligate--> PCR

Question 46

HI-C

Answer 46

crosslink, cut, fill ends with biotin, ligate, purify and shear, pull down biotin, sequence by pair ending

Question 47

chloroquinine

Answer 47

- induces positive supercoiling - nicked dna will still be relaxed - malaria treatment - to see assembled chromatin