module 9

Question 1

Epigenetics

Answer 1

the study of mechanisms that lead to changes in gene expression that can be passed from cell to cell and are reversible, but do not involve a change in the sequence of DNA

Question 2

genes can be targeted for epigenetic regulation via

Answer 2

transcription factors and noncoding RNA

Question 3

cis-epigenetic changes

Answer 3

are maintained at a specific site during cell division

Question 4

trans-epigenetic changes

Answer 4

are maintained by diffusible factors, such as transcription factors

Question 5

epigenetic gene regulation may occur as/be caused by

Answer 5

programed developmental change (genomic imprinting, x-chromosome inactivation, cell differentiation) or environmental agents (temperature, diet, toxins)

Question 6

euchromatin

Answer 6

chromosomal regions that are not stained during interphase, loop domains are not tightly packed, transcriptionally active

Question 7

heterchromatin

Answer 7

chromosomal regions that are stained during interphase, great level of compaction, inhibitory effect on gene expression

Question 8

constitutive heterochromatin

Answer 8

regions that are heterochromatic at the same location in all cell types

Question 9

facultative heterochromatin

Answer 9

heterochromatin that varies in its location among different cell types, allows for tissue specific gene regulation

Question 10

the genes that are contained with facultative heterochromatin are

Answer 10

usually silenced

Question 11

constitutive heterochromatin characteristics

Answer 11

close to centromere or telomere, generally composed of many short tandemly repeated sequences, highly methylated on cytosines in vertebrates and plants, H3K9me3 common in animals, H3K9me2 in plants

Question 12

facultative heterochromatin characteristics

Answer 12

formation is reversible, multiple sites between the centromere and the telomere, LINE-type repeats, methylation at CpG islands in gene regulatory regions (silences genes), H3K9me3 common

Question 13

Post-translational modifications (PTMs)

Answer 13

result in changes in chromatin structure, such as heterochromatin formation

Question 14

reader domains

Answer 14

bind specific proteins to particular PTMs in nucleosomes

Question 15

writer domains

Answer 15

addition of PTMs

Question 16

Eraser domains

Answer 16

remove PTMs

Question 17

recruitment domains

Answer 17

recruit other proteins, such as chromatin remodelers or chromatin-modifying enzymes

Question 18

heterochromatin formation involves multiple molecular events:

Answer 18

post-translational modifications of histones, binding of proteins to nucleosomes, chromatin remodeling, DNA methylation, binding of non-coding RNAs

Question 19

higher-order structural features of heterochromatin

Answer 19

1. has closer, more stable contacts of nucleosomes with each other via HP1 2. forms closer loop domains, binds to the nuclear lamina 3. may undergo liquid-liquid phase separation

Question 20

Nucleation

Answer 20

short chromosomal site bound by chromatin-modifying enzymes and chromatin-remodeling complexes

Question 21

Spreading

Answer 21

adjacent euchromatin is turned into heterochromatin

Question 22

Barrier

Answer 22

in interphase chromosomes, spreading stops when it reaches a barrier (common: Nucleosome free region)

Question 23

heterochromatin structure is maintained by

Answer 23

DNA methylation, histone modifications, DNA polymerase, local chromatin structure

Question 24

pioneer factors

Answer 24

category of transcription factors, can recognize and bind to DNA sequences exposed on the surface of a nucleosomes

Question 25

pioneer factors can

Answer 25

1. recruit chromatin-remodeling complexes and histone-modifying enzymes that carry out epigenetic changes 2. influence the ability of other transcription factors to bind to enhancer sequences 3. decrease the level of DNA methylation by binding to CpG islands thereby blocking DNA methyltransferases 4. be apart of gene activation/silencing

Question 26

Trithorax group (TrxG)

Answer 26

involved with gene activation

Question 27

Polycomb group (PcG)

Answer 27

involved with gene repression, two types: PRC1 and PRC2

Question 28

chromatin compaction

Answer 28

PRC1 may cause nucleosomes in the target gene to form a knot-like structure

Question 29

covalent modification of histones

Answer 29

PRC1 may covalently modify histone H2A by attaching ubiquitin molecules

Question 30

direct interaction with a transcription factor

Answer 30

PRC1 may directly inhibit proteins involved with transcription

Question 31

noncoding RNA functions

Answer 31

1. scaffold, binds to a group of proteins 2. guide, binds to a protein and guides it to a specific site in the cell 3. alteration of protein function or stability, binds to protein and alters structure 4. ribozyme, acts as a catalyst 5. blocker, physically prevents a cellular process from happening 6. decoy, recognizes another ncRNA and sequesters it

Question 32

types of ncRNA

Answer 32

long ncRNA (IncRNA), small regulatory RNA (short ncRNA), MicroRNA

Question 33

double-stranded RNA is ______ potent at silencing mRNA than antisense RNA

Answer 33

more

Question 34

RNA interference

Answer 34

the phenomenon in which double-stranded RNA causes the silencing of mRNA

Question 35

iRNA is mediated by

Answer 35

microRNAs and small interfering RNAs

Question 36

microRNAs

Answer 36

transcribed from endogenous eukaryotic genes (pri-miRNA) regulate gene expression

Question 37

siRNA

Answer 37

originates from exogenous sources (not made by cells) but can come from viruses

Question 38

RNA-Induced Silencing Complex (RISC)

Answer 38

1. inhibits translation without degrading mRNA 2. degradation of the mRNA through cleavage of Argonaute

Question 39

CRISPR-Cas System

Answer 39

defense against bacteriophages, plasmids, and transposons

Question 40

CRISPR-Cas System defense phases

Answer 40

1. Adaption 2. Expression 3. Interference

Question 41

Adaption phase

Answer 41

Cas protein complex cleaves bacteriophage DNA and inserts it into Crispr gene

Question 42

Expression phase

Answer 42

exposure to bacteriophage results in the expression of crispr, tracr, and Cas9 genes

Question 43

Interference phase

Answer 43

Cas system is able to recognize and bind to bacteriophages and inhibit proliferation