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MolCell Unit 2 > Iwafuchi 2 > Flashcards

Iwafuchi 2 Flashcards

Flashcards for Iwafuchi Lecture 2 (70 cards)

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1
Q

What type of histone helps to further condense chromatin structure?

A

Linker histone H1

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2
Q

Chromatin structure is highly _______, reflecting underlying genetic function.

A

dynamic

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3
Q

Regions of chromatin that are less compact and more accessible to transcription factors are called _______?

A

open chromatin

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4
Q

Histone modifications involve covalent additions of functional groups to _______?

A

amino acids of core histones

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5
Q

Histone modifications often, but not always, occur on which two amino acids?

A

Lysine (K) and arginine (R)

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6
Q

What process involves altering the interaction between histones and DNA, making specific DNA regions more or less accessible?

A

Chromatin remodeling

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7
Q

Chromatin remodeling is an _______ process that requires energy input.

A

ATP-dependent

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8
Q

Name one way that chromatin remodeling complexes can be recruited to specific chromatin regions.

A

Through interaction with epigenetic marks or transcription factors.

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9
Q

What type of chromatin remodeling complex promotes nucleosome sliding or ejection, making DNA more accessible?

A

SWI/SNF

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10
Q

Which type of chromatin remodeling complex helps to establish evenly spaced nucleosomes, potentially restricting access to DNA?

A

ISWI

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11
Q

The SWR1 complex can facilitate the insertion of _______ into nucleosomes.

A

variant core histones

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12
Q

Give two examples of variant core histones.

A

H2AZ, H3.1

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13
Q

Transcription factors that can bind to and open condensed chromatin, initiating changes in gene expression are called ______?

A

Pioneer TFs

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14
Q

Give four examples of pioneer transcription factors.

A

FOXA, GATA, OCT4, and SOX2.

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15
Q

Pioneer transcription factors can bind to DNA wrapped in _______, a characteristic that distinguishes them from other transcription factors.

A

nucleosomes

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16
Q

Pioneer transcription factors enable the binding of other regulatory proteins to DNA by making chromatin more _______?

A

accessible

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17
Q

True or False: Most histone writers, erasers, and chromatin remodelers have DNA-binding domains.

A

False

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18
Q

Histone writers, erasers, and chromatin remodelers are considered _______ because they regulate transcription but don’t bind directly to DNA.

A

transcription cofactors

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19
Q

Heterochromatin domains can range in size from _______ to _______.

A

Kilobases to megabases

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20
Q

Give three examples of genomic regions that are often packaged into heterochromatin.

A

Tissue-specific genes, lamin-associated domains, and repetitive DNA

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21
Q

Name the two main types of heterochromatin domains discussed in the source.

A

H2AK119ub/H3K27me3 and H3K9me3

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22
Q

What is the name of the protein complex that is a writer of the H3K27me3 histone modification?

A

Polycomb Repressive Complex 2 (PRC2)

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23
Q

PRC1 is responsible for writing which histone modification?

A

H2AK119ub

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24
Q

Mutations in PRC2 are lethal in mice shortly after what developmental stage?

A

gastrulation

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25
PRC1 mutant embryos in mice fail to develop beyond the _______ stage.
two-cell
26
What are the two main problems associated with current reprogramming techniques?
Incomplete repression of fibroblast genes and low efficiency/fidelity of reprogramming.
27
The addition of PRDM1 is being investigated for its ability to improve the _______ and _______ of cellular reprogramming.
efficiency, fidelity
28
What modification can neutralize the positive charge of lysine residues on histone tails?
Acetylation
29
Acetylation of lysine residues on histone tails can lead to a more ______ and _______ DNA template.
open, accessible
30
What specific histone modification is highly effective at inhibiting condensed chromatin fiber formation?
Acetylation of H4-lysine16
31
Besides charge neutralization, PTMs also serve as recognition sites for the binding of _______ or _______.
co-activators, co-repressors
32
What protein domain recognizes and binds to acetylated lysine residues?
Bromo domain
33
_______ domains are attracted to methylated lysine residues.
Chromo
34
The concept that specific combinations of histone modifications create a regulatory code that influences gene expression is called the _______?
histone code hypothesis
35
What three categories of enzymes are involved in writing, reading, and erasing the histone code?
Writers, readers, erasers
36
Histone acetyltransferases (HATs) and histone methyltransferases (HMTs) are examples of _______ of the histone code.
writers
37
_______, such as histone deacetylases (HDACs), are responsible for removing histone modifications.
Erasers
38
The inheritance of histone modifications and their associated gene expression patterns through cell division is part of the broader phenomenon known as _______.
epigenetics
39
Give an example of a pioneer transcription factor that is involved in both programming and reprogramming cell fate.
FOXA
40
What two cell types are used in the reprogramming experiments described in the source?
Skin fibroblasts, induced hepatocytes (iHeps)
41
What transcription factor, in addition to FOXA, is involved in the generation of induced hepatocytes from stem cells?
Hnf4a/1a
42
“Active”, “open” chromatin regions are depleted in _______ content.
histone H1
43
Compared to inactive, closed regions, active, open chromatin regions have a more _______ and ______ anatomy.
irregular, dynamic
44
Chromatin structure and epigenetic states are highly dynamic, reflecting the underlying ______ ______ functions.
gene regulatory
45
Some examples of epigenetic modifications for open euchromatin include _________.
H3K4 methylation, H3K27 acetylation
46
Some examples of epigenetic modifications for heterochromatin include _________.
H2AK119 ubiquitination, H3K27 methylation, H3K9 methylation
47
What can pioneer TFs do?
Access and scan closed chromatin, bind independently to nucleosomal DNA
48
When a TF binds to a nucleosome, it is known as ______.
primed
49
Rank pioneer TFs in terms of affinity to chromatin.
Foxa1 > Gata4 > > Nfi
50
What is mitotic bookmarking?
Pioneer TFs remain bound on mitotic chromosomes during mitosis when other TFs are excluded from chromosomes, suggesting a potential mechanism for maintaining transcriptional programs through the cell cycle.
51
Rank pioneer TFs in terms of slowest nuclear mobility.
Foxa1 < Gata4 < Nfi
52
In order to open chromatin, a pioneer TF must first _______ using its DNA-binding domain (DBD).
displace linker histone H1
53
After displacing linker histone H1, pioneer TFs _________ using their alpha helix.
interact with core histone residues
54
True or False: Active, open chromatin is depleted in histone H1 content.
True
55
True or False: Active, open chromatin is formed through chromatin perturbation, involving a combination of nucleosomal instability, remodeling, and post-translational modifications (epigenetic modifications).
True
56
In terms of epigenetic modifications, ________ can affect internucleosomal histone-histone and DNA-histone interaction, leading to a more open, accessible DNA template.
acetylation
57
True or False: PTM’s (including acetylation) provide crucial recognition and binding sites for a range of additional co-activators or co-repressors.
True
58
In the process known as chromatin remodeling, local ___________ interactions are disrupted such that the contact between them becomes much more fluid and/or dynamic; a DNA sequence can slide around the nucleosome core
histone-DNA
59
True or False: Chromatin remodeling is an ATP-independent process.
False, it requires ATP
60
There are several different families of chromatin remodeling complexes; each is a complex of several proteins, but all remodelers contain a subunit with an ____________, allowing energy derived from ATP hydrolysis to disrupt local DNA-histone interactions.
ATPase domain
61
Another type of remodeling complex, _______, can cause local nucleosome instability such that variant core histones (e.g., H2AZ, H3.1) can be inserted that may serve as local functional “marks” of relatively open or accessible chromatin.
SWR1
62
_______ remodeling allows an evenly spaced nucleosomal array to be established on the DNA, thereby inhibiting access of regulatory proteins to the DNA (note also that _______ subunit appears to promote association of linker histone H1 with chromatin).
ISWI-type, ISWI subunit
63
_________ remodeling causes nucleosome sliding or perhaps even nucleosome ejection, thereby allowing access of regulatory proteins (e.g., activators, repressors) to the DNA
SWI/SNF-type
64
Few histone writers, erasers, or chromatin remodelers have ___________ domains; they are transcription cofactors.
DNA-binding
65
__________ (H3K27me3 writer) mutant embryos die shortly after gastrulation
PRC2
66
________ (H2AK119ub writer) mutant embryos do not develop beyond the two-cell stage
PRC1
67
____________ are associated with H2AK119ub/H3K27me3.
Polycomb Repressive Complexes (PRC)
68
____________ are associated with H3K9me3.
Co-repressors & histone deacetylases
69
H3K9me3 heterochromatin domains occur on the _______ scale and cover tissue-specific genes and enhancers, lamin-associated domains, repetitive DNA near centrosome and telomeres, and transposable elements.
kilobase-megabase scale
70
H2AK119ub/H3K27me3 heterochromatin domains occur on the _______ scale and cover tissue-specific promoters and enhancers (for many transcription factor and cell-signaling-related genes), and inactive X chromosome.
kilobase scale

MolCell Unit 2 (13 decks)

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