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MolCell Unit 2 > Iwafuchi 2 > Flashcards

Iwafuchi 2 Flashcards

Flashcards for Iwafuchi Lecture 2

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
Q

PRC1 mutant embryos in mice fail to develop beyond the _______ stage.

A

two-cell

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26
Q

What are the two main problems associated with current reprogramming techniques?

A

Incomplete repression of fibroblast genes and low efficiency/fidelity of reprogramming.

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27
Q

The addition of PRDM1 is being investigated for its ability to improve the _______ and _______ of cellular reprogramming.

A

efficiency, fidelity

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28
Q

What modification can neutralize the positive charge of lysine residues on histone tails?

A

Acetylation

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29
Q

Acetylation of lysine residues on histone tails can lead to a more ______ and _______ DNA template.

A

open, accessible

30
Q

What specific histone modification is highly effective at inhibiting condensed chromatin fiber formation?

A

Acetylation of H4-lysine16

31
Q

Besides charge neutralization, PTMs also serve as recognition sites for the binding of _______ or _______.

A

co-activators, co-repressors

32
Q

What protein domain recognizes and binds to acetylated lysine residues?

A

Bromo domain

33
Q

_______ domains are attracted to methylated lysine residues.

A

Chromo

34
Q

The concept that specific combinations of histone modifications create a regulatory code that influences gene expression is called the _______?

A

histone code hypothesis

35
Q

What three categories of enzymes are involved in writing, reading, and erasing the histone code?

A

Writers, readers, erasers

36
Q

Histone acetyltransferases (HATs) and histone methyltransferases (HMTs) are examples of _______ of the histone code.

A

writers

37
Q

_______, such as histone deacetylases (HDACs), are responsible for removing histone modifications.

A

Erasers

38
Q

The inheritance of histone modifications and their associated gene expression patterns through cell division is part of the broader phenomenon known as _______.

A

epigenetics

39
Q

Give an example of a pioneer transcription factor that is involved in both programming and reprogramming cell fate.

A

FOXA

40
Q

What two cell types are used in the reprogramming experiments described in the source?

A

Skin fibroblasts, induced hepatocytes (iHeps)

41
Q

What transcription factor, in addition to FOXA, is involved in the generation of induced hepatocytes from stem cells?

A

Hnf4a/1a

42
Q

“Active”, “open” chromatin regions are depleted in _______ content.

A

histone H1

43
Q

Compared to inactive, closed regions, active, open chromatin regions have a more _______ and ______ anatomy.

A

irregular, dynamic

44
Q

Chromatin structure and epigenetic states are highly dynamic, reflecting the underlying ______ ______ functions.

A

gene regulatory

45
Q

Some examples of epigenetic modifications for open euchromatin include _________.

A

H3K4 methylation, H3K27 acetylation

46
Q

Some examples of epigenetic modifications for heterochromatin include _________.

A

H2AK119 ubiquitination, H3K27 methylation, H3K9 methylation

47
Q

What can pioneer TFs do?

A

Access and scan closed
chromatin, bind independently to nucleosomal DNA

48
Q

When a TF binds to a nucleosome, it is known as ______.

A

primed

49
Q

Rank pioneer TFs in terms of affinity to chromatin.

A

Foxa1 > Gata4 > > Nfi

50
Q

What is mitotic bookmarking?

A

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
Q

Rank pioneer TFs in terms of slowest nuclear mobility.

A

Foxa1 < Gata4 < Nfi

52
Q

In order to open chromatin, a pioneer TF must first _______ using its DNA-binding domain (DBD).

A

displace linker histone H1

53
Q

After displacing linker histone H1, pioneer TFs _________ using their alpha helix.

A

interact with core histone residues

54
Q

True or False: Active, open chromatin is depleted in histone H1 content.

A

True

55
Q

True or False: Active, open chromatin is formed through chromatin perturbation, involving a combination of
nucleosomal instability, remodeling, and post-translational modifications
(epigenetic modifications).

A

True

56
Q

In terms of epigenetic modifications, ________ can affect internucleosomal histone-histone and DNA-histone interaction, leading to a more open, accessible DNA template.

A

acetylation

57
Q

True or False: PTM’s (including acetylation) provide crucial recognition and binding
sites for a range of additional co-activators or co-repressors.

A

True

58
Q

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

A

histone-DNA

59
Q

True or False: Chromatin remodeling is an ATP-independent process.

A

False, it requires ATP

60
Q

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.

A

ATPase domain

61
Q

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.

A

SWR1

62
Q

_______ 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).

A

ISWI-type, ISWI subunit

63
Q

_________ remodeling causes nucleosome sliding
or perhaps even nucleosome ejection, thereby
allowing access of regulatory proteins (e.g., activators,
repressors) to the DNA

A

SWI/SNF-type

64
Q

Few histone writers, erasers, or chromatin remodelers have ___________ domains; they are transcription cofactors.

A

DNA-binding

65
Q

__________ (H3K27me3 writer) mutant embryos die shortly after gastrulation

A

PRC2

66
Q

________ (H2AK119ub writer) mutant embryos do not develop beyond the two-cell stage

A

PRC1

67
Q

____________ are associated with H2AK119ub/H3K27me3.

A

Polycomb Repressive Complexes (PRC)

68
Q

____________ are associated with H3K9me3.

A

Co-repressors &
histone deacetylases

69
Q

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.

A

kilobase-megabase scale

70
Q

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.

A

kilobase scale

MolCell Unit 2 (13 decks)

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