BCH5413 Exam 3 2026 Questions and
Answers
How is the change in gene expression caused by epigenetics different from changes
in gene expression caused by transcription factors? - Correct answer-transcription
factors bind to either activators or repressors and either act as an on or off switch.
They are dependent on DNA sequences specifically. Gene expression changes
caused by epigenetic factors regulate the chromatin structure around gene
regulatory areas.
Changes in gene expression patterns (or phenotype) that are not caused by changes
in DNA sequence (thus reversible) and heritable through cell division. - Correct
answer-Epigenetics
What are some examples of epigenetic modifications? - Correct answer-• histone
modifications and variants
• chromatin remodeling
• DNA methylation
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,• non-coding RNAs
• 3D genome architecture
In general, describe how the ChIP-Seq assay can be used to map histone marks
throughout the genome. - Correct answer-You need a DNA+protein with a stable
histone DNA interaction, chromatin is fragmented into small pieces, and antibodies
are added to be bound to specific histone modifications that you are interested in.
Then the isolated fragments are reversed crosslinked so they can release the
genomic DNA, then is purified for creating a sequencing library. Finally, the DNA
is aligned with a reference genome and the histone modifications can be mapped in
the reference genome.
Core histones are made up of 2 copies of each of these subunits per nucleosome: -
Correct answer-histone H2A - slightly lys rich
histone H2B - slightly lys rich
histone H3 - arg rich
histone H4 - arg rich
What are the three players and their functions in histone modification? - Correct
answer-Writers: These are histone modify enzymes that add a variety of covalent
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,modifications to histone tails. (histone acetyltransferases, histone
methyltransferases)
Erasers: They perform the opposite functions to writers, they remove histone
modifications. (histone deacetylaces, lysine demethylaces)
Readers: These are proteins that contain specific domains that can recognize
specific histone modifications. (bromodomains, chromodomains, PHD Fingers,
malignant brain tumor domains, tudor domains, PWWP domains)
How does lysine acetylation affect histone interaction with DNA? - Correct
answer-Lysine acetylation changes the charge from positively charged to
neutralized, affecting the interaction with negatively charged DNA.
Reduces electrostatic interaction between the histone tails and the negatively
charged phosphate backbone of DNA, resulting in loosening of chromatin.
What enzyme is responsible for acetylation? - Correct answer-Acetyl CoA
How is the acetylation removed from a lysine? - Correct answer-By a deacetylation
process
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, How is the action of p300/CBP (HATs) different in vitro and in vivo? - Correct
answer-Both of them have a catalytic domain. But when analyzed in vitro, it does
not have a strong substrate specificity. P300 and CBP can acetylate a lot of lysine
residues, in all histone tails, but in vivo, not many histone tails can be acetylated.
Describe both similarities and differences between histone acetylation and histone
methylation. - Correct answer-Both are writers. One transfers an acetyl group, and
the other transfers a methyl group.
Acetylation activates, methylation either suppresses or elevates gene expression.
Acetylation neutralizes the positive charge of lysine.
Methylation does not change net charge.Depending on the position and extent,
methylated residues act as specific histone marks and lead to different outcomes.
Methyltransferases are also highly specific.
In mammalian methyltransferases, what is the difference between the MLL1/2 and
MLL3/4 methytransferase complexes? - Correct answer-MLL1/2 are responsible
for H3K4 tri-methylation and are associated with active promotors. MLL3/4 are
responsible for H3K4 mono-methylation and are associated with enhancers.
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Answers
How is the change in gene expression caused by epigenetics different from changes
in gene expression caused by transcription factors? - Correct answer-transcription
factors bind to either activators or repressors and either act as an on or off switch.
They are dependent on DNA sequences specifically. Gene expression changes
caused by epigenetic factors regulate the chromatin structure around gene
regulatory areas.
Changes in gene expression patterns (or phenotype) that are not caused by changes
in DNA sequence (thus reversible) and heritable through cell division. - Correct
answer-Epigenetics
What are some examples of epigenetic modifications? - Correct answer-• histone
modifications and variants
• chromatin remodeling
• DNA methylation
©COPYRIGHT 2025, ALL RIGHTS RESERVED 1
,• non-coding RNAs
• 3D genome architecture
In general, describe how the ChIP-Seq assay can be used to map histone marks
throughout the genome. - Correct answer-You need a DNA+protein with a stable
histone DNA interaction, chromatin is fragmented into small pieces, and antibodies
are added to be bound to specific histone modifications that you are interested in.
Then the isolated fragments are reversed crosslinked so they can release the
genomic DNA, then is purified for creating a sequencing library. Finally, the DNA
is aligned with a reference genome and the histone modifications can be mapped in
the reference genome.
Core histones are made up of 2 copies of each of these subunits per nucleosome: -
Correct answer-histone H2A - slightly lys rich
histone H2B - slightly lys rich
histone H3 - arg rich
histone H4 - arg rich
What are the three players and their functions in histone modification? - Correct
answer-Writers: These are histone modify enzymes that add a variety of covalent
©COPYRIGHT 2025, ALL RIGHTS RESERVED 2
,modifications to histone tails. (histone acetyltransferases, histone
methyltransferases)
Erasers: They perform the opposite functions to writers, they remove histone
modifications. (histone deacetylaces, lysine demethylaces)
Readers: These are proteins that contain specific domains that can recognize
specific histone modifications. (bromodomains, chromodomains, PHD Fingers,
malignant brain tumor domains, tudor domains, PWWP domains)
How does lysine acetylation affect histone interaction with DNA? - Correct
answer-Lysine acetylation changes the charge from positively charged to
neutralized, affecting the interaction with negatively charged DNA.
Reduces electrostatic interaction between the histone tails and the negatively
charged phosphate backbone of DNA, resulting in loosening of chromatin.
What enzyme is responsible for acetylation? - Correct answer-Acetyl CoA
How is the acetylation removed from a lysine? - Correct answer-By a deacetylation
process
©COPYRIGHT 2025, ALL RIGHTS RESERVED 3
, How is the action of p300/CBP (HATs) different in vitro and in vivo? - Correct
answer-Both of them have a catalytic domain. But when analyzed in vitro, it does
not have a strong substrate specificity. P300 and CBP can acetylate a lot of lysine
residues, in all histone tails, but in vivo, not many histone tails can be acetylated.
Describe both similarities and differences between histone acetylation and histone
methylation. - Correct answer-Both are writers. One transfers an acetyl group, and
the other transfers a methyl group.
Acetylation activates, methylation either suppresses or elevates gene expression.
Acetylation neutralizes the positive charge of lysine.
Methylation does not change net charge.Depending on the position and extent,
methylated residues act as specific histone marks and lead to different outcomes.
Methyltransferases are also highly specific.
In mammalian methyltransferases, what is the difference between the MLL1/2 and
MLL3/4 methytransferase complexes? - Correct answer-MLL1/2 are responsible
for H3K4 tri-methylation and are associated with active promotors. MLL3/4 are
responsible for H3K4 mono-methylation and are associated with enhancers.
©COPYRIGHT 2025, ALL RIGHTS RESERVED 4
