BCH 5413 EXAM 3 | 88 QUESTIONS AND
CORRECT ANSWERS (VERIFIED ANSWERS)
| ALREADY GRADED A+ | LATEST UPDATE
2025-2026
How is the change in gene expression caused by epigenetics different from
changes in gene expression caused by transcription factors? - 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. -
ANSWER Epigenetics
What are some examples of epigenetic modifications? - ANSWER • histone
modifications and variants
• chromatin remodeling
• DNA methylation
• non-coding RNAs
• 3D genome architecture
In general, describe how the ChIP-Seq assay can be used to map histone marks
throughout the genome. - 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:
- 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? -
ANSWER Writers: These are histone modify enzymes that add a variety of
covalent 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? - 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? - ANSWER Acetyl CoA
How is the acetylation removed from a lysine? - ANSWER By a deacetylation
process
How is the action of p300/CBP (HATs) different in vitro and in vivo? - 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. - 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? - 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.
CORRECT ANSWERS (VERIFIED ANSWERS)
| ALREADY GRADED A+ | LATEST UPDATE
2025-2026
How is the change in gene expression caused by epigenetics different from
changes in gene expression caused by transcription factors? - 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. -
ANSWER Epigenetics
What are some examples of epigenetic modifications? - ANSWER • histone
modifications and variants
• chromatin remodeling
• DNA methylation
• non-coding RNAs
• 3D genome architecture
In general, describe how the ChIP-Seq assay can be used to map histone marks
throughout the genome. - 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:
- 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? -
ANSWER Writers: These are histone modify enzymes that add a variety of
covalent 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? - 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? - ANSWER Acetyl CoA
How is the acetylation removed from a lysine? - ANSWER By a deacetylation
process
How is the action of p300/CBP (HATs) different in vitro and in vivo? - 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. - 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? - 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.
