BCH5413 FINAL PAPER 2026 QUESTIONS WITH
ANSWERS GRADED A+
◉ 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.
ANSWERS GRADED A+
◉ 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.
