BCH5413 Exam 3 ACTUAL Exam
Questions and CORRECT 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
• 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
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
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.
In the polycomb repressor complexes, what is the difference between PRC1 and PRC2? -
CORRECT ANSWER - PRC1 = Recognizes H3K27me3. Also can catalyze mono-
ubiquitination of lysine (H2AK119)
PRC2 = Contains catalytic subunit for H3K27 trimethylation.
Together they condense chromatin.
What is the difference between constitutive and facultative heterochromatin in terms of
transcription and histone methylation? - CORRECT ANSWER - In terms of transcription,
constitutive heterochromatin is always condensed/transcriptionally inactive while facultative
heterochromatin may be converted into euchromatin. This means that facultative
heterochromatin has the potential to be transcribed or not. In terms of histone methylation
constitutive heterochromatin exhibits H3K9me3 and facultative heterochromatin exhibits
H3K27me3.
Describe the differences in histone methylation found at active vs. inactive gene promoters. What
is an enhancer element and what differences are found at enhancer elements that are inactive,
poised for activation, and those that are active? - CORRECT ANSWER - Generally,
methylation of H3K4, H3K36 and H3K79 is associated with actively transcribed genes, whereas
methylation of H3K27, H3K9 and H4K20 is associated with inactive genes.Within actively
transcribed genes, H3K4me3 is mainly found at the promoter area or around TSS, whereas
H3K36me3 is found in the gene bodies. On repressed genes, the H3K9 and H4K20 methylation
marks are relatively homogeneously distributed, whereas H3K27me3 is enriched at the
promoters.
Questions and CORRECT 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
• 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
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
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.
In the polycomb repressor complexes, what is the difference between PRC1 and PRC2? -
CORRECT ANSWER - PRC1 = Recognizes H3K27me3. Also can catalyze mono-
ubiquitination of lysine (H2AK119)
PRC2 = Contains catalytic subunit for H3K27 trimethylation.
Together they condense chromatin.
What is the difference between constitutive and facultative heterochromatin in terms of
transcription and histone methylation? - CORRECT ANSWER - In terms of transcription,
constitutive heterochromatin is always condensed/transcriptionally inactive while facultative
heterochromatin may be converted into euchromatin. This means that facultative
heterochromatin has the potential to be transcribed or not. In terms of histone methylation
constitutive heterochromatin exhibits H3K9me3 and facultative heterochromatin exhibits
H3K27me3.
Describe the differences in histone methylation found at active vs. inactive gene promoters. What
is an enhancer element and what differences are found at enhancer elements that are inactive,
poised for activation, and those that are active? - CORRECT ANSWER - Generally,
methylation of H3K4, H3K36 and H3K79 is associated with actively transcribed genes, whereas
methylation of H3K27, H3K9 and H4K20 is associated with inactive genes.Within actively
transcribed genes, H3K4me3 is mainly found at the promoter area or around TSS, whereas
H3K36me3 is found in the gene bodies. On repressed genes, the H3K9 and H4K20 methylation
marks are relatively homogeneously distributed, whereas H3K27me3 is enriched at the
promoters.
