BCH5413 3 Final Test A+ Questions and
Answers Verified Solutions Latest Update
2026/2027
Answer:
- composite of histone modification in promoter region of all genes
in human genome in CD4 T cells expressed in various levels
■Protein Readers that bind to methylated histone sites.
Answer:
1. chromodomain2. tudor domain3. WD40 repeat*each has a
different specificity
■Modes of chromatin modification/remodeling and promoter activation- order for yeast, human,
and alpha.
Answer:
Yeast- SWV/SNF opens promoter and allows HAT to enter and acetylate histones and form
PICHuman- HAT acts to acetylate nearby nucleosomes and recruits Pol II- then SWV/SNF comes
to open chromatin and form PICAlpha- form PIC first and recruit RNA Pol II, then acetylate with
HAT and remodel via SWV/SNF
■DNA methylation- what gets methylated- by what- what is the result- when does this occur-
methyl donor- what occurs with methyl donor.
Answer:
- deoxycytidine gets methylated at 5 position- by DNA
methyltransferase- yields 5-methyl-deoxycytidine- occurs in DNA after replication- methyl donor
is AdoMet- methyl group gets transferred to 5 position of cytosine - also results in AdoHcy
■DNA methylation ____ modifies ___.
Answer:
covalently modifies cytosines at CpG locations- symmetrical methylation
■Is there a genetic difference with DNA methylation?.
,Answer:
NO- epigenetic difference
■Maintenance of DNA methylation after cell division in mammals.
Answer:
- at replication, parental strands will be methylated but daughter
strands will not be- DNMT1 preferentially recognizes hemi-methylated DNA- methylates
non-methylated strand- regenerates original methylation pattern
■Can DNA methylation be transferred to following generations?.
Answer:
YES- through mitosis
■Functions of DNA methylation in mammals.
Answer:
- critical for normal embryogenesis/development- gene regulation
(hypermethylation of CpG promoter regions is associated with gene silencing)- chromatin
compaction- genome stability (silencing endogenous viral sequences and suppression of
homologous recombination between repeats)- genome defense- X chromosome inactivation
(females)- genomic imprinting
■Methylation of promoter regions with high CpG density is highly correlated with....
Answer:
gene silencing
■Methylation in promoter regions of low CpG density is not closely correlated with....
Answer:
gene silencing
■Intragenic and Intergenic DNA Methylation- Intragenic non-promoter DNA methylation has been
reported to....
Answer:
,- act as a positive regulator of gene transcription- regulate
alternative promoter usage- influence nucleosome positioning- affect transcription elongation-
regulate RNA splicing
■Intragenic and Intergenic DNA Methylation- Intergenic DNA methylation may regulate....
Answer:
the function of long range regulatory regions
■CpG Islands- what occurs here in mammals- representation in mammalian genome- %
methylated in mammalian genome- rich regions often associated with- how many islands in human
genome- how much of genome, CpG, and unmethylated cytosines.
Answer:
- DNA methylation in mammals occurs primarily within the CpG
sequence - CpG is underrepresented in the mammalian genome- 70% of all CpG's are methylated-
CpG islands are GC-rich regions of 500bp often associated with gene promoters (almost always
unmethylated)- 45,000 CpG islands in human genome- CpG islands are 1% of genome, 15% of
total CpG's, and 50% of total unmethylated cytosines
■The mammalian DNA methylation machinery is composed of multiple parts...
Answer:
1. DNA methyltransferase (DNMT): establish the methylation
mark in the genome2. Methyl-CpG binding proteins (MBD): read or interpret the methylation
mark3. DNA demethylation: erasing the methylation mark
■DNA Methyltransferases- three types and what they do.
Answer:
1. DNMT1- maintenance- methylate hemi-methylated to maintain
patterns in two daughter cells after DNA replication- localized to replication foci- recruited by
UHRF12. DNMT3A- de novo- put methyl groups on DNA that were previously unmethylated3.
DNMT3B- de novo- put methyl groups on DNA that were previously 4. DNMT3L- lacks
functional catalytic domain even though it has strong homology - still important b/c it interacts with
3A and 3B as regulator of their activity
■DNMT3A/B/L- domain.
Answer:
, ADD domain- recognizes unmethylated histone H3K4- methylates surrounding DNA
■De novo DNMT3A/B usually a part of larger....
Answer:
transcription repression complexes- HDAC and histone methyltransferase *interact with chromatin
and recruit DNMT to methylate
DNA
■Methylated DNA recognized and bound by two families of methylated DNA binding proteins.
Answer:
MBD and Kaiso- bind to methylated DNA and recruit transcriptional co-repressor complexes to
silence transcription
■MBD Family- have a common...- may also have..- MBD4 has glycosylase which....
Answer:
- methylated MBD domain that recognizes and binds to methylated
DNA- transcriptional repression domain- functions in excision repair
■What do you need to do to silence a gene...
Answer:
Recruit repressor complexes- MECP2 binds to methylated DNA and HDAC deacetylases
chromatinMethylate binding site of transcription factor- prevents it from binding
■MBD proteins and transcriptional silencing.
Answer:
- MBD1 binds to methylated DNA and recruits HDAC to
deacetylate nucleosomes to result in transcriptional silencing - MBD2 recruits Mr-2 and MBD3
complex that silences transcription - MBD3 lacks functional binding to methylated DNA but is part
of Mr-2 complex
■Pathways of DNA demethylation (erasers)- direct method?- result.
Answer:
- no direct mechanism- results in 5 methyl cytosine (5hmC) to
regular cytosine (5mC)
■5mC to 5hmC via hydroxylation- what proteins.
Answers Verified Solutions Latest Update
2026/2027
Answer:
- composite of histone modification in promoter region of all genes
in human genome in CD4 T cells expressed in various levels
■Protein Readers that bind to methylated histone sites.
Answer:
1. chromodomain2. tudor domain3. WD40 repeat*each has a
different specificity
■Modes of chromatin modification/remodeling and promoter activation- order for yeast, human,
and alpha.
Answer:
Yeast- SWV/SNF opens promoter and allows HAT to enter and acetylate histones and form
PICHuman- HAT acts to acetylate nearby nucleosomes and recruits Pol II- then SWV/SNF comes
to open chromatin and form PICAlpha- form PIC first and recruit RNA Pol II, then acetylate with
HAT and remodel via SWV/SNF
■DNA methylation- what gets methylated- by what- what is the result- when does this occur-
methyl donor- what occurs with methyl donor.
Answer:
- deoxycytidine gets methylated at 5 position- by DNA
methyltransferase- yields 5-methyl-deoxycytidine- occurs in DNA after replication- methyl donor
is AdoMet- methyl group gets transferred to 5 position of cytosine - also results in AdoHcy
■DNA methylation ____ modifies ___.
Answer:
covalently modifies cytosines at CpG locations- symmetrical methylation
■Is there a genetic difference with DNA methylation?.
,Answer:
NO- epigenetic difference
■Maintenance of DNA methylation after cell division in mammals.
Answer:
- at replication, parental strands will be methylated but daughter
strands will not be- DNMT1 preferentially recognizes hemi-methylated DNA- methylates
non-methylated strand- regenerates original methylation pattern
■Can DNA methylation be transferred to following generations?.
Answer:
YES- through mitosis
■Functions of DNA methylation in mammals.
Answer:
- critical for normal embryogenesis/development- gene regulation
(hypermethylation of CpG promoter regions is associated with gene silencing)- chromatin
compaction- genome stability (silencing endogenous viral sequences and suppression of
homologous recombination between repeats)- genome defense- X chromosome inactivation
(females)- genomic imprinting
■Methylation of promoter regions with high CpG density is highly correlated with....
Answer:
gene silencing
■Methylation in promoter regions of low CpG density is not closely correlated with....
Answer:
gene silencing
■Intragenic and Intergenic DNA Methylation- Intragenic non-promoter DNA methylation has been
reported to....
Answer:
,- act as a positive regulator of gene transcription- regulate
alternative promoter usage- influence nucleosome positioning- affect transcription elongation-
regulate RNA splicing
■Intragenic and Intergenic DNA Methylation- Intergenic DNA methylation may regulate....
Answer:
the function of long range regulatory regions
■CpG Islands- what occurs here in mammals- representation in mammalian genome- %
methylated in mammalian genome- rich regions often associated with- how many islands in human
genome- how much of genome, CpG, and unmethylated cytosines.
Answer:
- DNA methylation in mammals occurs primarily within the CpG
sequence - CpG is underrepresented in the mammalian genome- 70% of all CpG's are methylated-
CpG islands are GC-rich regions of 500bp often associated with gene promoters (almost always
unmethylated)- 45,000 CpG islands in human genome- CpG islands are 1% of genome, 15% of
total CpG's, and 50% of total unmethylated cytosines
■The mammalian DNA methylation machinery is composed of multiple parts...
Answer:
1. DNA methyltransferase (DNMT): establish the methylation
mark in the genome2. Methyl-CpG binding proteins (MBD): read or interpret the methylation
mark3. DNA demethylation: erasing the methylation mark
■DNA Methyltransferases- three types and what they do.
Answer:
1. DNMT1- maintenance- methylate hemi-methylated to maintain
patterns in two daughter cells after DNA replication- localized to replication foci- recruited by
UHRF12. DNMT3A- de novo- put methyl groups on DNA that were previously unmethylated3.
DNMT3B- de novo- put methyl groups on DNA that were previously 4. DNMT3L- lacks
functional catalytic domain even though it has strong homology - still important b/c it interacts with
3A and 3B as regulator of their activity
■DNMT3A/B/L- domain.
Answer:
, ADD domain- recognizes unmethylated histone H3K4- methylates surrounding DNA
■De novo DNMT3A/B usually a part of larger....
Answer:
transcription repression complexes- HDAC and histone methyltransferase *interact with chromatin
and recruit DNMT to methylate
DNA
■Methylated DNA recognized and bound by two families of methylated DNA binding proteins.
Answer:
MBD and Kaiso- bind to methylated DNA and recruit transcriptional co-repressor complexes to
silence transcription
■MBD Family- have a common...- may also have..- MBD4 has glycosylase which....
Answer:
- methylated MBD domain that recognizes and binds to methylated
DNA- transcriptional repression domain- functions in excision repair
■What do you need to do to silence a gene...
Answer:
Recruit repressor complexes- MECP2 binds to methylated DNA and HDAC deacetylases
chromatinMethylate binding site of transcription factor- prevents it from binding
■MBD proteins and transcriptional silencing.
Answer:
- MBD1 binds to methylated DNA and recruits HDAC to
deacetylate nucleosomes to result in transcriptional silencing - MBD2 recruits Mr-2 and MBD3
complex that silences transcription - MBD3 lacks functional binding to methylated DNA but is part
of Mr-2 complex
■Pathways of DNA demethylation (erasers)- direct method?- result.
Answer:
- no direct mechanism- results in 5 methyl cytosine (5hmC) to
regular cytosine (5mC)
■5mC to 5hmC via hydroxylation- what proteins.
