APG Exam II Study Guide
1. What is a key fac- Genome plasticity; several diploid ancestors have contributed to the genome
tor in the success of of modern wheat, allowing it to survive lots of environmental conditions
polyploid wheat un-
der domestication?
2. Explain the writer, Covalent modifications of histones and genomic DNA (like methylations)
eraser, and reader control the accessibility of chromatin to transcription factors/regulatory pro-
concept. teins. Writer, reader, and eraser proteins interact, and these interactions are
essential gene expression control.
Writers: proteins that introduce the chromatin marks
Readers: proteins that interpret the marks
Erasers: proteins that remove the marks
3. Describe the three 1) de novo DNA methylation: initiates new sites of cytosine methylation
steps in DNA methy- 2) maintenance: mitosis and meiosis propagate the methylation marks
lation. 3) reprogramming/demethylation: specific methylation sites are removed
4. Name the mecha- RNA-directed DNA methylation (RdDM) involves non-coding RNA molecules
nism of de novo directing the addition of DNA methylation to specific DNA sequences.
DNA methylation. In
one sentence, how
does it work?
5. Why is RdDM impor- It plays adds DNA methylation over new transposable element (TE) insertions
tant? to silence them and reinforces DNA methylation over existing TEs, which
inhibits transposition and maintains long-term genome stability
6. Describe the canon- 1) sRNA production: Pol IV generates ssRNAs from transposons and repeats,
ical RdDM pathway. which are converted into double-stranded small interfering RNAs (sRNAs).
2) DNA methylation: The sRNAs a protein to create a duplex and interact
with Pol V, which transcribes intergenic non-coding regions (functions as a
, APG Exam II Study Guide
scaffold). The sRNA transcript duplex is recognized by a protein that recruits
a methyltransferase, DRM2, for DNA methylation.
7. What is the main The non-canonical pathway has multiple sources of sRNAs, including from the
difference between RNAi (RNA interference)/post-transcriptional gene silencing (PTGS). plants
the non-canonical with RNAi/PTGS showed accumulation of sRNA species in different silencing
and the canoni- backgrounds. Co-suppressed transgenic plants produce small RNAs, which
cal RdDM pathways? hybridize to both sense and antisense probes, implicating small dsRNA in
Explain. gene silencing.
8. Describe the RNAi 1) RNA dependent RNA polymerase (RdRP) initiates RNAi from aberrant
pathway. ssRNAs by making them dsRNAs.
2) DICER cleaves long dsRNA into shorter bp molecules, and siRNAs are
assembled into the RNA Induced Silencing Complex (RISC) and activated.
3) RISC binds and cleaves the target mRNA, preventing protein production
(critical protein = AGO).
4) RdRP primes the synthesis of new dsRNA molecules, amplifying the siRNA
signal.
9. Describe the modes 1) Post-transcriptional gene silencing: RNA degradation
of silencing by siR- 2) Transcriptional gene silencing: inhibition of transcription/translation, DNA
NAs. methylation (RdDM), chromatin modification
10. How are DNA Passive demethylation: during cell division newly-synthesized DNA lacks
methylation path- methylation until it is re-added by a maintenance DNA methylation pathway.
ways opposed? De-
scribe the differ- Active demethylation: DNA glycosylases remove methylated cytosines through
ence between these base excision repair. Four proteins: ROS1, DME, DML2, DML3
methods.
11. Describe how ROS1 When RdDM targets a repeat in the ROS1 promoter, the ROS1 protein
contributes to demethylates the entire genome, as well as the methylstat, which results
demethylation. in the downregulation of ROS1 expression (stopping demethylation). The
, APG Exam II Study Guide
degree of methylation of the methylstat element regulates the degree of
expression of ROS1.
12. Describe the mech- RdDM represses the FWA gene, which allows for the proper timing of flow-
anism of the late ering. FWA promoter contains tandem repeats that are usually unmethylated
flowering pheno- by RdDM, leading to transcriptional repression. Losing this methylation re-
type in Arabidopsis activates FWA, which causes late flowering.
(FWA gene). What
do you call this type This can be stably transmitted to progeny without any changes in the DNA
of inherited trait? sequence (only through methylation, an epigenetic change), which makes it
considered an epiallele.
13. How do you find epi- You can use MethylC-seq.
alleles?
14. What could be the Transgenerational epigenetic instability
source of new epial-
leles?
15. How can you Both = dCas9-SunTag system. The SunTag scaffold can be fused to GFP, which
articficially methy- then are fused to protein of interest (methyltransferase). gRNAs are used to
late DNA in a guide complex to methylate the DNA of interest.
site-specific man-
ner? Demethylate?
16. Explain the "re- In pollen grains, transposons are only reactivated in the vegetative nucleus to
inforcement of only silence transposons in sperm cells through high degrees of methyla-
gene-silencing the- tion.
ory" during plant
gametogenesis In the embryo sac, transposons are reactivated in the central cell. siRNAS from
the central cell reinforce transposon silencing in the egg and embryo.
17. What is imprinting? It is an epigenetic phenomenon by which genetically identical alleles are
expressed differently depending on the parent of origin.
1. What is a key fac- Genome plasticity; several diploid ancestors have contributed to the genome
tor in the success of of modern wheat, allowing it to survive lots of environmental conditions
polyploid wheat un-
der domestication?
2. Explain the writer, Covalent modifications of histones and genomic DNA (like methylations)
eraser, and reader control the accessibility of chromatin to transcription factors/regulatory pro-
concept. teins. Writer, reader, and eraser proteins interact, and these interactions are
essential gene expression control.
Writers: proteins that introduce the chromatin marks
Readers: proteins that interpret the marks
Erasers: proteins that remove the marks
3. Describe the three 1) de novo DNA methylation: initiates new sites of cytosine methylation
steps in DNA methy- 2) maintenance: mitosis and meiosis propagate the methylation marks
lation. 3) reprogramming/demethylation: specific methylation sites are removed
4. Name the mecha- RNA-directed DNA methylation (RdDM) involves non-coding RNA molecules
nism of de novo directing the addition of DNA methylation to specific DNA sequences.
DNA methylation. In
one sentence, how
does it work?
5. Why is RdDM impor- It plays adds DNA methylation over new transposable element (TE) insertions
tant? to silence them and reinforces DNA methylation over existing TEs, which
inhibits transposition and maintains long-term genome stability
6. Describe the canon- 1) sRNA production: Pol IV generates ssRNAs from transposons and repeats,
ical RdDM pathway. which are converted into double-stranded small interfering RNAs (sRNAs).
2) DNA methylation: The sRNAs a protein to create a duplex and interact
with Pol V, which transcribes intergenic non-coding regions (functions as a
, APG Exam II Study Guide
scaffold). The sRNA transcript duplex is recognized by a protein that recruits
a methyltransferase, DRM2, for DNA methylation.
7. What is the main The non-canonical pathway has multiple sources of sRNAs, including from the
difference between RNAi (RNA interference)/post-transcriptional gene silencing (PTGS). plants
the non-canonical with RNAi/PTGS showed accumulation of sRNA species in different silencing
and the canoni- backgrounds. Co-suppressed transgenic plants produce small RNAs, which
cal RdDM pathways? hybridize to both sense and antisense probes, implicating small dsRNA in
Explain. gene silencing.
8. Describe the RNAi 1) RNA dependent RNA polymerase (RdRP) initiates RNAi from aberrant
pathway. ssRNAs by making them dsRNAs.
2) DICER cleaves long dsRNA into shorter bp molecules, and siRNAs are
assembled into the RNA Induced Silencing Complex (RISC) and activated.
3) RISC binds and cleaves the target mRNA, preventing protein production
(critical protein = AGO).
4) RdRP primes the synthesis of new dsRNA molecules, amplifying the siRNA
signal.
9. Describe the modes 1) Post-transcriptional gene silencing: RNA degradation
of silencing by siR- 2) Transcriptional gene silencing: inhibition of transcription/translation, DNA
NAs. methylation (RdDM), chromatin modification
10. How are DNA Passive demethylation: during cell division newly-synthesized DNA lacks
methylation path- methylation until it is re-added by a maintenance DNA methylation pathway.
ways opposed? De-
scribe the differ- Active demethylation: DNA glycosylases remove methylated cytosines through
ence between these base excision repair. Four proteins: ROS1, DME, DML2, DML3
methods.
11. Describe how ROS1 When RdDM targets a repeat in the ROS1 promoter, the ROS1 protein
contributes to demethylates the entire genome, as well as the methylstat, which results
demethylation. in the downregulation of ROS1 expression (stopping demethylation). The
, APG Exam II Study Guide
degree of methylation of the methylstat element regulates the degree of
expression of ROS1.
12. Describe the mech- RdDM represses the FWA gene, which allows for the proper timing of flow-
anism of the late ering. FWA promoter contains tandem repeats that are usually unmethylated
flowering pheno- by RdDM, leading to transcriptional repression. Losing this methylation re-
type in Arabidopsis activates FWA, which causes late flowering.
(FWA gene). What
do you call this type This can be stably transmitted to progeny without any changes in the DNA
of inherited trait? sequence (only through methylation, an epigenetic change), which makes it
considered an epiallele.
13. How do you find epi- You can use MethylC-seq.
alleles?
14. What could be the Transgenerational epigenetic instability
source of new epial-
leles?
15. How can you Both = dCas9-SunTag system. The SunTag scaffold can be fused to GFP, which
articficially methy- then are fused to protein of interest (methyltransferase). gRNAs are used to
late DNA in a guide complex to methylate the DNA of interest.
site-specific man-
ner? Demethylate?
16. Explain the "re- In pollen grains, transposons are only reactivated in the vegetative nucleus to
inforcement of only silence transposons in sperm cells through high degrees of methyla-
gene-silencing the- tion.
ory" during plant
gametogenesis In the embryo sac, transposons are reactivated in the central cell. siRNAS from
the central cell reinforce transposon silencing in the egg and embryo.
17. What is imprinting? It is an epigenetic phenomenon by which genetically identical alleles are
expressed differently depending on the parent of origin.
