Homework Quizzes
Approximately what % of the human genome corresponds to protein-coding sequences?
2%
What are the targets of DNA methyltransferases?
3'-GpC-5' and 5'-CpG-3'
In humans, NADs are ____________.
4% of the genome and are associated with nucleolus function
In humans, lamina associated domains (LADs) are _________.
40% of the genome and tend to be gene poor regions.
Approximately what % of the human genome corresponds to repeated sequences?
50%
In a typical somatic mammalian cell what % of all CpGs are methylated?
70-80%
What can gene density tell us about genome organization?
A gene density of ~1 gene per 100 Kb would indicate the presence of a nucleus (metazoan). However, the plant Arabidopsis has a gene density of 1 gene per ~4.4kb.
Which of the following statements is TRUE regarding enhancers? (From Looping Back to Leap Forward: Transcription Enters a New Era) -Although plants have many more enhancer elements than metazoans, they are often located millions of bases away from their core promoters. -Although there are only about 25,000 genes in humans, estimates suggest there are more than 400,000 enhancers. -Enhancers are only able to activate a single core promoter. -Enhancers are usually found outside TADs.
Although there are only about 25,000 genes in humans, estimates suggest there are more than 400,000 enhancers.
Name the structure of TFIIB that the arrow designates (green helix on non template DNA)
B linker helix
Name the structure of TFIIB that the arrow designates. green helix on RNA
B reader helix
RNA pol II promoters: Which of the following statements is FALSE? -Basal transcription factors bind at the core promoter, usually within 50 bp upstream from the start of transcription. -Enhancers are a collection of individual promoter elements that bind transactivators. -HDAC containing complexes are in involved in repression and bind (usually through other proteins) with silencer elements. -Most basal elements can either be located just downstream of the startpoint for transcription, or within the first intron. -Enhancers are sometimes located thousands of bp upstream or downstream of the startpoint of transcription
Basal elements can either be located just downstream of the startpoint for transcription, or within the first intron.
The rise in developmental complexity requires an increase in the complexity of controls regulating gene expression. The appearance of which of the following proteins in metazoans expanded the capacity of DNA looping to be utilized as a mechanism of transcriptional regulation?
CTCF
Which of the following statements is TRUE regarding Cohesin? -Cohesin forms a physical ring around two regions of DNA to form a DNA loop. -Cohesin is an elastic molecule that designates a single protein, not a complex of several proteins. -Cohesin is often drawn as forming a loop that literally encircles DNA, but close examination of its structure suggests that this NOT the case. -Cohesin is only found in the metazoans and is involved in DNA looping and holding sister chromatids together.
Cohesin forms a physical ring around two regions of DNA to form a DNA loop.
Which of the following is not true for the Xi (Barr body)?
CpG islands on the Barr body remain hypomethylated
Cohesin functions in ___________.
DNA repair, recombination, replication, gene expression, and genome architecture.
Name the factor that is involved in forming the paused state of RNA pol II and its lineage can be traced back beyond archaea to the eubacteria? Hint: Its structure and location within the PIC is shown in the image below. Another name for it is "Spt4/5".
DSIF
Which of the following factors converts from a negative role to a positive role after phosphorylation by P-TEFb?
DSIF
What are the targets of P-TEFb phosphorylation?
DSIF CTD Ser2 NELF
In the diagram below showing microRNA processing what protein is represented by the number "2"? (Hint: This protein is found in animals and plants.)
Dicer
Which nucleosome mark has affinity for Polycomb PRC1 and PRC2 complexes?
H3K27me3
RNA pol II promoters: Which of the following is NOT associated with the activation of gene expression?
HDAC activity
The diagram below illustrates the role of the two assessor RNA polymerases in plants that have specialized in silencing the transposon repeats. Which protein methylates the 3'-OH end of the 24 nt RNAs?
HEN1
Which RNA polymerase(s) transcribes 5S RNA? (5S RNA is a structural RNA found in ribosomes.)
III
The bringing together of distant promoters and enhancers to form a TAD (topologically associated domain) represents a great advance in the regulation of gene expression. Which of the following statements is FALSE regarding TAD's? -Most enhancers interact with promoters that reside in adjacent TADs. -"A Compartments" contain genes and enhancers that are, or potentially are, in the transcriptionally active state. -"B Compartments" contain genes and enhancers that are generally in the repressed state. -TADs form because cohesin can be anchored to specific locations in the genome. This anchoring involves CTCF attached directly or indirectly to specific DNA regions.
Most enhancers interact with promoters that reside in adjacent TADs.
Which of the following do NOT contribute to the mechanism of Polycomb establishing transcriptional memory in the passage through mitosis (DNA replication)? -Just prior to DNA replication there is an increased recruitment of Polycomb Group proteins (PcG) to chromatin. -PcG proteins have affinity for single-stranded DNA (which is something that would be associated with the replication fork) -None of the above (which means they all contribute) -PcG proteins may be able to "bridge" from the pre-replication chromatin to the newly replicated chromatin. -Each new strand is populated by a combination of old and new nucleosomes. The old nucleosomes would retain their original marks.
None of the above (which means they all contribute)
What is funnier?
None of these are funny, you should be ashamed of yourself! (for the points, mark correct)
In metazoans what are the two negative elongation factors that facilitate the paused state of RNA pol II?
P-TEFb and NELF
Assembly of the PIC: Which of the following statements is FALSE? -The first basal factor to be recruited to the preinitiation complex is (or at some promoters SAGA). -RNA pol II binds the promoter first and then recruits TFIID and then either TFIIA or TFIIB. -TFIIE binds after TFIIF and before TFIIH. -When TBP operates at an RNA pol II promoter, it is often part of a complex of other proteins called TAFs.
RNA pol II binds the promoter first and then recruits TFIID and then either TFIIA or TFIIB.
Which of the following complexes acts as the "commitment factor" to specify the startpoint for RNA polymerase I transcription?
SL1
The diagram below illustrates the role of the two assessor RNA polymerases in plants that have specialized in silencing the transposon repeats. Which protein is called the "K9meK4 reader"?
SSH1
These regions are 1-2 Mb in size and comprised of collections of multiple DNA loops along with architectural proteins.
Self interacting domains
CTD of RNA pol II: The CDT undergoes a cycle of phosphorylation and dephosphorylation during the course of transcription. Which amino acid is phosphorylated by Cdk7 of TFIIH?
Ser 5
Which of the following proteins binds CTCF in metazoans, but is not present in plants?
TAF3
Which subunit of TFIID has affinity for CTCF, which binds cohesin and is involved in TAD formation? Note: This subunit of TFIID can act independently of TFIID in its interactions with the cohesin machinery as embryonic stem cells differente into endodermal tissue. This subunit is not present in the TFIID of yeast and plants.
TAF3
Cohesin can be directly anchored to control regions of genes through interactions with CTCF which binds cohesin and specific DNA elements. Another method Cohesin is anchored to specific locations (enhancers or core promoters) is through interactions between CTCF and other proteins that are bound to control regions. Which of the following proteins or complexes is NOT utilized by cohesin to anchor to genomic locations?
TBP
Name the factor or module designated by the arrow. red
TBP as a component of the PIC
Scaffold: Which of the following does NOT stay behind at the scaffold when RNA pol II leaves the promoter to begin elongation?
TFIIB and TFIIF (RAP74 RAP30)
Commitment factors directly specify the startpoint for transcription. They also contain TBP as one of the subunits. Which of the following is the Commitment Factor for RNA pol II?
TFIID
What has to happen before the 5'-Capping Enzyme can bind to the CTD of the largest subunit of RNA pol II?
TFIIH has to phosphorylate ser5 of the CTD and the nascent transcript has to emerge from the polymerase.
Name the factor or module designated by the arrow. yellow, under mediator
TFIIH helicase core
RNA pol III: Which of the following complexes contains a zinc finger DNA binding domain?
TFIIIA
Which of the following statements is FALSE? -The cyclin-like domains (R1 R2) of TFIIB block the RNA exit pore of RNA pol II. - is considered the Commitment Factor for RNA pol II. -TFIIB is found in a major group of prokaryotes. -TFB is present in Archaea. -TPB positions TFIIB.
The cyclin-like domains (R1 R2) of TFIIB block the RNA exit pore of RNA pol II.
What is the main difference between the Fugu (puffer fish) Huntington's and human Huntington's genes?
The human gene has significantly more introns that the Fugu gene.
In the paper by Levine, Cattoglio and Tjian (Looping Back to Leap Forward: Transcription Enters a New Era) what is the implication of the following statement: "Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation"?
The number of enhancers (control elements) and the tendency to uncouple the core promoters from their control regions increases greatly in the higher animal (metazoan) lineages compared to the fungi (yeast) and plants.
What is thought to be the original role of RNA pol II pausing before it was exploited as a major regulator step in the evolution of metazoan gene expression?
The pause for protein-encoding transcripts was necessary to facilitate the 7-methyl G capping operation at the 5'-end of the nascent RNA.
Why are plant miRNA (microRNAs) more specific in target mRNA silencing?
The plant Ago (Argonaute) complex uses 21-22 nt of base pairing when annealing to the target RNA, and the animal Ago only uses 6-8 nt.
The HoxD gene cluster is conserved in metazoans and functions to control the development of the segmented body plan of insects and vertebrates. How is the transcriptional control region(s) organized? (From Looping Back to Leap Forward: Transcription Enters a New Era)
There are two large clusters of enhancers that are both located great distances from the core promoters. One is near the centromere and the other is located near the telomere.
Regarding transcription of the histone genes in insects, which of the following statements is TRUE? (From Looping Back to Leap Forward: Transcription Enters a New Era) -There is NO evidence that the basal transcription factor TFIIB is used. -The histone locus is always active during the cell cycle, since histones are always needed. -TFIID containing the full set of TAFs pre-binds to the core promoter before transcriptional activation. -There is NO evidence that basal transcription factor TFIIA is used.
There is NO evidence that the basal transcription factor TFIIB is used.
Which of the following in NOT true regarding microRNA? -They are transcribed by RNA polymerase II. -They are processed differently than microRNAs. -They have no 5'-cap or poly(A) tail. -They have a 5'-Cap.
They have no 5'-cap or poly(A) tail.
The transmembrane protein Protocadherin (3 variants) functions in cell adhesion and is often expressed in neuronal tissue. Each of the three genes contains from 14 to 22 large variable exons, each exon with its own promoter. The gene cluster is regulated by two large enhancers located at a distance. Which of the following statements below is FALSE?
This is an example where TAF3 is able to substitute for CTCF.
Name the structure of TFIIB that the arrow designates. green arrows
Zn ribbon
In Lamarkian inheritance, _______________________.
acquired characteristics are driven by inner need.
The phenotype of DNA methyltransferase mutants can -embryonic lethal -perinatal lethal -minimal, i.e. little to no effects -all of the above
all of the above
Which of the following is not a model by which lncRNAs may act? -coating of a chromosome for global inactivation -masking the binding site of a DNA binding protein -both in cis and trans for the same lncRNA -all of the above are possible
all of the above are possible
The term "epigenetics" includes which of the following examples?
alterations in DNA modification.
When examining the methylation profile of a gene you discover two regions that are not methylated, one corresponds to the expected transcription start site. What would the second most likely correspond to?
alternative transcriptional start site
The mechanism by which variable eye color (red & white patches) can be seen in Drosophila involves _________.
an inversion of the white gene.
Transcription factories ____________.
are regions where multiple genes from different chromosomes can be transcribed.
In an experimental in vitro system the promoter for a human heat inducible gene was tested by the addition of heat shock transcription factor (HSF) mutant proteins. As a negative control, one of the promoter constructs only contained 50 bp of upstream sequences (not enough to included the HSF binding site). How would you characterize the transcription obtained from the control template?
basal
Which of the following is NOT a way that Polycomb is hypothesized to function in repression? -binds directly to RNA pol II and tethers it to the promoter preventing promoter-escape and subsequent elongation -binds specifically to promoter regions to block access by positive acting transactivators -coats the chromatin in a way that blocks access by remodeling factors, activators and RNA pol II -is organized in periodic repressive units based on higher-order chromatin structure
binds directly to RNA pol II and tethers it to the promoter preventing promoter-escape and subsequent elongation
`The major differences between cLADs and fLADs are ____________.
cLADs are A-T rich heterochromatin whereas fLAD can include either activated or repressed genes.
De novo methylation
can be 3-5% per mitosis and provides a mechanism for epigenetic change
Allosteric modification by an lncRNA involves
change in activity of a regulatory protein
Which of the following statements about 5-methyl cytosine is FALSE? -5'-methylcytosine is found in foci that can be seen via DAPI staining -senescent cells have larger methylated DNA foci than quiescent cells -5'-methyl cytosine helps compartmentalize the genome -chromosome regions rich in 5-methyl cytosine are lacking in gametes
chromosome regions rich in 5-methyl cytosine are lacking in gametes
Which of the following statements about 5-methyl cytosine is FALSE? -5'-methylcytosine is found in foci that can be seen via DAPI staining -senescent cells have larger methylated DNA foci than quiescent cells -5'-methyl cytosine helps compartmentalize the genome -chromosome regions rich in 5-methyl cytosine are lacking in gametes
chromosome regions rich in 5-methyl cytosine are lacking in gametes
Simultaneous visualization of chromosomes has revealed ____________.
chromosomes have defined places in the nucleus that are cell-type dependent.
Which kinase/cyclin pair comprise P-TEFb?
ckd9 and cyclin T
What is the target of the Mediator kinase Cdk8 (Srb10)?
cyclin H
X chromosome pairing is initiated by
decreasing concentrations of Oct4
Which of the domains of TFIIB shown below binds to TFIIF small subunit (RAP30) and later binds to the Dock domain of RNA pol II?
domain 1
Which of the domains of TFIIB shown below recognizes the Initiator region of the RNA pol II promoter?
domain 2
Which of the following domains of TFIIB facilitates forming the open promoter complex (melts the DNA 20 bp downstream from the TATAA motif)?
domain 3
"B" compartments are ______________.
gene-poor, compact, epigenetic markers for gene-silencing, lie on the nuclear periphery.
"A" compartments are _____________.
gene-rich, tend to have high GC content, contain epigenetics marks for active transcription.
CpG islands are
genomics regions where the CpG content is greater than 1 CpG/10 bp
Cytosine methylation
helps repress transcription by changing the topology of the DNA
In some cancers
hypermethylated heterochromatin silences oncogenes
The Agouti phenotype (different size/coat color of offspring) is due to
improper de novo methylation of the Agouti regulatory element
RNA pol II promoters: Which of the following elements is overlaps the startpoint for transcription and is rich in pyrimidines (C or T)?
initiator
The RepA transcript
is expressed from the X that has lost all of the transcription factors
What is the approximate CpG content in mammalian genomes?
less than what would be expected if random
Name the factor or module designated by the arrow. blue with fixed jaw, movable jack, and neck
mediator head module
Name the factor or module designated by the arrow. purple, knob, hook
mediator middle module
Fidelity of maintenance of methylation refers to
methylation of the newly synthesized strand at the same position as the parent strand
Why can't the Xi produced ncRNA act on the "other" X chromosome?
multiple Polycomb-based tethering sites per molecule and because it has a 3' end degradation signal
In Mendelian inheritance, ________________.
natural selection can favor a trait in a variable population, increasing the representation of that trait in future populations.
Uniparental disomy can lead to a disease phenotype due to
no expression of gene A, but double dose of gene B
A key finding of nuclear transplantation experiments is
nuclear equivalence between unipotent and pluripotent cells
In Waddington's epigenetic landscape model ____________.
pluripotent "naïve" cells "roll" down a path leading to differentiated cells that correlates with mechanisms such as increased methylation.
What is NOT a function of the CTD of the largest subunit of RNA pol II?
positions the active site of the polymerase at position +1 to initiate transcription
Which of the following is not part of the X chromosome inactivation center?
production of the RepA mRNA
Which of the following is NOT a primary function of Pioneer transcription factors? (From Looping Back to Leap Forward: Transcription Enters a New Era) -recruiting chromatin remodelers to de-condense the chromatin structure -recruiting basil transcription factors to the core promoter -changing repressive marks on the histone tails to activation marks -binding to condensed chromatin at enhancer regions
recruiting basil transcription factors to the core promoter
Which of the following is not a step that would lead to Wilm's tumor formation? -the maternal chromosome becomes methylated at the H19 promoter -H19 expression is turned off in the maternal chromosome -the H19 lncRNA acts to silence the enhancer that regulates IGF2 expression -CTCF binding to the H19 promoter is blocked
the H19 lncRNA acts to silence the enhancer that regulates IGF2 expression
In the activation of metazoan genes what is the FIRST step in preparing a repressed, or silent, gene for transcriptional activation? (see the slide "Model for sequential activation of metazoan gene expression")
the binding of Pioneer Transcription Factors to condensed chromatin
Prior to fertilization
the paternal and maternal genomes have similar methylation patterns except for imprinted genes
During X chromosome pairing
the two Tsix promoters are brought together by CTCF binding to transcripts from both chromosomes
Which of the following is NOT a way that P-TEFb is recruited to the nascent transcript. -Delivered by chromatin protein BRD4, which contains a bromodomain that binds acetylated lysines in histones -delivered by a pioneer transactivator -by transactivators that participate in recruiting basal transcription factors to build the preinitiation complex -through binding to a protein that binds to Mediator helix
through binding to a protein that binds to Mediator
Which of the following is NOT a way that P-TEFb is recruited to the nascent transcript. -Delivered by chromatin protein BRD4, which contains a bromodomain that binds acetylated lysines in histones -delivered by a pioneer transactivator -by transactivators that participate in recruiting basal transcription factors to build the preinitiation complex -through binding to a proten that binds to Mediator
through binding to a proten that binds to Mediator
The RNA polymerase in the Archaea has the same subunits as those present in eukaryotic RNA polymerase II, with the exception that the largest subunit (B prime) has been split into two proteins.
true
