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Exercise for BCM-1
Week 10 (Constam)
November 17, 2014
1) True/false: CpG islands are regions in the genome that are protected
against de novo methylation both in early embryos and in gametes by
specific TFs such as Sp1
2)
a.
b.
c.
d.
DNase Hypersensitivity Assays are useful
to identify relatively open regions in chromatin
to map candidate gene regulatory regions
to distinguish regions of CpG methylation from CpG islands
to determine the DNA footprint of a transcription factor
3) True/false: A role for GATA-1 in megakaryocytes has been confirmed by
a. the accumulation of undifferentiated, rapidly proliferating
megakaryocyte/erythrocyte progenitors in a subset of leukemia patients
b. the lack of blood platelets in female mice lacking one copy of Gata1
c. targeted deletion of a hematopoietic cell-specific enhancer in the Gata1
regulatory region
d. promoter bashing studies showing that a fragment of the Gata1
regulatory region can direct lacZ expression in megakaryocytes
4) Feed-forward loops in gene regulatory networks
a. describe the behavior e.g. of AP-1 complexes or myogenic TFs such as
MyoD to amplify their own expression
b. accelerate the induction of target genes
c. delay the induction of target genes and filter specific signals from
randomly fluctuating inputs ('noise')
d. often act on super-enhancers
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5) In mammalian embryos, Sox2 and the POU domain factor Oct4 are
required at the blastocyst stage to specify the pluripotent inner cell mass
(ICM) cells that give rise to all cells and tissues of the future body. Forced
expression of these 2 factors together with c-Myc and Klf4 (a Krüppel-like
zinc finger TF) in differentiated cells is sufficient to induce their
"reprogramming". Which one of the following statements is not entirely
correct:
a. Reprogramming describes a process of induced cell de-differentiation to
a pluripotent state
b. All of these reprogramming factors ('KSOM') activate genes that control
specific developmental processes and stem cell self-renewal
c. Multiple reprogramming factors synergize by simultaneously binding to
so-called super-enhancers
d. ES cell-specific super-enhancers facilitate the recruitment of such
pioneer factors to closed chromatin
e. Reprogramming factors recruit Tet enzymes to convert 5-methyl
cytosines to 5-hydroxymethyl cytosine and thereby trigger CpG
demethylation
6) R26RLSL reporter mice carry the stop-floxed lacZ cassette in the
ubiquitously expressed Rosa26 locus. The R26RLSL reporter has been
engineered for genetic lineage tracing, e.g. to trace the fate of MyoDexpressing myoblasts. If you cross R26RLSL reporter into Sox2+/Cre mice which
express Cre recombinase from the Sox2 locus, which cells and tissues will
switch on the lacZ reporter allele?
7) True/false: Dosage compensation of sex chromosomes in mammals is
achieved by
a. by inactivating one X-chromosome of female cells in so-called 'Barr
bodies'
b. by transcribing the long non-coding Xist RNA from the XIC region on the
X-chromosome
c. by recruiting a repressive histone (macroH2A) and repressive histone
methyl-transferases to the inactive X
d. through widespread de novo DNA methylation
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