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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 1 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 2