The Venn diagram on the right shows results from RNA-seq and ChiP-seq experiment

Question

The Venn diagram on the right shows results from RNA-seq and ChiP-seq experiments designed to find Pax6 target genes, as we discussed in class. Transcription factors have two major domains: a protein-protein interaction domain and a sequence-specific binding damain. In total, 559 genes (483 + 76 in venn Diagram) were found by RNA-seq to be differentially expressed in wild type vs. Pax6 mutant eye precursor cells. Of these genes, only 76 were identified in the ChlP-seq experiment. Therefore the majority of differentially expressed genes identified by the RNA-seq experiment are: (circle best answer) direct/indirect targets of Pax6. 2235 (2259 + 76 in Venn Diagram) genes were immunoprecipitated in the Pax6 Chip-seq experiment, indicating that Pax6 binds in their vicinity in eye precursor cells. However, of these genes, only 76 were found to be differentially expressed in the RNA-seq experiment. Therefore, Pax6 is: (circle best answer) necessary unnecessary for expression of the majority of genes it is bound to in eye precursor cells. Imagine that Pax6 directly activates the expression of Gene X and that Gene X encodes a transcription factor. "TF-X", that directly activates Gene Y. In this scenario, Pax6 does not bind anywhere near Gene Y In the Venn Diagram above, Gene X would be in which set? (circle best answer) A B C In the Venn Diagram above, Gene Y would be in which set? (circle best answer) A B C E. Using DNA diagrams like the ones in part D above. draw an illustration of what a gene in Group C (from the above Venn diagram) would look like.

Explanation / Answer

1. Transcription factor is modular in structure and contains the following domains: DNA binding domain(DBD), which attaches to specific sequences of DNA. Trans activating domain (TAD), which contains binding sites for other proteins. So, the answer is DNA binding domain.

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