Define “histone code hypothesis” and give two examples.

  Question 1: (2 pts) Define “histone code hypothesis” and give two examples. Question 2: (4 pts) Describe mechanisms by which a sequence-specific DNA-binding transcription activator may activate transcription. Question 3: (3 pts) Describe three mechanisms how the activity of a given transcription factors can be regulated. Question 4: (11 pts) You are studying structure-function relationship of a novel transcription factor, Ying. Ying was isolated as an interacting partner of another transcription factor, Yang, through a yeast twohybrid screen. Ying and Yang form heterodimers to bind DNA that contains a 5’-AGGTCA-XXXXXAGGTCA-3’ motif. Sequence analyses indicate that such sequence motif is present between 450 to 500 base pairs upstream of transcription initiation site of gene PEACE. You hypothesize that gene PEACE is a putative target gene of the Ying:Yang heterodimers. You need to include all the controls in your answers. Assume that you have all the necessary reagents for your experiments. 1. (3 pts) Name and describe an in vitro assay that allows you to conclude that the Ying:Yang heterodimers directly bind this putative binding site of PEACE. 2. (3 pts) Your collaborator has recently identified the hormone Harmony (H) as a physiological ligand for Ying. You hypothesize that hormone H binds and activates transcription activity of Ying:Yang heterodimers. Name a cell-based assay and describe the experiments and the anticipated results to test your hypothesis. 3. (5 pts) Unliganded Ying is localized in the cytosol. Harmony (H)-bound Ying translocates to the nucleus, where it heterodimerizes with Yang and binds their cognate sites. Ying:Yang heterodimers bind the “putative” binding site in the regulatory region of the gene PEACE in response to H treatment (see figure). PCAF is a potent histone H3-K9 acetyltransferase. You recently showed that H-bound Ying:Yang heterodimers bind PCAF in vitro. You hypothesize that in vivo (cells), Ying:Yang recruits PCAF to the “putative” binding site of PEACE in response to the hormone H. If this model is correct, describe an assay and the anticipated results to test your hypothesi