Instructions: Answer all questions to the best of your ability; partial credit will be granted where appropriate. You may write or type your responses on additional sheets. You may consult your textbook and your notes. You may NOT consult other individuals or the broader internet. Your signature (typed or electronically signed) at the end confirms your willingness to abide by these rules. (40 points total). All of the questions of this project relate to the following abstract. The sentences of the abstract have been numbered to help you organize your answers. (1) WUSCHEL (WUS) is critical for plant meristem maintenance and determinacy in Arabidopsis, and the regulation of its spatiotemporal expression patterns is complex. (2) We previously found that AGAMOUS (AG), a key transcription factor in floral organ identity and floral meristem determinacy, can directly suppress WUS expression through the recruitment of the Polycomb group (PcG) protein TERMINAL FLOWER 2 (TFL2) at the WUS locus; however, the mechanism by which WUS is repressed remains unclear. (3) Here, we found that two specific regions flanking the WUS gene body bound by AG and TFL2 form a chromatin loop that is directly promoted by AG during flower development in a manner independent of the physical distance and sequence content of the intervening region. (4) Moreover, AG physically interacts with TFL2, and TFL2 binding to the chromatin loop is dependent on AG. (5) By mutating the regulatory region, we showed that the WUS chromatin loop represses gene expression by blocking the recruitment of RNA polymerase II at the locus. (6) The findings uncover the WUS chromatin loop as another regulatory mechanism controlling WUS expression, and also shed light on the factors required for chromatin conformation change and their recruitment. Part A: Use your notes to answer each of these to the best of your ability. Answers should be between 1 sentence and 1 paragraph. (3 points each) 1. In a previous genome-wide study, WUS was one of many genes that increased in gene expression in response to changing temperature. In a genomics experiment, multiple-test correction is used. Why is multiple test correction necessary? Describe one way in which it could be completed. 2. Clustering is a tool for organizing large datasets, and can be considered “hypothesis generating”. Describe two kinds of information can you infer from clusters of genomic data. 3. TFL2 is known to repress FLC, a gene required for vernalization (plants knowing that winter is passed before flowering). Draw or describe the mechanism by which FLC is repressed by cold temperatures. Make sure to discuss at least two epigenetic mechanisms involved in this repression. 4. Flowering plants must regenerate new cell types (flowers) each season. This requires maintaining a population of stem cells that retains the information for future differentiation. Assuming that plant stem cells are similar to mammalian stem cells, how might these stem cells maintain ‘poised’ gene expression, which can be resolved (active or repressed) during final differentiation?
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