Faculty Leader: Cliff Lowell

Microbiology 204 Discussion Session #2 October 12, 2016 1-2:30PM HSW1057 Faculty leader: Cliff Lowell

Koues et al., Distinct gene regulatory pathways for human innate versus adaptive lymphoid cells. Cell 165:1134-1146, 2016 Everyone should read this paper before coming to class. You do not need to read the supplemental materials and supplemental figures, although the Discussion Leader may choose to have the class discuss one or a few supplemental figures.

See below if you have an assignment, in which case you have some additional preparation for class. Assignments rotate among the students.

LEARNING OBJECTIVES: To learn some of the lineage relationships between ILCs and conventional T-cells. To become acquainted with whole genome methodologies for analysis of gene expression/function.

STUDENT ASSIGNMENTS 1. Discussion leader (see instruction page for advice on leading the discussion) 2. Describe the methods and results for Fig. 1. What is PCA analysis? You will have to look this up in Wikipedia or something and explain to the group how it works! 3. In Fig. 1F, describe the ingenuity pathway analysis. How does signaling in ILCs differ from that of Th subsets? What are the primary ligands that drive ILCs versus Th cells? 4. For Fig. 2, describe the methods used. What is ATAC-seq? What is Chip-seq using H3K4me3 and H3K27Ac marks? What do you conclude from this figure and how does it compare to Fig. 1? 5. For Fig. 3, what is HOMER? How does the data in this figure compare to Fig. 1 and Fig. 2 6. Review Fig 4. What are the differences between super enhancers and conventional enhancers and which are more “unique” to any give ILC or Th cell lineage. Compare the lineage specificity of super enhancers versus conventional enhancers. 7. In Fig. 4, what lineage restricted cells are revealed by analysis of super enhancers? 8. In Fig. 6, they compare location of super enhancers with SNPs for autoimmunity as determined by GWAS. Describe what SNP and GWAS are and how many SNPs ended up in super enhancer regions. What function do these SNPs usually affect (gene coding regions or gene regulatory regions?).

Student assignment #s

1. Camille Simoneau 10. Germain Yong 2. Patrick Schupp 11. Didi Zhu 3. Elise Wollf 12. Jeanmarie Gonzalez 4. Cindy Tian 13. Parinaz Fozouni 5. Kristine Tan 14. Priya Mohindra 6. Joe Hiatt 7. Theo Ross 8. Tina Solvik 9. Ariane Panzer

(NOTE : if you will miss a discussion session, inform Dr. Lowell in advance; if assignments have already been made, you should additionally make a trade with one of your classmates who does not have an assignment that week so that your assignment is covered).