Skim through A comparative encyclopedia of DNA elements in the mouse genome: http://www.nature.com/nature/journal/v515/n7527/pdf/nature13992.pdf and answer the following questions.
1) What types of experimental techniques were used to investigate the mouse regulatory landscape?
2) How does the conservation between mouse and human of the cis-regulatory regions differ from that of the transcription factor network?
3) Based upon the paper and what you learned from the phylogenetic or BLAST lab, briefly describe how mouse-human orthologs may have been determined.
4) What is significant about immune system related genes in terms of their level of conservation? Why may this be?
Part 2: Enhancers & Epigenetics
Skim the following paper on enhancers: http://www.nature.com/nrg/journal/v15/n4/full/nrg3682.html and answer the following questions.
1) What is an enhancer?
2) What epigenetic marks are characteristic of an enhancer? What other features can be used to identify enhancers?