The geneticist in Q5. identified a new developmental gene called gappy. When the gene is deleted it completely abolished the latter half of developing mosquito larvae.

Question

Excited at the new results the geneticist was interested in searching for the cis regulatory elements that control the expression of gappy. The geneticist heard genetic regions called conserved noncoding sequences (CNS) during a meeting and was interested in finding the CNS surrounding the gappy gene. (A) How would the geneticist look for CNS around the gappy gene region? (B) Once identified how would the geneticist test a CNS is regulating gappy gene?

Answer 1

 I would recommend an RNA-Seq over a microarray, since the purpose is to identify "undescribed genes." RNA-Seq offers greater specificity and is therefore better at detecting different isoforms. Likewise, RNA-seq has greater sensitivity then microarray which will allow you to identify more detect differential expression patterns.