Updated and validated global cis-regulatory element map which includes the M/m sex-determining region of Aedes aegypti

Formaldehyde assisted isolation of regulatory element (FAIRE) enrichment was used to recover open chromatin from A. aegypti embryos. Next-generation sequencing of FAIRE DNA was performed. Computational detection and analysis of FAIRE-enriched DNA sequences followed. For each of three biological replicates, A. aegypti eggs were collected for two hours and aged until 49-51 hrs after egg laying, at which point they were used as starting material for preparation of FAIRE-enriched DNA. The FAIRE DNA enrichment protocol involved formaldehyde crosslinking and shearing of chromatin, followed by phenol chloroform extraction to recover open promoter regions from the aqueous phase. Next-generation Illumina sequencing followed by computational detection and analysis of FAIRE-enriched sequences followed.