iDamIDseq and iDEAR: An improved method and a computational pipeline to profile chromatin-binding proteins of developing organisms

DNA adenine methyltransferase identification (DamID) has emerged as an alternative for profiling protein-DNA interactions, however critical issues in the method limit its applicability. Here we present iDamIDseq, a protocol that improves specificity and robustness making its use compatible with developing organisms. In addition, we present the analysis tool iDEAR (iDamIDseq Enrichment Analysis with R) to determine protein-DNA interactions genome wide. The combination of both allows establishing highly reliable transcription factor profiles, even in transient assays. For tissue specific expression we improved the Dam coding sequence to overcome predominant aberrant splicing of Dam fusions we discovered with the commonly used sequence.