RT Journal Article
SR Electronic
T1 iDamIDseq and iDEAR: An improved method and a computational pipeline to profile chromatin-binding proteins of developing organisms
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 062208
DO 10.1101/062208
A1 Jose Arturo Gutierrez-Triana
A1 Juan L. Mateo
A1 David Ibberson
A1 Joachim Wittbrodt
YR 2016
UL http://biorxiv.org/content/early/2016/07/05/062208.abstract
AB 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 iDamlDseq, a protocol that improves specificity and robustness making its use compatible with developing organisms. In addition, we present the analysis tool iDEAR (iDamlDseq 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.