Jul 5, 2016

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

BioRxiv : the Preprint Server for Biology
Jose Arturo Gutierrez-TrianaJoachim Wittbrodt

Abstract

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.

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Mentioned in this Paper

Computer Software
Genome
DNA Modification Methylases
Protein-Protein Interaction
Binding Protein
Nuclear mRNA Cis Splicing, via Spliceosome
RNA Splicing
Chromatin Location
Methyltransferase
Analysis

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