Identification of Tox chromatin binding properties and downstream targets by DamID-Seq

Benedetta Artegiani, António Miguel de Jesus Domingues, Andreas Dahl, Federico Calegari

Onderzoeksoutput: Bijdrage aan tijdschriftArtikelpeer review

Samenvatting

In recent years, DNA adenine methyltransferase identification (DamID) has emerged as a powerful tool to profile protein-DNA interaction on a genome-wide scale. While DamID has been primarily combined with microarray analyses, which limits the spatial resolution and full potential of this technique, our group was the first to combine DamID with sequencing (DamID-Seq) for characterizing the binding loci and properties of a transcription factor (Tox) (sequencing data available at NCBI's Gene Expression Omnibus under the accession number GSE64240). Our approach was based on the combination and optimization of several bioinformatics tools that are here described in detail. Analysis of Tox proximity to transcriptional start sites, profiling on enhancers and binding motif has allowed us to identify this transcription factor as an important new regulator of neural stem cells differentiation and newborn neurons maturation during mouse cortical development. Here we provide a valuable resource to study the role of Tox as a novel key determinant of mammalian somatic stem cells during development of the nervous and lymphatic system, in which this factor is known to be active, and describe a useful pipeline to perform DamID-Seq analyses for any other transcription factor.

Originele taal-2Engels
Pagina's (van-tot)264-8
Aantal pagina's5
TijdschriftGenomics data
Volume7
DOI's
StatusGepubliceerd - mrt. 2016
Extern gepubliceerdJa

Vingerafdruk

Duik in de onderzoeksthema's van 'Identification of Tox chromatin binding properties and downstream targets by DamID-Seq'. Samen vormen ze een unieke vingerafdruk.

Citeer dit