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Identification of Rx2 binding loci in medaka by iDamID-seq

ABSTRACT: We have improved the DamID method to make it applicable for vertebrate life specimens. We use iDamID-seq to profile the binding profile of the transcription factor Rx2 in medaka embryos at stage 22 of development. We compare two replicates of the fusion Dam-Rx2 against two replicates of the fusion Dam-GFP as control. Medaka embryos at 1-cell stage were injected with mRNA transcribed in vitro from one of the two Dam fusions. The embryos were allowed to grow in normal conditions up to stage 22. The genomic DNA was isolated and treated to extract only the DpnI fragments that had adenine methylation. These fragments were subjected to deep sequencing.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryzias latipes

SUBMITTER: Arturo Gutierrez-Triana

PROVIDER: E-MTAB-4610 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins.

Gutierrez-Triana Jose Arturo JA Mateo Juan L JL Ibberson David D Ryu Soojin S Wittbrodt Joachim J

Development (Cambridge, England) 20161005 22

DNA adenine methyltransferase identification (DamID) has emerged as an alternative method to profile protein-DNA interactions; however, critical issues limit its widespread applicability. Here, we present iDamIDseq, a protocol that improves specificity and sensitivity by inverting the steps DpnI-DpnII and adding steps that involve a phosphatase and exonuclease. To determine genome-wide protein-DNA interactions efficiently, we present the analysis tool iDEAR (iDamIDseq Enrichment Analysis with R) ...[more]

PMID: 27707796

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