Literature DB >> 35103969

Profiling Protein-DNA Interactions Cell-Type-Specifically with Targeted DamID.

Owen J Marshall1, Caroline Delandre2.   

Abstract

Targeted DamID (TaDa) is a means of profiling the binding of any DNA-associated protein cell-type specifically, including transcription factors, RNA polymerase, and chromatin-modifying proteins. The technique is highly sensitive, highly reproducible, requires no mechanical disruption, cell isolation or antibody purification, and can be performed by anyone with basic molecular biology knowledge. Here, we describe the TaDa method and downstream bioinformatics data processing.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  DamID; Gene transcription; Protein-DNA interactions; Targeted DamID; Transcription factors

Mesh：

Substances：

Year:  2022        PMID： 35103969     DOI： 10.1007/978-1-0716-2140-0_11

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  15 in total

1.  Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase.

Authors:  B van Steensel; S Henikoff
Journal:  Nat Biotechnol       Date:  2000-04       Impact factor: 54.908

2.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.

Authors:  Lars Guelen; Ludo Pagie; Emilie Brasset; Wouter Meuleman; Marius B Faza; Wendy Talhout; Bert H Eussen; Annelies de Klein; Lodewyk Wessels; Wouter de Laat; Bas van Steensel
Journal:  Nature       Date:  2008-05-07       Impact factor: 49.962

3.  Chromatin profiling using targeted DNA adenine methyltransferase.

Authors:  B van Steensel; J Delrow; S Henikoff
Journal:  Nat Genet       Date:  2001-03       Impact factor: 38.330

4.  Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing.

Authors:  Owen J Marshall; Tony D Southall; Seth W Cheetham; Andrea H Brand
Journal:  Nat Protoc       Date:  2016-08-04       Impact factor: 13.491

5.  DNA N6-methyladenine in metazoans: functional epigenetic mark or bystander?

Authors:  Guan-Zheng Luo; Chuan He
Journal:  Nat Struct Mol Biol       Date:  2017-06-06       Impact factor: 15.369

6.  damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.

Authors:  Owen J Marshall; Andrea H Brand
Journal:  Bioinformatics       Date:  2015-06-25       Impact factor: 6.937

7.  Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells.

Authors:  Tony D Southall; Katrina S Gold; Boris Egger; Catherine M Davidson; Elizabeth E Caygill; Owen J Marshall; Andrea H Brand
Journal:  Dev Cell       Date:  2013-06-20       Impact factor: 12.270

8.  Chromatin state changes during neural development revealed by in vivo cell-type specific profiling.

Authors:  Owen J Marshall; Andrea H Brand
Journal:  Nat Commun       Date:  2017-12-22       Impact factor: 14.919

9.  RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites.

Authors:  Seth W Cheetham; Andrea H Brand
Journal:  Nat Struct Mol Biol       Date:  2017-12-18       Impact factor: 15.369

10.  Drosophila intestinal stem and progenitor cells are major sources and regulators of homeostatic niche signals.

Authors:  David P Doupé; Owen J Marshall; Hannah Dayton; Andrea H Brand; Norbert Perrimon
Journal:  Proc Natl Acad Sci U S A       Date:  2018-11-07       Impact factor: 11.205
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