RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

• DOI: 10.1101/681924
• Publication Date: 2019-06-28T02:34:39Z
• Authors: Alessandro Bonetti; Federico Agostini; Ana Maria Suzuki; Kosuke Hashimoto; Giovanni Pascarella; Juliette Gimenez; Leonie Roos; Alex J. Nash; Marco Ghilotti; Christopher JF Ca...; Matthew Valentine; Yulia A Medvedeva; Shuhei Noguchi; Eneritz Agirre; Kaori Kashi; Samudyata; Joachim Luginbuehl; Riccardo Cazzoli; Saumya Agrawal; Nicholas M Luscombe; Mathieu Blanchette; Takeya Kasukawa; Michiel De Hoon; Erik Arner; Boris Lenhard; Charles Plessy; Gonçalo Castelo-B...; Valerio Orlando; Piero Carninci
• Keywords: ChIA-PET; ENCODE; Transcription; Chromosome conformation capture

Abstract Mammalian genomes encode tens of thousands noncoding RNAs. Most transcripts exhibit nuclear localization and several have been shown to play a role in the regulation gene expression chromatin remodelling. To investigate function such RNAs, methods massively map genomic interacting sites multiple developed. However, they still present some limitations. Here, we introduce R NA A nd D Interacting C omplexes L igated seq uenced (RADICL-seq), technology that maps genome-wide RNA-chromatin interactions intact nuclei. RADICL-seq is proximity ligation-based methodology reduces bias for nascent transcription, while increasing coverage unique mapping rate efficiency compared existing methods. identifies distinct patterns genome occupancy different classes as well cell type-specific interactions, emphasizes transcription establishment structure.