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

A. Bonetti, F. Agostini, A.M. Suzuki, K. Hashimoto, G. Pascarella, J. Gimenez, L. Roos, A.J. Nash, M. Ghilotti, C.J.F. Cameron, M. Valentine, Y.A. Medvedeva, S. Noguchi, E. Agirre, K. Kashi, Samudyata, J. Luginbühl, R. Cazzoli, S. Agrawal, N.M. LuscombeM. Blanchette, T. Kasukawa, M. Hoon, E. Arner, B. Lenhard, C. Plessy, G. Castelo-Branco, V. Orlando, P. Carninci

Research output: Contribution to journalArticlepeer-review


Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed; however, these methods have some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA–chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared with existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type–specific RNA-chromatin interactions, and highlights the role of transcription in the establishment of chromatin structure. © 2020, The Author(s).
Original languageEnglish
JournalNat. Commun.
Issue number1
Publication statusPublished - 2020


  • cell
  • complexity
  • DNA
  • gene expression
  • genome
  • ligand
  • RNA
  • article
  • chromatin structure
  • transcription initiation
  • animal
  • cell line
  • cell nucleus
  • chromatin
  • chromatin assembly and disassembly
  • chromosomal mapping
  • gene library
  • genetic transcription
  • genetics
  • high throughput sequencing
  • metabolism
  • mouse
  • mouse embryonic stem cell
  • procedures
  • sequence analysis
  • Mammalia
  • untranslated RNA
  • Animals
  • Cell Line
  • Cell Nucleus
  • Chromatin
  • Chromatin Assembly and Disassembly
  • Chromosome Mapping
  • Gene Library
  • High-Throughput Nucleotide Sequencing
  • Mice
  • Mouse Embryonic Stem Cells
  • RNA, Untranslated
  • Sequence Analysis, RNA
  • Transcription, Genetic


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