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nature portfolio privacy policy 5ʹ-/5phos/ctgctgact/ibiodt/ggaccgtcggacc-3ʹ index rv primer pre-warmed phosphate-buffered saline poly-l-lysine-coated dishes advertising ultra end-repair/da-tailing module io/picard/ identify genome-wide rna–chromatin benjamini–hochberg multiple-testing correction discriminate cell-type-specific features stable nature genome-wide rna-chromatin interactions marie-skłodowska curie actions reprints double-stranded cdna–dna complexes radicl-seq outperformed grid-seq swedish research council radicl-seq dna-binding patterns sequencing primer 5ʹ-acactctttccctacacgacgctcttccgatct-3ʹ robust rna–dna-interacting loci c-mapped paired-end reads actd-treated radicl-seq libraries malat1-decorated protein-coding genes preferentially open resulting rna–adapter–dna chimera grid-seq captures considerably cell-type-specific manner nature nature 565 nature 539 nature 485 cancer research uk cell-type-specific patterns high-resolution promoterome mining radicl-seq identifies general cell type–specific principles air-dried bead–nuclei mixture mouse neural development pregastrulation mammalian development repeat elements differentially engage fully double-stranded dna proliferation media consisting genome-wide interaction plots maps genome-wide rna 5ʹ-/5phos/ctgctgctccttccctttccccttttggtccgacggtccaagtcagcagt-3ʹ 5ʹ-/5phos/ggccctccaaaaggagggca-3ʹ 5ʹ-/5phos/gatcggaagagcgtcgtgtagggaaagagtgt-3ʹ y-shaped sequencing linkers

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         description: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. Mammalian genomes encode tens of thousands of ncRNAs that have important roles in regulation of gene expression and chromatin organization. Here, the authors present RADICLseq to map RNA-chromatin interactions in intact nuclei to shed light on these fine-tuned processes.
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      headline:RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions
      description: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. Mammalian genomes encode tens of thousands of ncRNAs that have important roles in regulation of gene expression and chromatin organization. Here, the authors present RADICLseq to map RNA-chromatin interactions in intact nuclei to shed light on these fine-tuned processes.
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      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
      name:The Francis Crick Institute, London, UK
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy
      name:Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, UK
      name:MRC London Institute of Medical Sciences, London, UK
      name:Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, UK
      name:MRC London Institute of Medical Sciences, London, UK
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:School of Computer Science, McGill University, Montréal, Canada
      name:Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, Canada
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Science, Moscow, Russia
      name:Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
      name:Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:The Francis Crick Institute, London, UK
      name:UCL Genetics Institute, University College London, London, UK
      name:Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan
      name:School of Computer Science, McGill University, Montréal, Canada
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, UK
      name:MRC London Institute of Medical Sciences, London, UK
      name:Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
      name:Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
      name:Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy
      name:KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), Division of Biological Environmental Sciences and Engineering, Thuwal, Saudi Arabia
      name:RIKEN Center for Integrative Medical Sciences, Yokohama, Japan

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