RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions
| Autor: | Charles Plessy, Mathieu Blanchette, Yulia A. Medvedeva, Marco Ghilotti, Samudyata, Piero Carninci, Saumya Agrawal, Gonçalo Castelo-Branco, Alessandro Bonetti, Erik Arner, Valerio Orlando, Takeya Kasukawa, Shuhei Noguchi, Nicholas M. Luscombe, Matthew Valentine, Kosuke Hashimoto, Kaori Kashi, Juliette Gimenez, Joachim Luginbuehl, Federico Agostini, Michiel J. L. de Hoon, Alexander J Nash, Eneritz Agirre, Leonie Roos, Giovanni Pascarella, Boris Lenhard, Christopher J. F. Cameron, Riccardo Cazzoli, Ana Maria Suzuki |
|---|---|
| Jazyk: | angličtina |
| Předmět: |
0301 basic medicine
RNA Untranslated Transcription Genetic Science General Physics and Astronomy Computational biology Biology ENCODE Genome Article General Biochemistry Genetics and Molecular Biology Chromatin remodeling DNA sequencing Cell Line chemistry.chemical_compound 03 medical and health sciences Mice 0302 clinical medicine Transcription (biology) Animals Genomic library lcsh:Science Author Correction 030304 developmental biology Gene Library Regulation of gene expression Cell Nucleus 0303 health sciences Multidisciplinary Sequence Analysis RNA Biological techniques RNA Chromosome Mapping High-Throughput Nucleotide Sequencing Mouse Embryonic Stem Cells General Chemistry Chromatin Assembly and Disassembly Chromatin 030104 developmental biology chemistry lcsh:Q DNA Nuclear localization sequence 030217 neurology & neurosurgery |
| Zdroj: | Nature Communications Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020) |
| ISSN: | 2041-1723 |
| DOI: | 10.1038/s41467-020-14337-6 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|