Blar i Bergen Open Research Archive på forfatter "Carninci, Piero"

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    • CAGEr: Precise TSS data retrieval and high-resolution promoterome mining for integrative analyses 

      Haberle, Vanja; Forrest, Alistair R.R.; Hayashizaki, Yoshihide; Carninci, Piero; Lenhard, Boris (Peer reviewed; Journal article, 2015)
      Cap analysis of gene expression (CAGE) is a high-throughput method for transcriptome analysis that provides a single base-pair resolution map of transcription start sites (TSS) and their relative usage. Despite their high ...

    • Complex Loci in Human and Mouse Genomes 

      Engström, Pär G.; Suzuki, Harukazu; Ninomiya, Norika; Akalin, Altuna; Sessa, Luca; Lavorgna, Giovanni; Brozzi, Alessandro; Luzi, Lucilla; Lam Tan, Sin; Yang, Liang; Kunarso, Galih; Lian-Chong, Edwin Ng; Batalov, Serge; Wahlestedt, Claes; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Wells, Christine; Bajic, Vladimir B.; Orlando, Valerio; Reid, James F.; Lenhard, Boris; Lipovich, Leonard (Peer reviewed; Journal article, 2006-04-28)
      Mammalian genomes harbor a larger than expected number of complex loci, in which multiple genes are coupled by shared transcribed regions in antisense orientation and/or by bidirectional core promoters. To determine the ...

    • Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis 

      Nepal, Chirag; Hadzhiev, Yavor; Previti, A. Christopher; Haberle, Vanja; Li, Nan; Takahashi, Hazuki; Suzuki, Ana Maria; Sheng, Ying; Abdelhamid, Rehab; Anand, Santosh; Gehrig, Jochen; Akalin, Altuna; Kockx, Christel E.M.; van der Sloot, Antoine A.J.; van Ijcken, Wilfred F.J.; Armant, Olivier; Rastegar, Sepand; Watson, Craig; Strähle, Uwe; Stupka, Elia; Carninci, Piero; Lenhard, Boris; Müller, Ferenc (Peer reviewed; Journal article, 2013)
      Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in ...

    • Evolutionary turnover of mammalian transcription start sites 

      Frith, Martin C.; Ponjavic, Jasmina; Fredman, David; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Sandelin, Albin (Peer reviewed; Journal article, 2006-05-06)
      Alignments of homologous genomic sequences are widely used to identify functional genetic elements and study their evolution. Most studies tacitly equate homology of functional elements with sequence homology. This assumption ...

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

      Bonetti, Alessandro; Agostini, Federico; Suzuki, Ana Maria; Hashimoto, Kosuke; Pascarella, Giovanni; Gimenez, Juliette; Roos, Leonie; Nash, Alex J.; Ghilotti, Marco; Cameron, Christopher J.  F.; Valentine, Matthew; Medvedeva, Yulia A.; Noguchi, Shuhei; Agirre, Eneritz; Kashi, Kaori; Samudyata, Samudyata; Luginbühl, Joachim; Cazzoli, Riccardo; Agrawal, Saumya; Luscombe, Nicholas M.; Blanchette, Mathieu; Kasukawa, Takeya; de Hoon, Michiel; Arner, Erik; Lenhard, Boris; Plessy, Charles; Castelo-Branco, Gonçalo; Orlando, Valerio; Carninci, Piero (Journal article; Peer reviewed, 2020)
      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. ...