Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA von Fadloun, Anas, Le Gras, Stéphanie, Jost, Bernard, Ziegler-Birling, Céline, Takahashi, Hazuki, Gorab, Eduardo, Carninci, Piero, Torres-Padilla, Maria-Elena

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An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs von Ohyama, Takako, Takahashi, Hazuki, Sharma, Harshita, Yamazaki, Toshio, Gustincich, Stefano, Ishii, Yoshitaka, Carninci, Piero

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Drosophila Piwi distinguishes transposons from mRNAs by piRNA complementarity and abundance von Ariura, Masaru, Solberg, Therese, Ishizu, Hirotsugu, Takahashi, Hazuki, Carninci, Piero, Siomi, Haruhiko, Iwasaki, Yuka W.

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CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing von Carbonell-Sala, Sílvia, Perteghella, Tamara, Lagarde, Julien, Nishiyori, Hiromi, Palumbo, Emilio, Arnan, Carme, Takahashi, Hazuki, Carninci, Piero, Uszczynska-Ratajczak, Barbara, Guigó, Roderic

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Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation von Sharma, Harshita, Valentine, Matthew N. Z., Toki, Naoko, Sueki, Hiromi Nishiyori, Gustincich, Stefano, Takahashi, Hazuki, Carninci, Piero

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Low Quantity Single Strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters von Takahashi, Hazuki, Nishiyori-Sueki, Hiromi, Ramilowski, Jordan A., Itoh, Masayoshi, Carninci, Piero

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Characterization of piRNAs across postnatal development in mouse brain von Ghosheh, Yanal, Seridi, Loqmane, Ryu, Taewoo, Takahashi, Hazuki, Orlando, Valerio, Carninci, Piero, Ravasi, Timothy

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Genome-wide analysis of promoter architecture in Drosophila melanogaster von Hoskins, Roger A, Landolin, Jane M, Brown, James B, Sandler, Jeremy E, Takahashi, Hazuki, Lassmann, Timo, Yu, Charles, Booth, Benjamin W, Zhang, Dayu, Wan, Kenneth H, Yang, Li, Boley, Nathan, Andrews, Justen, Kaufman, Thomas C, Graveley, Brenton R, Bickel, Peter J, Carninci, Piero, Carlson, Joseph W, Celniker, Susan E

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Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites von Haberman, Nejc, Digby, Holly, Faraway, Rupert, Cheung, Rebecca, Chakrabarti, Anob M., Jobbins, Andrew M., Parr, Callum, Yasuzawa, Kayoko, Kasukawa, Takeya, Yip, Chi Wai, Kato, Masaki, Takahashi, Hazuki, Carninci, Piero, Vernia, Santiago, Ule, Jernej, Sibley, Christopher R., Martinez-Sanchez, Aida, Lenhard, Boris

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Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation von Takahashi, Hazuki, Kozhuharova, Ana, Sharma, Harshita, Hirose, Masakazu, Ohyama, Takako, Fasolo, Francesca, Yamazaki, Toshio, Cotella, Diego, Santoro, Claudio, Zucchelli, Silvia, Gustincich, Stefano, Carninci, Piero

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Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis von Nepal, Chirag, Hadzhiev, Yavor, Previti, Christopher, Haberle, Vanja, Li, Nan, Takahashi, Hazuki, Suzuki, Ana Maria M, Sheng, Ying, Abdelhamid, Rehab F, 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

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CAGE (Cap Analysis of Gene Expression): A Protocol for the Detection of Promoter and Transcriptional Networks von Takahashi, Hazuki, Kato, Sachi, Murata, Mitsuyoshi, Carninci, Piero

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His166 Is the Schiff Base Proton Acceptor in Attractant Phototaxis Receptor Sensory Rhodopsin I von Sasaki, Jun, Takahashi, Hazuki, Furutani, Yuji, Sineshchekov, Oleg A, Spudich, John L, Kandori, Hideki

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Widespread genome transcription: New possibilities for RNA therapies von Takahashi, Hazuki, Carninci, Piero

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5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing von Takahashi, Hazuki, Lassmann, Timo, Murata, Mitsuyoshi, Carninci, Piero

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Structural Changes of Salinibacter Sensory Rhodopsin I upon Formation of the K and M Photointermediates von Suzuki, Daisuke, Sudo, Yuki, Furutani, Yuji, Takahashi, Hazuki, Homma, Michio, Kandori, Hideki

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Antisense RNAs during early vertebrate development are divided in groups with distinct features von Pillay, Sanjana, Takahashi, Hazuki, Carninci, Piero, Kanhere, Aditi

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Synthetic in vitro transcribed lncRNAs (SINEUPs) with chemical modifications enhance target mRNA translation von Toki, Naoko, Takahashi, Hazuki, Zucchelli, Silvia, Gustincich, Stefano, Carninci, Piero

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Sensory Rhodopsin-I as a Bidirectional Switch: Opposite Conformational Changes from the Same Photoisomerization von Sasaki, Jun, Takahashi, Hazuki, Furutani, Yuji, Kandori, Hideki, Spudich, John L.

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The status of the human gene catalogue von Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M., Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L., Hatzigeorgiou, Artemis G., Johnson, Rory, Murphy, Terence D., Pertea, Mihaela, Pruitt, Kim D., Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A., Yandell, Mark, Carninci, Piero, Salzberg, Steven L.

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