Annotation of nuclear lncRNAs based on chromatin interactions.

Autor: Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Howard Y Chang, Josée Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J Makeev, Mickaël Mendez, Yasushi Okazaki, Jordan A Ramilowski, Andrey I Sigorskikh, Lisa J Strug, Ken Yagi, Kayoko Yasuzawa, Chi Wai Yip, Chung Chau Hon, Michael M Hoffman, Chikashi Terao, Ivan V Kulakovskiy, Takeya Kasukawa, Jay W Shin, Piero Carninci, Michiel J L de Hoon

Publikováno v: PLoS ONE, Vol 19, Iss 5, p e0295971 (2024)

The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory comp

Externí odkaz: https://doaj.org/article/cd55b6045f20467eb83991410871c30d

Abundant capped RNAs are derived from mRNA cleavage at 3’UTR G-Quadruplexes

Autor: Nejc Haberman, Holly Digby, Rupert Faraway, Rebecca Cheung, Andrew M Jobbins, Callum Parr, Kayoko Yasuzawa, Takeya Kasukawa, Chi Wai Yip, Masaki Kato, Hazuki Takahashi, Piero Carninci, Santiago Vernia, Jernej Ule, Christopher R Sibley, Aida Martinez-Sanchez, Boris Lenhard

SummaryThe 3’ untranslated region (3’UTR) plays a crucial role in determining mRNA stability, localisation, translation and degradation. Cap analysis gene expression (CAGE), a method for the detection of capped 5’ ends of mRNAs, additionally re

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18bb72c57a82b070076c02347f548466
http://hdl.handle.net/10044/1/105362

Systematic identification of cis-interacting lncRNAs and their targets

Autor: Saumya Agrawal, Ivan V. Kulakovskiy, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Andrey Buyan, Howard Y. Chang, Josee Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J. Makeev, Mickaël Mendez, Yasushi Okazaki, Jordan A. Ramilowski, Andrey I. Sigorskikh, Lisa J. Strug, Ken Yagi, Kayoko Yasuzawa, Chi Wai Yip, Chung Chau Hon, Michael M. Hoffman, Chikashi Terao, Takeya Kasukawa, Jay W. Shin, Piero Carninci, Michiel JL de Hoon

The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Studying lncRNAs is challenging due to their low expression level, cell type-

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::4f5c41a30cef5b93213ba6062a7d02d3
https://doi.org/10.1101/2021.01.13.426305

Functional annotation of human long noncoding RNAs via molecular phenotyping

Autor: Jayson Harshbarger, Hideya Kawaji, Diego Garrido, Michiel J. L. de Hoon, Tsugumi Kawashima, Lusy Handoko, Masayoshi Itoh, John F. Ouyang, Michihira Tagami, Kosuke Hashimoto, Andreas Petri, Patrizia Rizzu, Christopher J. F. Cameron, Tetsuro Hirose, Marina Lizio, Beatrice Borsari, Robert Young, Vidisha Tripathi, Chung-Chau Hon, Joachim Luginbühl, Ryan Cardenas, Jasmine Li Ching Ooi, Chikashi Terao, Vsevolod J. Makeev, Aki Minoda, Colin A. Semple, Alexander V. Favorov, Yasushi Okazaki, Kazuhiro R. Nitta, Mitsuyoshi Murata, Juha Kere, Harukazu Suzuki, Bogumil Kaczkowski, Fernando López-Redondo, Ivan Antonov, Mickaël Mendez, Diego Fernando Sánchez Martinez, Michael M. Hoffman, Chi Wai Yip, Imad Abugessaisa, Pillay Sanjana, Sakari Kauppinen, Erik Arner, Denis Paquette, Norihito Hayatsu, Ramil N. Nurtdinov, Mariola Kurowska-Stolarska, Luigi Marchionni, Takahiro Suzuki, Claudio Schneider, J Kenneth Baillie, Andrew T. Kwon, Saumya Agrawal, Carlo Vittorio Cannistraci, Roberto Verardo, Suzannah C. Szumowski, Frank Brombacher, Tsukasa Kouno, Boris Lenhard, Noa Gil, Manuel Muñoz-Aguirre, Shiori Maeda, Luca Ducoli, Emily Kawabata, Valerio Orlando, Leonie Roos, Divya M. Sivaraman, Youtaro Shibayama, Supat Thongjuea, Piero Carninci, Kayoko Yasuzawa, Jeffrey T. Leek, Alexandre Fort, Hidemasa Bono, Peter Heutink, Takeya Kasukawa, Alessandro Bonetti, Jen-Chien Chang, Josée Dostie, Naoto Kondo, Ferenc Müller, Nicholas J. Parkinson, Haruhiko Koseki, Malte Thodberg, Callum J.C. Parr, Anton Kratz, Miki Kojima, Reto Guler, Jordan A. Ramilowski, Alistair R. R. Forrest, Owen J. L. Rackham, Igor Ulitsky, Yari Ciani, Howard Y. Chang, Roderic Guigó, Jay W. Shin, Andreas Lennartsson, Ivan V. Kulakovskiy, Jessica Severin, Ilya E. Vorontsov, Melissa Cardon, Ken Yagi, Chinatsu Yamamoto, Yukihiko Noro, Juliette Gimenez, Shuhei Noguchi, Yuki Hasegawa, Eddie Luidy Imada, Martin S. Taylor, Yulia A. Medvedeva, Altuna Akalin, Albin Sandelin, Aditi Kanhere, S. Thomas Kelly, Hiromi Nishiyori, Akira Hasegawa

Publikováno v: Ramilowski, J A, Yip, C W, Agrawal, S, Chang, J-C, Ciani, Y, Kulakovskiy, I V, Mendez, M, Ooi, J L C, Ouyang, J F, Parkinson, N, Petri, A, Roos, L, Severin, J, Yasuzawa, K, Abugessaisa, I, Akalin, A, Antonov, I V, Arner, E, Bonetti, A, Bono, H, Borsari, B, Brombacher, F, Cameron, C JF, Cannistraci, C V, Cardenas, R, Cardon, M, Chang, H, Dostie, J, Ducoli, L, Favorov, A, Fort, A, Garrido, D, Gil, N, Gimenez, J, Guler, R, Handoko, L, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, K, Hayatsu, N, Heutink, P, Hirose, T, Imada, E L, Itoh, M, Kaczkowski, B, Kanhere, A, Kawabata, E, Kawaji, H, Kawashima, T, Kelly, S T, Kojima, M, Kondo, N, Koseki, H, Kouno, T, Kratz, A, Kurowska-Stolarska, M, Kwon, A T J, Leek, J, Lennartsson, A, Lizio, M, López-Redondo, F, Luginbühl, J, Maeda, S, Makeev, V J, Marchionni, L, Medvedeva, Y A, Minoda, A, Müller, F, Muñoz-Aguirre, M, Murata, M, Nishiyori, H, Nitta, K R, Noguchi, S, Noro, Y, Nurtdinov, R, Okazaki, Y, Orlando, V, Paquette, D, Parr, C J C, Rackham, O J L, Rizzu, P, Sánchez Martinez, D F, Sandelin, A, Sanjana, P, Semple, C A M, Shibayama, Y, Sivaraman, D M, Suzuki, T, Szumowski, S C, Tagami, M, Taylor, M S, Terao, C, Thodberg, M, Thongjuea, S, Tripathi, V, Ulitsky, I, Verardo, R, Vorontsov, I E, Yamamoto, C, Young, R S, Baillie, J K, Forrest, A R R, Guigó, R, Hoffman, M M, Hon, C C, Kasukawa, T, Kauppinen, S, Kere, J, Lenhard, B, Schneider, C, Suzuki, H, Yagi, K, de Hoon, M J L, Shin, J W & Carninci, P 2020, ' Functional annotation of human long noncoding RNAs via molecular phenotyping ', Genome Research, vol. 30, no. 7, pp. 1060-1072 . https://doi.org/10.1101/gr.254219.119
Genome Research
Ramilowski, J A, Yip, C W, Agrawal, S, Chang, J-C, Ciani, Y, Kulakovskiy, I V, Mendez, M, Ooi, J L C, Ouyang, J F, Parkinson, N, Petri, A, Roos, L, Severin, J, Yasuzawa, K, Abugessaisa, I, Akalin, A, Antonov, I V, Arner, E, Bonetti, A, Bono, H, Borsari, B, Brombacher, F, Cameron, C J F, Cannistraci, C V, Cardenas, R, Cardon, M, Chang, H, Dostie, J, Ducoli, L, Favorov, A, Fort, A, Garrido, D, Gil, N, Gimenez, J, Guler, R, Handoko, L, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, K, Hayatsu, N, Heutink, P, Hirose, T, Imada, E L, Itoh, M, Kaczkowski, B, Kanhere, A, Kawabata, E, Kawaji, H, Kawashima, T, Kelly, S T, Kojima, M, Kondo, N, Koseki, H, Kouno, T, Kratz, A, Kurowska-Stolarska, M, Kwon, A T J, Leek, J, Lennartsson, A, Lizio, M, López-Redondo, F, Luginbühl, J, Maeda, S, Makeev, V J, Marchionni, L, Medvedeva, Y A, Minoda, A, Müller, F, Muñoz-Aguirre, M, Murata, M, Nishiyori, H, Nitta, K R, Noguchi, S, Noro, Y, Nurtdinov, R, Okazaki, Y, Orlando, V, Paquette, D, Parr, C J C, Rackham, O J L, Rizzu, P, Sánchez Martinez, D F, Sandelin, A, Sanjana, P, Semple, C A M, Shibayama, Y, Sivaraman, D M, Suzuki, T, Szumowski, S C, Tagami, M, Taylor, M S, Terao, C, Thodberg, M, Thongjuea, S, Tripathi, V, Ulitsky, I, Verardo, R, Vorontsov, I E, Yamamoto, C, Young, R S, Baillie, J K, Forrest, A R R, Guigó, R, Hoffman, M M, Hon, C C, Kasukawa, T, Kauppinen, S, Kere, J, Lenhard, B, Schneider, C, Suzuki, H, Yagi, K, de Hoon, M J L, Shin, J W & Carninci, P 2020, ' Functional annotation of human long noncoding RNAs via molecular phenotyping ', Genome Research, vol. 30, pp. 1060-1072 . https://doi.org/10.1101/gr.254219.119
Ramilowski, J A, Yip, C W, Agrawal, S, Chang, J-C, Ciani, Y, Kulakovskiy, I V, Mendez, M, Ooi, J L C, Ouyang, J F, Parkinson, N, Petri, A, Roos, L, Severin, J, Yasuzawa, K, Abugessaisa, I, Akalin, A, Antonov, I V, Arner, E, Bonetti, A, Bono, H, Borsari, B, Brombacher, F, Cameron, C J F, Cannistraci, C V, Cardenas, R, Cardon, M, Chang, H, Dostie, J, Ducoli, L, Favorov, A, Fort, A, Garrido, D, Gil, N, Gimenez, J, Guler, R, Handoko, L, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, K, Hayatsu, N, Heutink, P, Hirose, T, Imada, E L, Itoh, M, Kaczkowski, B, Kanhere, A, Kawabata, E, Kawaji, H, Kawashima, T, Kelly, S T, Kojima, M, Kondo, N, Koseki, H, Kouno, T, Kratz, A, Kurowska-Stolarska, M, Kwon, A T J, Leek, J, Lennartsson, A, Lizio, M, López-Redondo, F, Luginbühl, J, Maeda, S, Makeev, V J, Marchionni, L, Medvedeva, Y A, Minoda, A, Müller, F, Muñoz-Aguirre, M, Murata, M, Nishiyori, H, Nitta, K R, Noguchi, S, Noro, Y, Nurtdinov, R, Okazaki, Y, Orlando, V, Paquette, D, Parr, C J C, Rackham, O J L, Rizzu, P, Sánchez Martinez, D F, Sandelin, A, Sanjana, P, Semple, C A M, Shibayama, Y, Sivaraman, D M, Suzuki, T, Szumowski, S C, Tagami, M, Taylor, M S, Terao, C, Thodberg, M, Thongjuea, S, Tripathi, V, Ulitsky, I, Verardo, R, Vorontsov, I E, Yamamoto, C, Young, R S, Baillie, J K, Forrest, A R R, Guigó, R, Hoffman, M M, Hon, C C, Kasukawa, T, Kauppinen, S, Kere, J, Lenhard, B, Schneider, C, Suzuki, H, Yagi, K, de Hoon, M J L, Shin, J W & Carninci, P 2020, ' Functional annotation of human long noncoding RNAs via molecular phenotyping ', Genome Research . https://doi.org/10.1101/gr.254219.119
Ramilowski, J A, Yip, C W, Agrawal, S, Chang, J-C, Ciani, Y, Kulakovskiy, I V, Mendez, M, Ooi, J L C, Ouyang, J F, Parkinson, N, Petri, A, Roos, L, Severin, J, Yasuzawa, K, Abugessaisa, I, Akalin, A, Antonov, I V, Arner, E, Bonetti, A, Bono, H, Borsari, B, Brombacher, F, Cameron, C J F, Cannistraci, C V, Cardenas, R, Cardon, M, Chang, H, Dostie, J, Ducoli, L, Favorov, A, Fort, A, Garrido, D, Gil, N, Gimenez, J, Guler, R, Handoko, L, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, K, Hayatsu, N, Heutink, P, Hirose, T, Imada, E L, Itoh, M, Kaczkowski, B, Kanhere, A, Kawabata, E, Kawaji, H, Kawashima, T, Kelly, S T, Kojima, M, Kondo, N, Koseki, H, Kouno, T, Kratz, A, Kurowska-Stolarska, M, Kwon, A T J, Leek, J, Lennartsson, A, Lizio, M, Lopez-Redondo, F, Luginbühl, J, Maeda, S, Makeev, V J, Marchionni, L, Medvedeva, Y A, Minoda, A, Müller, F, Muñoz-Aguirre, M, Murata, M, Nishiyori, H, Nitta, K R, Noguchi, S, Noro, Y, Nurtdinov, R, Okazaki, Y, Orlando, V, Paquette, D, Parr, C J C, Rackham, O J L, Rizzu, P, Martinez, D F S, Sandelin, A, Sanjana, P, Semple, C A M, Shibayama, Y, Sivaraman, D M, Suzuki, T, Szumowski, S C, Tagami, M, Taylor, M S, Terao, C, Thodberg, M, Thongjuea, S, Tripathi, V, Ulitsky, I, Verardo, R, Vorontsov, I E, Yamamoto, C, Young, R S, Baillie, J K, Forrest, A R R, Guigó, R, Hoffman, M M, Hon, C C, Kasukawa, T, Kauppinen, S, Kere, J, Lenhard, B, Schneider, C, Suzuki, H, Yagi, K, de Hoon, M J L, Shin, J W & Carninci, P 2020, ' Functional annotation of human long noncoding RNAs via molecular phenotyping ', Genome Research, vol. 30, no. 7, pp. 1060-1072 . https://doi.org/10.1101/gr.254219.119
Genome Res
Genome research 30(7), 1060-1072 (2020). doi:10.1101/gr.254219.119

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human derm

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9cf2df2c4fb7df1b0612e3c14c9242a6
https://vbn.aau.dk/da/publications/9945d8a2-24bb-4411-ada7-c0664ae247f1

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

Autor: Howard Y. Chang, Manuel Muñoz-Aguirre, Roderic Guigó, Andreas Lennartsson, Chinatsu Yamamoto, Robert Young, Ramil N. Nurtdinov, Jasmine Li Ching Ooi, Christopher J. F. Cameron, Andreas Petri, Valerio Orlando, Tetsuro Hirose, Vidisha Tripathi, Tsugumi Kawashima, Joachim Luginbühl, Ilya E. Vorontsov, Diego Garrido, Jeffrey T. Leek, Alexandre Fort, Ryan Cardenas, Colin A. Semple, Aki Minoda, Takeya Kasukawa, Michiel J. L. de Hoon, Alexander V. Favorov, Peter Heutink, Harukazu Suzuki, Jordan A. Ramilowski, Alistair R. R. Forrest, Michihira Tagami, Imad Abugessaisa, Malte Thodberg, J Kenneth Baillie, Andrew T. Kwon, Juha Kere, Ivan V. Kulakovskiy, Jen-Chien Chang, Yuki Hasegawa, Melissa Cardon, Kazuhiro R. Nitta, John F. Ouyang, Jay W. Shin, Noa Gil, Jessica Severin, Reto Guler, Shiori Maeda, Eddie Luidy Imada, Emily Kawabata, Sakari Kauppinen, Hideya Kawaji, Pillay Sanjana, Miki Kojima, Yulia A. Medvedeva, Igor Ulitsky, Suzannah C. Szumowski, Martin S. Taylor, Michael M. Hoffman, Denis Paquette, Yari Ciani, Yukihiko Noro, S. Thomas Kelly, Mickaël Mendez, Diego Fernando Sánchez Martinez, Lusy Handoko, Jayson Harshbarger, Roberto Verardo, Owen J. L. Rackham, Bogumil Kaczkowski, Ivan Antonov, Frank Brombacher, Akira Hasegawa, Tsukasa Kouno, Fernando López-Redondo, Mariola Kurowska-Stolarska, Luigi Marchionni, Supat Thongjuea, N. Hayatsu, Ken Yagi, Juliette Gimenez, Anton Kratz, Hiromi Nishiyori, Shuhei Noguchi, Kayoko Yasuzawa, Chi Wai Yip, Chung-Chau Hon, Altuna Akalin, Albin Sandelin, Aditi Kanhere, Marina Lizio, Beatrice Borsari, Chikashi Terao, Vsevolod J. Makeev, Luca Ducoli, Alessandro Bonetti, Josée Dostie, Divya M. Sivaraman, Masayoshi Itoh, Piero Carninci, Hidemasa Bono, Erik Arner, Kosuke Hashimoto, Yasushi Okazaki, Patrizia Rizzu, Mitsuyoshi Murata, Callum J.C. Parr, Boris Lenhard, Ferenc Müller, Claudio Schneider, Youtaro Shibayama, Saumya Agrawal, Carlo Vittorio Cannistraci, Leonie Roos, Naoto Kondo, Nicholas J. Parkinson, Haruhiko Koseki, Takahiro Suzuki

Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes and yet, their functions remain largely unknown. We systematically knockdown 285 lncRNAs expression in human dermal fibroblasts and quantified cellular gro

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4a46b53a4c59f5aa48e139d767d36993