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Global reference mapping of human transcription factor footprints

mercredi 29 juillet 2020 par Jeff Vierstra, John Lazar, Richard Sandstrom, Jessica Halow, Kristen Lee, Daniel Bates, Morgan Diegel, Douglas Dunn, Fidencio Neri, Eric Haugen, Eric Rynes, Alex Reynolds, Jemma Nelson, Audra Johnson, Mark Frerker, Michael Buckley, Rajinder Kaul, Wouter Meuleman, John A. Stamatoyannopoulos
Nature, Published online: 29 July 2020; doi:10.1038/s41586-020-2528-xA high-density DNase I cleavage map from 243 human cell and tissue types provides a genome-wide, nucleotide-resolution map of human transcription factor footprints.

Perspectives on ENCODE

mercredi 29 juillet 2020 par Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal, Bronwen Aken, Jennifer A. Akiyama, Omar Al Jammal, Henry Amrhein, Stacie M. Anderson, Gregory R. Andrews, Igor Antoshechkin, Kristin G. Ardlie, Joel Armstrong, Matthew Astley, Budhaditya Banerjee, Amira A. Barkal, If H. A. Barnes, Iros Barozzi, Daniel Barrell, Gemma Barson, Daniel Bates, Ulugbek K. Baymuradov, Cassandra Bazile, Michael A. Beer, Samantha Beik, M. A. Bender, Ruth Bennett, Louis Philip Benoit Bouvrette, Bradley E. Bernstein, Andrew Berry, Anand Bhaskar, Alexandra Bignell, Steven M. Blue, David M. Bodine, Carles Boix, Nathan Boley, Tyler Borrman, Beatrice Borsari, Alan P. Boyle, Laurel A. Brandsmeier, Alessandra Breschi, Emery H. Bresnick, Jason A. Brooks, Michael Buckley, Christopher B. Burge, Rachel Byron, Eileen Cahill, Lingling Cai, Lulu Cao, Mark Carty, Rosa G. Castanon, Andres Castillo, Hassan Chaib, Esther T. Chan, Daniel R. Chee, Sora Chee, Hao Chen, Huaming Chen, Jia-Yu Chen, Songjie Chen, J. Michael Cherry, Surya B. Chhetri, Jyoti S. Choudhary, Jacqueline Chrast, Dongjun Chung, Declan Clarke, Neal A. L. Cody, Candice J. Coppola, Julie Coursen, Anthony M. D’Ippolito, Stephen Dalton, Cassidy Danyko, Claire Davidson, Jose Davila-Velderrain, Carrie A. Davis, Job Dekker, Alden Deran, Gilberto DeSalvo, Gloria Despacio-Reyes, Colin N. Dewey, Diane E. Dickel, Morgan Diegel, Mark Diekhans, Vishnu Dileep, Bo Ding, Sarah Djebali, Alexander Dobin, Daniel Dominguez, Sarah Donaldson, Jorg Drenkow, Timothy R. Dreszer, Yotam Drier, Michael O. Duff, Douglass Dunn, Catharine Eastman, Joseph R. Ecker, Matthew D. Edwards, Nicole El-Ali, Shaimae I. Elhajjajy, Keri Elkins, Andrew Emili, Charles B. Epstein, Rachel C. Evans, Iakes Ezkurdia, Kaili Fan, Peggy J. Farnham, Nina Farrell, Elise A. Feingold, Anne-Maud Ferreira, Katherine Fisher-Aylor, Stephen Fitzgerald, Paul Flicek, Chuan Sheng Foo, Kevin Fortier, Adam Frankish, Peter Freese, Shaliu Fu, Xiang-Dong Fu, Yu Fu, Yoko Fukuda-Yuzawa, Mariateresa Fulciniti, Alister P. W. Funnell, Idan Gabdank, Timur Galeev, Mingshi Gao, Carlos Garcia Giron, Tyler H. Garvin, Chelsea Anne Gelboin-Burkhart, Grigorios Georgolopoulos, Mark B. Gerstein, Belinda M. Giardine, David K. Gifford, David M. Gilbert, Daniel A. Gilchrist, Shawn Gillespie, Thomas R. Gingeras, Peng Gong, Alvaro Gonzalez, Jose M. Gonzalez, Peter Good, Alon Goren, David U. Gorkin, Brenton R. Graveley, Michael Gray, Jack F. Greenblatt, Ed Griffiths, Mark T. Groudine, Fabian Grubert, Mengting Gu, Roderic Guigó, Hongbo Guo, Yu Guo, Yuchun Guo, Gamze Gursoy, Maria Gutierrez-Arcelus, Jessica Halow, Ross C. Hardison, Matthew Hardy, Manoj Hariharan, Arif Harmanci, Anne Harrington, Jennifer L. Harrow, Tatsunori B. Hashimoto, Richard D. Hasz, Meital Hatan, Eric Haugen, James E. Hayes, Peng He, Yupeng He, Nastaran Heidari, David Hendrickson, Elisabeth F. Heuston, Jason A. Hilton, Benjamin C. Hitz, Abigail Hochman, Cory Holgren, Lei Hou, Shuyu Hou, Yun-Hua E. Hsiao, Shanna Hsu, Hui Huang, Tim J. Hubbard, Jack Huey, Timothy R. Hughes, Toby Hunt, Sean Ibarrientos, Robbyn Issner, Mineo Iwata, Osagie Izuogu, Tommi Jaakkola, Nader Jameel, Camden Jansen, Lixia Jiang, Peng Jiang, Audra Johnson, Rory Johnson, Irwin Jungreis, Madhura Kadaba, Maya Kasowski, Mary Kasparian, Momoe Kato, Rajinder Kaul, Trupti Kawli, Michael Kay, Judith C. Keen, Sunduz Keles, Cheryl A. Keller, David Kelley, Manolis Kellis, Pouya Kheradpour, Daniel Sunwook Kim, Anthony Kirilusha, Robert J. Klein, Birgit Knoechel, Samantha Kuan, Michael J. Kulik, Sushant Kumar, Anshul Kundaje, Tanya Kutyavin, Julien Lagarde, Bryan R. Lajoie, Nicole J. Lambert, John Lazar, Ah Young Lee, Donghoon Lee, Elizabeth Lee, Jin Wook Lee, Kristen Lee, Christina S. Leslie, Shawn Levy, Bin Li, Hairi Li, Nan Li, Xiangrui Li, Yang I. Li, Ying Li, Yining Li, Yue Li, Jin Lian, Maxwell W. Libbrecht, Shin Lin, Yiing Lin, Dianbo Liu, Jason Liu, Peng Liu, Tingting Liu, X. Shirley Liu, Yan Liu, Yaping Liu, Maria Long, Shaoke Lou, Jane Loveland, Aiping Lu, Yuheng Lu, Eric Lécuyer, Lijia Ma, Mark Mackiewicz, Brandon J. Mannion, Michael Mannstadt, Deepa Manthravadi, Georgi K. Marinov, Fergal J. Martin, Eugenio Mattei, Kenneth McCue, Megan McEown, Graham McVicker, Sarah K. Meadows, Alex Meissner, Eric M. Mendenhall, Christopher L. Messer, Wouter Meuleman, Clifford Meyer, Steve Miller, Matthew G. Milton, Tejaswini Mishra, Dianna E. Moore, Helen M. Moore, Jill E. Moore, Samuel H. Moore, Jennifer Moran, Ali Mortazavi, Jonathan M. Mudge, Nikhil Munshi, Rabi Murad, Richard M. Myers, Vivek Nandakumar, Preetha Nandi, Anil M. Narasimha, Aditi K. Narayanan, Hannah Naughton, Fabio C. P. Navarro, Patrick Navas, Jurijs Nazarovs, Jemma Nelson, Shane Neph, Fidencio Jun Neri, Joseph R. Nery, Amy R. Nesmith, J. Scott Newberry, Kimberly M. Newberry, Vu Ngo, Rosy Nguyen, Thai B. Nguyen, Tung Nguyen, Andrew Nishida, William S. Noble, Catherine S. Novak, Eva Maria Novoa, Briana Nuñez, Charles W. O’Donnell, Sara Olson, Kathrina C. Onate, Ericka Otterman, Hakan Ozadam, Michael Pagan, Tsultrim Palden, Xinghua Pan, Yongjin Park, E. Christopher Partridge, Benedict Paten, Florencia Pauli-Behn, Michael J. Pazin, Baikang Pei, Len A. Pennacchio, Alexander R. Perez, Emily H. Perry, Dmitri D. Pervouchine, Nishigandha N. Phalke, Quan Pham, Doug H. Phanstiel, Ingrid Plajzer-Frick, Gabriel A. Pratt, Henry E. Pratt, Sebastian Preissl, Jonathan K. Pritchard, Yuri Pritykin, Michael J. Purcaro, Qian Qin, Giovanni Quinones-Valdez, Ines Rabano, Ernest Radovani, Anil Raj, Nisha Rajagopal, Oren Ram, Lucia Ramirez, Ricardo N. Ramirez, Dylan Rausch, Soumya Raychaudhuri, Joseph Raymond, Rozita Razavi, Timothy E. Reddy, Thomas M. Reimonn, Bing Ren, Alexandre Reymond, Alex Reynolds, Suhn K. Rhie, John Rinn, Miguel Rivera, Juan Carlos Rivera-Mulia, Brian Roberts, Jose Manuel Rodriguez, Joel Rozowsky, Russell Ryan, Eric Rynes, Denis N. Salins, Richard Sandstrom, Takayo Sasaki, Shashank Sathe, Daniel Savic, Alexandra Scavelli, Jonathan Scheiman, Christoph Schlaffner, Jeffery A. Schloss, Frank W. Schmitges, Lei Hoon See, Anurag Sethi, Manu Setty, Anthony Shafer, Shuo Shan, Eilon Sharon, Quan Shen, Yin Shen, Richard I. Sherwood, Minyi Shi, Sunyoung Shin, Noam Shoresh, Kyle Siebenthall, Cristina Sisu, Teri Slifer, Cricket A. Sloan, Anna Smith, Valentina Snetkova, Michael P. Snyder, Damek V. Spacek, Sharanya Srinivasan, Rohith Srivas, George Stamatoyannopoulos, John A. Stamatoyannopoulos, Rebecca Stanton, Dave Steffan, Sandra Stehling-Sun, J. Seth Strattan, Amanda Su, Balaji Sundararaman, Marie-Marthe Suner, Tahin Syed, Matt Szynkarek, Forrest Y. Tanaka, Danielle Tenen, Mingxiang Teng, Jeffrey A. Thomas, Dave Toffey, Michael L. Tress, Diane E. Trout, Gosia Trynka, Junko Tsuji, Sean A. Upchurch, Oana Ursu, Barbara Uszczynska-Ratajczak, Mia C. Uziel, Alfonso Valencia, Benjamin Van Biber, Arjan G. van der Velde, Eric L. Van Nostrand, Yekaterina Vaydylevich, Jesus Vazquez, Alec Victorsen, Jost Vielmetter, Jeff Vierstra, Axel Visel, Anna Vlasova, Christopher M. Vockley, Simona Volpi, Shinny Vong, Hao Wang, Mengchi Wang, Qin Wang, Ruth Wang, Tao Wang, Wei Wang, Xiaofeng Wang, Yanli Wang, Nathaniel K. Watson, Xintao Wei, Zhijie Wei, Hendrik Weisser, Sherman M. Weissman, Rene Welch, Robert E. Welikson, Zhiping Weng, Harm-Jan Westra, John W. Whitaker, Collin White, Kevin P. White, Andre Wildberg, Brian A. Williams, David Wine, Heather N. Witt, Barbara Wold, Maxim Wolf, James Wright, Rui Xiao, Xinshu Xiao, Jie Xu, Jinrui Xu, Koon-Kiu Yan, Yongqi Yan, Hongbo Yang, Xinqiong Yang, Yi-Wen Yang, Galip Gürkan Yardımcı, Brian A. Yee, Gene W. Yeo, Taylor Young, Tianxiong Yu, Feng Yue, Chris Zaleski, Chongzhi Zang, Haoyang Zeng, Weihua Zeng, Daniel R. Zerbino, Jie Zhai, Lijun Zhan, Ye Zhan, Bo Zhang, Jialing Zhang, Jing Zhang, Kai Zhang, Lijun Zhang, Peng Zhang, Qi Zhang, Xiao-Ou Zhang, Yanxiao Zhang, Zhizhuo Zhang, Yuan Zhao, Ye Zheng, Guoqing Zhong, Xiao-Qiao Zhou, Yun Zhu, Jared Zimmerman
Nature, Published online: 29 July 2020; doi:10.1038/s41586-020-2449-8The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous (...)

A simple test could extend cystic-fibrosis treatments to those left behind

mercredi 29 juillet 2020 par Steven M. Rowe
Nature, Published online: 29 July 2020; doi:10.1038/d41586-020-02107-9Sweat-chloride measurements could be used to develop and approve drugs for rare mutations in cystic fibrosis.

Na+ controls hypoxic signalling by the mitochondrial respiratory chain

mercredi 29 juillet 2020 par Pablo Hernansanz-Agustín, Carmen Choya-Foces, Susana Carregal-Romero, Elena Ramos, Tamara Oliva, Tamara Villa-Piña, Laura Moreno, Alicia Izquierdo-Álvarez, J. Daniel Cabrera-García, Ana Cortés, Ana Victoria Lechuga-Vieco, Pooja Jadiya, Elisa Navarro, Esther Parada, Alejandra Palomino-Antolín, Daniel Tello, Rebeca Acín-Pérez, Juan Carlos Rodríguez-Aguilera, Plácido Navas, Ángel Cogolludo, Iván López-Montero, Álvaro Martínez-del-Pozo, Javier Egea, Manuela G. López, John W. Elrod, Jesús Ruíz-Cabello, Anna Bogdanova, José Antonio Enríquez, Antonio Martínez-Ruiz
Nature, Published online: 29 July 2020; doi:10.1038/s41586-020-2551-yNa+ controls the function of the mitochondrial oxidative phosphorylation system and hypoxic redox signalling through an unexpected interaction with phospholipids.

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

mercredi 29 juillet 2020 par Yupeng He, Manoj Hariharan, David U. Gorkin, Diane E. Dickel, Chongyuan Luo, Rosa G. Castanon, Joseph R. Nery, Ah Young Lee, Yuan Zhao, Hui Huang, Brian A. Williams, Diane Trout, Henry Amrhein, Rongxin Fang, Huaming Chen, Bin Li, Axel Visel, Len A. Pennacchio, Bing Ren, Joseph R. Ecker
Nature, Published online: 29 July 2020; doi:10.1038/s41586-020-2119-xAnalysis of 168 methylomes from 12 mouse tissues at 9 developmental stages sheds light on the epigenetic and regulatory landscape during mammalian fetal development.

How much protein function needs to be restored in cystic fibrosis?

mercredi 29 juillet 2020 par Benjamin Plackett
Nature, Published online: 29 July 2020; doi:10.1038/d41586-020-02114-wKnowing the percentage of function that is required to eliminate disease symptoms could help to shape treatment in the coming years and ensure sufferers don’t slip through the (...)

Lysosome-targeting chimaeras for degradation of extracellular proteins

mercredi 29 juillet 2020 par Steven M. Banik, Kayvon Pedram, Simon Wisnovsky, Green Ahn, Nicholas M. Riley, Carolyn R. Bertozzi
Nature, Published online: 29 July 2020; doi:10.1038/s41586-020-2545-9Lysosome-targeting chimaeras—in which a small molecule or antibody is connected to a glycopeptide ligand to form a conjugate that can bind a cell-surface lysosome-shuttling receptor and a protein target—are used to achieve the (...)

Why skin grows bigger as you stretch it

mercredi 29 juillet 2020 par Nick Howe, Shamini Bundell
Nature, Published online: 29 July 2020; doi:10.1038/d41586-020-02253-0Skin's unusual response to stretching is finally explained, and the latest in a huge effort to map DNA.

Association of COVID-19 inflammation with activation of the C5a–C5aR1 axis

mercredi 29 juillet 2020 par Julien Carvelli, Olivier Demaria, Frédéric Vély, Luciana Batista, Nassima Chouaki Benmansour, Joanna Fares, Sabrina Carpentier, Marie-Laure Thibult, Ariane Morel, Romain Remark, Pascale André, Agnès Represa, Christelle Piperoglou, Laura Assante Miranda, William Baron, Nourhène Belaid, Clarisse Caillet, Flavien Caraguel, Barbara Carrette, Florent Carrette, Fabien Chanuc, Rachel Courtois, Aurore Fenis, Marilyn Giordano, Mathilde Girard-Madoux, Marc Giraudon-Paoli, Nicolas Gourdin, Gwendoline Grondin, Franceline Guillot, Guillaume Habif, Solène Jaubert, Julie Lopez, Mélanie Le Van, Naouel Lovera, Marine Mansuy, Elodie Bonnet, Audrey Sansaloni, Annick Reboul, Emmanuel Mitry, Camille Nekkar-Constant, Valentine Péri, Paul Ricaut, Léa Simon, Jean-Baptiste Vallier, Marie Vétizou, Robert Zerbib, Pierre Yves Cordier, Erwan Le Dault, Christophe Guervilly, Pierre Simeone, Marc Gainnier, Yannis Morel, Mikael Ebbo, Nicolas Schleinitz, Eric Vivier, Sophie Ugolini, Marion Etiennot, Justine Galluso, Luc Lyonnet, Jean-Marie Forel, Laurent Papazian, Lionel Velly, Baptiste André, Antoine Briantais, Benoit Faucher, Estelle Jean, Julie Seguier, Veronique Veit, Jean-Robert Harlé, Boris Pastorino, Clémence Delteil, Laurent Daniel, Jean-Paul Boudsocq, Axelle Clerc, Emmanuel Delmond, Pierre-Olivier Vidal, Hélène Savini, Bruno Coutard
Nature, Published online: 29 July 2020; doi:10.1038/s41586-020-2600-6Association of COVID-19 inflammation with activation of the C5a–C5aR1 axis

Night-time measurements of astronomical seeing at Dome A in Antarctica

mercredi 29 juillet 2020 par Bin Ma, Zhaohui Shang, Yi Hu, Keliang Hu, Yongjiang Wang, Xu Yang, Michael C. B. Ashley, Paul Hickson, Peng Jiang
Nature, Published online: 29 July 2020; doi:10.1038/s41586-020-2489-0The night-time seeing (the extent to which a star’s light is blurred by the atmosphere) at Dome A, the highest part on the Antarctic plateau, can be as good as 0.13 arcseconds above a height of only 8 (...)

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