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ELIMÄKI Locus Is Required for Vertical Proprioceptive Response in Birch Trees

Current Biology 2020年第4期30卷 589-599.e5页

作者： Alonso-Serra, Juan Shi, Xueping Peaucelle, Alexis Rastas, Pasi Bourdon, Matthieu Immanen, Juha Takahashi, Junko Koivula, Hanna Eswaran, Gugan Muranen, Sampo Help, Hanna Smolander, Olli-Pekka Su, Chang Safronov, Omid Gerber, Lorenz Salojärvi, Jarkko Hagqvist, Risto Mähönen, Ari Pekka Helariutta, Ykä Nieminen, Kaisa Organismal and Evolutionary Biology Research Program Faculty of Biological and Environmental Sciences Viikki Plant Science Centre University of Helsinki Helsinki 00014 Finland Institute of Biotechnology HiLIFE University of Helsinki Helsinki 00014 Finland Key Laboratory of Horticultural Plant Biology of Ministry of Education College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China Sainsbury Laboratory University of Cambridge Cambridge CB2 1LR United Kingdom Institut Jean-Pierre Bourgin INRA AgroParisTech CNRS Université Paris-Saclay Versailles 78000 France Production Systems Natural Resources Institute Finland (Luke) Helsinki 00790 Finland Umeå Plant Science Center Department of Forest Genetics and Plant Physiology Swedish University of Agricultural Sciences Umeå 901 83 Sweden Department of Food and Nutrition Faculty of Agriculture and Forestry University of Helsinki Helsinki 00014 Finland Department of Physics Division of Materials Sciences X-ray Laboratory University of Helsinki Helsinki 00014 Finland Department of Chemistry and Biotechnology School of Science Tallinn University of Technology Tallinn Estonia Genome Institute of Singapore Singapore 138672 Singapore Singapore Centre for Environmental Life Sciences Engineering Nanyang Technological University Singapore 63755 Singapore

Tree architecture has evolved to support a top-heavy above-ground biomass, but this integral feature poses a weight-induced challenge to trunk stability. Maintaining an upright stem is expected to require vertical proprioception through feedback between sensing stem weight and responding with radial growth. Despite its apparent importance, the principle by which plant stems respond to vertical loading forces remains largely unknown. Here, by manipulating the stem weight of downy birch (Betula pubescens) trees, we show that cambial development is modulated systemically along the stem. We carried out a genetic study on the underlying regulation by combining an accelerated birch flowering program with a recessive mutation at the ELIMÄKI locus (EKI), which causes a mechanically defective response to weight stimulus resulting in stem collapse after just 3 months. We observed delayed wood morphogenesis in eki compared with WT, along with a more mechanically elastic cambial zone and radial compression of xylem cell size, indicating that rapid tissue differentiation is critical for cambial growth under mechanical stress. Furthermore, the touch-induced mechanosensory pathway was transcriptionally misregulated in eki, indicating that the ELIMÄKI locus is required to integrate the weight-growth feedback regulation. By studying this birch mutant, we were able to dissect vertical proprioception from the gravitropic response associated with reaction wood formation. Our study provides evidence for both local and systemic responses to mechanical stimuli during secondary plant development. Alonso-Serra et al. use birch trees to explore vertical proprioception, the growth response of stems to changes in aerial body weight. They identify a genetic locus, which is required for this developmental response, and study the consequences of cambial growth under mechanical stress. © 2019 Elsevier Ltd

关键词： Betula forward genetics mechanosensing proprioception radial growth trees wood formation

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Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

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Nature 2022年第7909期605卷 E3页

作者： Jill E Moore Michael J Purcaro Henry E Pratt Charles B Epstein Noam Shoresh Jessika Adrian Trupti Kawli Carrie A Davis Alexander Dobin Rajinder Kaul Jessica Halow Eric L Van Nostrand Peter Freese David U Gorkin Yin Shen Yupeng He Mark Mackiewicz Florencia Pauli-Behn Brian A Williams Ali Mortazavi Cheryl A Keller Xiao-Ou Zhang Shaimae I Elhajjajy Jack Huey Diane E Dickel Valentina Snetkova Xintao Wei Xiaofeng Wang Juan Carlos Rivera-Mulia Joel Rozowsky Jing Zhang Surya B Chhetri Jialing Zhang Alec Victorsen Kevin P White Axel Visel Gene W Yeo Christopher B Burge Eric Lécuyer David M Gilbert Job Dekker John Rinn Eric M Mendenhall Joseph R Ecker Manolis Kellis Robert J Klein William S Noble Anshul Kundaje Roderic Guigó Peggy J Farnham J Michael Cherry Richard M Myers Bing Ren Brenton R Graveley Mark B Gerstein Len A Pennacchio Michael P Snyder Bradley E Bernstein Barbara Wold Ross C Hardison Thomas R Gingeras John A Stamatoyannopoulos Zhiping Weng University of Massachusetts Medical School Program in Bioinformatics and Integrative Biology Worcester MA USA. The Broad Institute of Harvard and MIT Cambridge MA USA. Department of Genetics School of Medicine Stanford University Palo Alto CA USA. Cold Spring Harbor Laboratory Functional Genomics Cold Spring Harbor NY USA. Altius Institute for Biomedical Sciences Seattle WA USA. Department of Medicine University of Washington School of Medicine Seattle WA USA. Department of Cellular and Molecular Medicine Institute for Genomic Medicine Stem Cell Program Sanford Consortium for Regenerative Medicine University of California San Diego La Jolla CA USA. Program in Computational and Systems Biology Massachusetts Institute of Technology Cambridge MA USA. Center for Epigenomics Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA. Ludwig Institute for Cancer Research University of California San Diego La Jolla CA USA. Institute for Human Genetics Department of Neurology University of California San Francisco San Francisco CA USA. Genomics Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA. HudsonAlpha Institute for Biotechnology Huntsville AL USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA. Department of Developmental and Cell Biology University of California Irvine Irvine CA USA. Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. Department of Genetics and Genome Sciences Institute for Systems Genomics UConn Health Farmington CT USA. Département de Biochimie et Médecine Moléculaire Université de Montréal Montréal Quebec Canada. Division of Experimental Medicine McGill University Montreal Quebec Canada. Institut de Recherches Cliniques de Montréal (IR

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Author Correction: The bromodomain containing protein BRD-9 orchestrates RAD51-RAD54 complex formation and regulates homologous recombination-mediated repair

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Nature communications 2022年第1期13卷 7190页

作者： Qin Zhou Jinzhou Huang Chao Zhang Fei Zhao Wootae Kim Xinyi Tu Yong Zhang Somaira Nowsheen Qian Zhu Min Deng Yuping Chen Bo Qin Kuntian Luo Baohua Liu Zhenkun Lou Robert W Mutter Jian Yuan Department of Oncology Mayo Clinic Rochester MN 55905 USA. Department of Radiation Oncology Hubei Cancer Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan 430022 China. Mayo Medical Scientist Training Program Mayo Clinic School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences Mayo Clinic Rochester MN 55905 USA. Department of Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Rochester MN 55905 USA. Research Center for Translational Medicine East Hospital Tongji University School of medicine Shanghai 200120 China. Key Laboratory of Arrhythmias of the Ministry of Education of China East Hospital Tongji University School of Medicine Shanghai 200120 China. Guangdong Key Laboratory of Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen 518055 China. Department of Radiation Oncology Mayo Clinic Rochester MN 55905 USA. Mutter.Robert@mayo.edu. Research Center for Translational Medicine East Hospital Tongji University School of medicine Shanghai 200120 China. yuanjian229@***. Key Laboratory of Arrhythmias of the Ministry of Education of China East Hospital Tongji University School of Medicine Shanghai 200120 China. yuanjian229@***.

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Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

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Nature genetics 2023年第6期55卷 1080页

作者： Bernardo Rodriguez-Martin Eva G Alvarez Adrian Baez-Ortega Jorge Zamora Fran Supek Jonas Demeulemeester Martin Santamarina Young Seok Ju Javier Temes Daniel Garcia-Souto Harald Detering Yilong Li Jorge Rodriguez-Castro Ana Dueso-Barroso Alicia L Bruzos Stefan C Dentro Miguel G Blanco Gianmarco Contino Daniel Ardeljan Marta Tojo Nicola D Roberts Sonia Zumalave Paul A Edwards Joachim Weischenfeldt Montserrat Puiggròs Zechen Chong Ken Chen Eunjung Alice Lee Jeremiah A Wala Keiran M Raine Adam Butler Sebastian M Waszak Fabio C P Navarro Steven E Schumacher Jean Monlong Francesco Maura Niccolo Bolli Guillaume Bourque Mark Gerstein Peter J Park David C Wedge Rameen Beroukhim David Torrents Jan O Korbel Iñigo Martincorena Rebecca C Fitzgerald Peter Van Loo Haig H Kazazian Kathleen H Burns Peter J Campbell Jose M C Tubio Department of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela Santiago de Compostela Spain. Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain. Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Transmissible Cancer Group Department of Veterinary Medicine University of Cambridge Cambridge UK. The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain. Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK. Genome Data Science Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. The Francis Crick Institute London UK. Department of Human Genetics University of Leuven Leuven Belgium. Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea. Cancer Ageing and Somatic Mutation Programme Wellcome Sanger Institute Cambridge UK. Department of Biochemistry Genetics and Immunology University of Vigo Vigo Spain. Galicia Sur Health Research Institute Vigo Spain. Faculty of Science and Technology University of Vic-Central University of Catalonia (UVic-UCC) Vic Spain. Barcelona Supercomputing Center (BSC) Barcelona Spain. Experimental Cancer Genetics Wellcome Sanger Institute Cambridge UK. Oxford Big Data Institute University of Oxford Oxford UK. DNA Repair and Genome Integrity Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Department of Biochemistry and Molecular Biology Universidade de Santiago de Compostela Santiago de Compostela Spain. Medical R

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Author Correction: Examining the healthy human microbiome concept

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Nature reviews. Microbiology 2025年第3期23卷 206页

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Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

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Nature genetics 2023年第3期55卷 519-520页

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The ELIMÄKI Locus is Required for Vertical Proprioception in Birch Trees

SSRN

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SSRN 2019年

作者： Alonso-Serra, Juan Shi, Xueping Peaucelle, Alexis Rastas, Pasi Bourdon, Matthieu Immanen, Juha Takahashi, Junko Koivula, Hanna Eswaran, Gugan Muranen, Sampo Help, Hanna Smolander, Olli-Pekka Su, Chang Safronov, Omid Gerber, Lorenz Salojärvi, Jarkko Hagqvist, Risto Mähonen, Ari Pekka Nieminen, Kaisa Helariutta, Ykä Organismal and Evolutionary Biology Research Program Faculty of Biological and Environmental Sciences Viikki Plant Science Centre University of Helsinki Helsinki Finland Institute of Biotechnology HiLIFE University of Helsinki Helsinki Finland Key Laboratory of Horticultural Plant Biology of Ministry of Education College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan430070 China Sainsbury Laboratory University of Cambridge Cambridge United Kingdom Institut Jean-Pierre Bourgin INRA AgroParisTech CNRS Université Paris-Saclay Versailles78000 France Helsinki Finland Umeå Plant Science Center Department of Forest Genetics and Plant Physiology Swedish University of Agricultural Sciences Umeå Sweden Department of Food and Nutrition Faculty of Agriculture and Forestry University of Helsinki Finland Department of Physics Division of Materials Sciences X-ray Laboratory University of Helsinki Helsinki Finland Department of Chemistry and Biotechnology School of Science Tallinn University of Technology Tallinn Estonia Genome Institute of Singapore Singapore138672 Singapore Singapore Centre for Environmental Life Sciences Engineering Nanyang Technological University Singapore63755 Singapore

Tree architecture has evolved to support a top-heavy above-ground biomass, but this integral feature poses a weight-induced challenge to trunk stability. Maintaining an upright stem is expected to require vertical proprioception through feedback between sensing stem weight and modulating radial growth. Despite its apparent importance, the principle by which plant stems respond to vertical loading forces remains largely unknown. Here, by manipulating the stem weight of downy birch (Betula pubescens) trees, we show that cambial development is modulated systemically along the stem. We carried out a genetic study on the underlying regulation by combining an accelerated birch flowering program with a recessive mutation at the ELIMÄKI locus (EKI), which causes a mechanically defective response to weight stimulus resulting in stem collapse after just three months. We observed delayed wood morphogenesis in eki compared with WT, along with a more mechanically elastic cambial zone and radial compression of xylem cell size, indicating that timely tissue differentiation is critical for cambial growth under mechanical stress. Furthermore, the touch-induced mechanosensory pathway was transcriptionally misregulated in eki, indicating that the ELIMÄKI locus is required to integrate the weight-growth feedback regulation. By studying this birch mutant, we were able to dissect vertical proprioception from the gravitropic response associated with reaction wood formation. Taken together, our study provides evidence for both local and systemic responses to mechanical stimuli during secondary plant development. © 2019, The Authors. All rights reserved.

关键词： Forestry

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Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex

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Nature 2024年第7996期625卷 E26页

作者： Nathan R Zemke Ethan J Armand Wenliang Wang Seoyeon Lee Jingtian Zhou Yang Eric Li Hanqing Liu Wei Tian Joseph R Nery Rosa G Castanon Anna Bartlett Julia K Osteen Daofeng Li Xiaoyu Zhuo Vincent Xu Lei Chang Keyi Dong Hannah S Indralingam Jonathan A Rink Yang Xie Michael Miller Fenna M Krienen Qiangge Zhang Naz Taskin Jonathan Ting Guoping Feng Steven A McCarroll Edward M Callaway Ting Wang Ed S Lein M Margarita Behrens Joseph R Ecker Bing Ren Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA. Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA. Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. Genomic Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA. Division of Biological Sciences University of California San Diego La Jolla CA USA. Computational Neurobiology Laboratory The Salk Institute for Biological Studies La Jolla CA USA. Department of Genetics The Edison Family Center for Genome Sciences & Systems Biology Washington University School of Medicine St Louis MO USA. Princeton Neuroscience Institute Princeton University Princeton NJ USA. Department of Genetics Harvard Medical School Boston USA. Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA. McGovern Institute for Brain Research Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA USA. Allen Institute for Brain Science Seattle WA USA. Systems Neurobiology Laboratories The Salk Institute for Biological Studies La Jolla CA USA. Department of Neurosciences University of California San Diego La Jolla CA USA. McDonnell Genome Institute Washington University School of Medicine St. Louis MO USA. Department of Neurological Surgery University of Washington Seattle WA USA. Genomic Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA. ecker@salk.edu. Howard Hughes Medical Institute The Salk Institute for Biological Studies La Jolla CA USA. ecker@salk.edu. Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA. biren@ucsd.edu. Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA. biren@ucsd.edu. Institute of Genomic Medicine Moores Cancer C

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TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A (vol 603, pg 131, 2022)

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NATURE 2024年第8020期631卷 E7-E7页

作者： Brown, Anna-Leigh Wilkins, Oscar G. Keuss, Matthew J. Hill, Sarah E. Zanovello, Matteo Lee, Weaverly Colleen Bampton, Alexander Lee, Flora C. Y. Masino, Laura Qi, Yue A. Bryce-Smith, Sam Gatt, Ariana Hallegger, Martina Fagegaltier, Delphine Phatnani, Hemali Phatnani, Hemali Newcombe, Jia Gustavsson, Emil K. Seddighi, Sahba Reyes, Joel F. Coon, Steven L. Ramos, Daniel Schiavo, Giampietro Fisher, Elizabeth M. C. Raj, Towfique Secrier, Maria Lashley, Tammaryn Ule, Jernej Buratti, Emanuele Humphrey, Jack Ward, Michael E. Fratta, Pietro UCL Queen Square Motor Neuron Disease Centre Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology UCL London UK The Francis Crick Institute London UK UK Dementia Research Institute University College London London UK Department of Molecular Biology and Nanobiotechnology National Institute of Chemistry Ljubljana Slovenia National Institute of Neurological Disorders and Stroke NIH Bethesda MD USA Medical Scientist Training Program Johns Hopkins University School of Medicine Baltimore MD USA Center for Alzheimer’s and Related Dementias National Institutes of Health Bethesda MD USA Queen Square Brain Bank UCL Queen Square Institute of Neurology University College London London UK Department of Neurodegenerative Disease UCL Queen Square Institute of Neurology University College London London UK Great Ormond Street Institute of Child Health Genetics and Genomic Medicine University College London London UK Center for Genomics of Neurodegenerative Disease New York Genome Center (NYGC) New York NY USA NeuroResource Department of Neuroinflammation UCL Queen Square Institute of Neurology London UK Molecular Genomics Core Eunice Kennedy Shriver National Institute of Child Health and Human Development NIH Bethesda MD USA Nash Family Department of Neuroscience and Friedman Brain Institute Icahn School of Medicine at Mount Sinai New York NY USA Ronald M. Loeb Center for Alzheimer’s Disease Icahn School of Medicine at Mount Sinai New York NY USA Department of Pathology Fishberg Department of Neuroscience Icahn School of Medicine at Mount Sinai New York NY USA Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology Icahn School of Medicine at Mount Sinai New York NY USA Estelle and Daniel Maggin Department of Neurology Icahn School of Medicine at Mount Sinai New York NY USA Department of Genetics Evolution and Environment UCL Genetics Institute University College London London UK Mole

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Author Correction: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

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Nature communications 2021年第1期12卷 3128页

作者： Alessandro Bonetti Federico Agostini Ana Maria Suzuki Kosuke Hashimoto Giovanni Pascarella Juliette Gimenez Leonie Roos Alex J Nash Marco Ghilotti Christopher J F Cameron Matthew Valentine Yulia A Medvedeva Shuhei Noguchi Eneritz Agirre Kaori Kashi Joachim Luginbühl Riccardo Cazzoli Saumya Agrawal Nicholas M Luscombe Mathieu Blanchette Takeya Kasukawa Michiel de Hoon Erik Arner Boris Lenhard Charles Plessy Gonçalo Castelo-Branco Valerio Orlando Piero Carninci RIKEN Center for Integrative Medical Sciences Yokohama Kanagawa 230-0045 Japan. alessandro.bonetti@riken.jp. Laboratory of Molecular Neurobiology Department Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden. alessandro.bonetti@riken.jp. The Francis Crick Institute 1 Midland Road London NW1 1AT UK. RIKEN Center for Integrative Medical Sciences Yokohama Kanagawa 230-0045 Japan. Department of Medicine (H7) Karolinska Institutet Stockholm 141 86 Sweden. Epigenetics and Genome Reprogramming Laboratory IRCCS Fondazione Santa Lucia Rome Italy. Faculty of Medicine Imperial College London Institute of Clinical Sciences London W12 0NN UK. MRC London Institute of Medical Sciences London W12 0NN UK. School of Computer Science McGill University Montréal QC Canada. Department of Biochemistry and Goodman Cancer Research Centre McGill University Montréal QC Canada. Institute of Bioengineering Research Centre of Biotechnology Russian Academy of Science 117312 Moscow Russia. Department of Computational Biology Vavilov Institute of General Genetics Russian Academy of Science 119991 Moscow Russia. Department of Biological and Medical Physics Moscow Institute of Physics and Technology 141701 Dolgoprudny Moscow Region Russia. Laboratory of Molecular Neurobiology Department Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden. Department of Experimental Oncology IEO European Institute of Oncology IRCCS Milan Italy. UCL Genetics Institute University College London London WC1E 6BT UK. Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha Onna-son Kunigami-gun Okinawa 904-0495 Japan. Sars International Centre for Marine Molecular Biology University of Bergen 5008 Bergen Norway. Epigenetics and Genome Reprogramming Laboratory IRCCS Fondazione Santa Lucia Rome Italy. valerio.orlando@kaust.edu.sa. KAUST Environmental Epigenetics Program King Abdullah University of Science and Technology (KAUS

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