IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v489y2012i7414d10.1038_nature11233.html
   My bibliography  Save this article

Landscape of transcription in human cells

Author

Listed:
  • Sarah Djebali

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Carrie A. Davis

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Angelika Merkel

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Alex Dobin

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Timo Lassmann

    (RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Ali Mortazavi

    (California Institute of Technology, 2 Beckman Institute
    University of California Irvine, 2300 Biological Sciences III, Irvine, California 92697, USA)

  • Andrea Tanzer

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Julien Lagarde

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Wei Lin

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Felix Schlesinger

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Chenghai Xue

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Georgi K. Marinov

    (California Institute of Technology, 2 Beckman Institute)

  • Jainab Khatun

    (Boise State University, College of Arts & Sciences, 1910 University Drive)

  • Brian A. Williams

    (California Institute of Technology, 2 Beckman Institute)

  • Chris Zaleski

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Joel Rozowsky

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Maik Röder

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Felix Kokocinski

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Rehab F. Abdelhamid

    (RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Tyler Alioto

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Centro Nacional de Análisis Genómico (CNAG), C/ Baldiri Reixac 4, Torre I, Barcelona 08028, Catalonia, Spain)

  • Igor Antoshechkin

    (California Institute of Technology, 2 Beckman Institute)

  • Michael T. Baer

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Nadav S. Bar

    (Norwegian University of Science and Technology, Trondheim NO-7491, Norway)

  • Philippe Batut

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Kimberly Bell

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Ian Bell

    (Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA)

  • Sudipto Chakrabortty

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Xian Chen

    (University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, USA)

  • Jacqueline Chrast

    (University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne 1015, Switzerland)

  • Joao Curado

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Thomas Derrien

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Jorg Drenkow

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Erica Dumais

    (Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA)

  • Jacqueline Dumais

    (Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA)

  • Radha Duttagupta

    (Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA)

  • Emilie Falconnet

    (University of Geneva Medical School, 1 rue Michel-Servet, Geneva 1211, Switzerland)

  • Meagan Fastuca

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Kata Fejes-Toth

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Pedro Ferreira

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Sylvain Foissac

    (Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA)

  • Melissa J. Fullwood

    (Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore)

  • Hui Gao

    (Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA)

  • David Gonzalez

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Assaf Gordon

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Harsha Gunawardena

    (University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, USA)

  • Cedric Howald

    (University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne 1015, Switzerland)

  • Sonali Jha

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Rory Johnson

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain)

  • Philipp Kapranov

    (Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA
    St Laurent Institute, One Kendall Square)

  • Brandon King

    (California Institute of Technology, 2 Beckman Institute)

  • Colin Kingswood

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Centro Nacional de Análisis Genómico (CNAG), C/ Baldiri Reixac 4, Torre I, Barcelona 08028, Catalonia, Spain)

  • Oscar J. Luo

    (Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore)

  • Eddie Park

    (University of California Irvine, 2300 Biological Sciences III, Irvine, California 92697, USA)

  • Kimberly Persaud

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Jonathan B. Preall

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Paolo Ribeca

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Centro Nacional de Análisis Genómico (CNAG), C/ Baldiri Reixac 4, Torre I, Barcelona 08028, Catalonia, Spain)

  • Brian Risk

    (Boise State University, College of Arts & Sciences, 1910 University Drive)

  • Daniel Robyr

    (University of Geneva Medical School, 1 rue Michel-Servet, Geneva 1211, Switzerland)

  • Michael Sammeth

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Centro Nacional de Análisis Genómico (CNAG), C/ Baldiri Reixac 4, Torre I, Barcelona 08028, Catalonia, Spain)

  • Lorian Schaffer

    (California Institute of Technology, 2 Beckman Institute)

  • Lei-Hoon See

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Atif Shahab

    (Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore)

  • Jorgen Skancke

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Norwegian University of Science and Technology, Trondheim NO-7491, Norway)

  • Ana Maria Suzuki

    (RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Hazuki Takahashi

    (RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Hagen Tilgner

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Present address: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.)

  • Diane Trout

    (California Institute of Technology, 2 Beckman Institute)

  • Nathalie Walters

    (University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne 1015, Switzerland)

  • Huaien Wang

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • John Wrobel

    (Boise State University, College of Arts & Sciences, 1910 University Drive)

  • Yanbao Yu

    (University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, USA)

  • Xiaoan Ruan

    (Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore)

  • Yoshihide Hayashizaki

    (RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Jennifer Harrow

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Mark Gerstein

    (Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
    Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA)

  • Tim Hubbard

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Alexandre Reymond

    (University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne 1015, Switzerland)

  • Stylianos E. Antonarakis

    (University of Geneva Medical School, 1 rue Michel-Servet, Geneva 1211, Switzerland)

  • Gregory Hannon

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA)

  • Morgan C. Giddings

    (Boise State University, College of Arts & Sciences, 1910 University Drive
    University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, USA)

  • Yijun Ruan

    (Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore)

  • Barbara Wold

    (California Institute of Technology, 2 Beckman Institute)

  • Piero Carninci

    (RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Roderic Guigó

    (Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain)

  • Thomas R. Gingeras

    (Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
    Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA)

Abstract

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Suggested Citation

  • Sarah Djebali & Carrie A. Davis & Angelika Merkel & Alex Dobin & Timo Lassmann & Ali Mortazavi & Andrea Tanzer & Julien Lagarde & Wei Lin & Felix Schlesinger & Chenghai Xue & Georgi K. Marinov & Jaina, 2012. "Landscape of transcription in human cells," Nature, Nature, vol. 489(7414), pages 101-108, September.
    • Handle: RePEc:nat:nature:v:489:y:2012:i:7414:d:10.1038_nature11233
    DOI: 10.1038/nature11233
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature11233
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature11233?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Gavin J. Sutton & Daniel Poppe & Rebecca K. Simmons & Kieran Walsh & Urwah Nawaz & Ryan Lister & Johann A. Gagnon-Bartsch & Irina Voineagu, 2022. "Comprehensive evaluation of deconvolution methods for human brain gene expression," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Claudia Ctortecka & Natalie M. Clark & Brian W. Boyle & Anjali Seth & D. R. Mani & Namrata D. Udeshi & Steven A. Carr, 2024. "Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    3. Zhantao Shao & Jack Hu & Allison Jandura & Ronit Wilk & Matthew Jachimowicz & Lingfeng Ma & Chun Hu & Abby Sundquist & Indrani Das & Phillip Samuel-Larbi & Julie A. Brill & Henry M. Krause, 2024. "Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Jie Liao & Jingyang Qian & Yin Fang & Zhuo Chen & Xiang Zhuang & Ningyu Zhang & Xin Shao & Yining Hu & Penghui Yang & Junyun Cheng & Yang Hu & Lingqi Yu & Haihong Yang & Jinlu Zhang & Xiaoyan Lu & Li , 2022. "De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    5. Wei Hu & Yangjun Wu & Qili Shi & Jingni Wu & Deping Kong & Xiaohua Wu & Xianghuo He & Teng Liu & Shengli Li, 2022. "Systematic characterization of cancer transcriptome at transcript resolution," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    6. Ravneet Jaura & Ssu-Yu Yeh & Kaitlin N. Montanera & Alyssa Ialongo & Zobia Anwar & Yiming Lu & Kavindu Puwakdandawa & Ho Sung Rhee, 2022. "Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    7. Robert Atkinson & Maria Georgiou & Chunbo Yang & Katarzyna Szymanska & Albert Lahat & Elton J. R. Vasconcelos & Yanlong Ji & Marina Moya Molina & Joseph Collin & Rachel Queen & Birthe Dorgau & Avril W, 2024. "PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5´-splice-site selection causing tissue-specific defects," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    8. Clarice K. Y. Hong & Yawei Wu & Alyssa A. Erickson & Jie Li & Arnold J. Federico & Barak A. Cohen, 2024. "Massively parallel characterization of insulator activity across the genome," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Marco Luciani & Chiara Garsia & Stefano Beretta & Ingrid Cifola & Clelia Peano & Ivan Merelli & Luca Petiti & Annarita Miccio & Vasco Meneghini & Angela Gritti, 2024. "Human iPSC-derived neural stem cells displaying radial glia signature exhibit long-term safety in mice," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    10. Kota Hamamoto & Yusuke Umemura & Shiho Makino & Takashi Fukaya, 2023. "Dynamic interplay between non-coding enhancer transcription and gene activity in development," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    11. Letizia Pitto & Francesca Gorini & Fabrizio Bianchi & Elena Guzzolino, 2020. "New Insights into Mechanisms of Endocrine-Disrupting Chemicals in Thyroid Diseases: The Epigenetic Way," IJERPH, MDPI, vol. 17(21), pages 1-18, October.
    12. Morgane Boone & Pathmanaban Ramasamy & Jasper Zuallaert & Robbin Bouwmeester & Berre Moer & Davy Maddelein & Demet Turan & Niels Hulstaert & Hannah Eeckhaut & Elien Vandermarliere & Lennart Martens & , 2021. "Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    13. Edie-Rosmin Wu & Ming-Ju Hsieh & Whei-Ling Chiang & Kuan-Chun Hsueh & Shun-Fa Yang & Shih-Chi Su, 2019. "Association of lncRNA CCAT2 and CASC8 Gene Polymorphisms with Hepatocellular Carcinoma," IJERPH, MDPI, vol. 16(16), pages 1-11, August.
    14. Anne-Emmanuelle Foucher & Leila Touat-Todeschini & Ariadna B. Juarez-Martinez & Auriane Rakitch & Hamida Laroussi & Claire Karczewski & Samira Acajjaoui & Montserrat Soler-López & Stephen Cusack & Cam, 2022. "Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    15. Luke Hoberecht & Pirunthan Perampalam & Aaron Lun & Jean-Philippe Fortin, 2022. "A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    16. Annkatrin Bressin & Olga Jasnovidova & Mirjam Arnold & Elisabeth Altendorfer & Filip Trajkovski & Thomas A. Kratz & Joanna E. Handzlik & Denes Hnisz & Andreas Mayer, 2023. "High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    17. Shurong Liu & Junhong Huang & Jie Zhou & Siyan Chen & Wujian Zheng & Chang Liu & Qiao Lin & Ping Zhang & Di Wu & Simeng He & Jiayi Ye & Shun Liu & Keren Zhou & Bin Li & Lianghu Qu & Jianhua Yang, 2024. "NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions," Nature Communications, Nature, vol. 15(1), pages 1-21, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:489:y:2012:i:7414:d:10.1038_nature11233. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.