A multi-scale map of cell structure fusing protein images and interactions.

Antigens, Nuclear / genetics Chromatin / genetics Chromosomes / metabolism Humans Nuclear Matrix-Associated Proteins / metabolism Proteome / metabolism RNA, Ribosomal RNA-Binding Proteins / genetics

Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
12 2021
Historique:
received: 18 06 2020
accepted: 08 10 2021
pubmed: 26 11 2021
medline: 23 4 2022
entrez: 25 11 2021
Statut: ppublish

Résumé

The cell is a multi-scale structure with modular organization across at least four orders of magnitude

Identifiants

DOI: 10.1038/s41586-021-04115-9 PMID: 34819669 PMC: PMC9053732
pubmed: 34819669
doi: 10.1038/s41586-021-04115-9
pii: 10.1038/s41586-021-04115-9
pmc: PMC9053732
mid: NIHMS1784657
doi:

Substances chimiques

Antigens, Nuclear 0
Chromatin 0
Nuclear Matrix-Associated Proteins 0
Proteome 0
RNA, Ribosomal 0
RNA-Binding Proteins 0
SRRM1 protein, human 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

536-542

Subventions

Organisme : NCI NIH HHS
ID : R50 CA243885
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL137223
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG006673
Pays : United States
Organisme : NCI NIH HHS
ID : F99 CA264422
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG009889
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG004659
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG009979
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA209891
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA067754
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM103504
Pays : United States
Organisme : NIMH NIH HHS
ID : U01 MH115747
Pays : United States

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

Références

Harold, F. M. Molecules into cells: specifying spatial architecture. Microbiol. Mol. Biol. Rev. 69, 544–564 (2005).
doi: 10.1128/MMBR.69.4.544-564.2005
Mori, H. & Cardiff, R. D. Methods of immunohistochemistry and immunofluorescence: converting invisible to visible. In The Tumor Microenvironment, Methods in Molecular Biology Vol. 1458 (eds Ursini-Siegel, J. & Beauchemin, N.) 1–12 (Humana Press, 2016).
Aebersold, R. & Mann, M. Mass-spectrometric exploration of proteome structure and function. Nature 537, 347–355 (2016).
doi: 10.1038/nature19949
Thul, P. J. et al. A subcellular map of the human proteome. Science 356, eaal3321 (2017).
doi: 10.1126/science.aal3321
Huttlin, E. L. et al. Architecture of the human interactome defines protein communities and disease networks. Nature 545, 505–509 (2017).
doi: 10.1038/nature22366
Schaffer, L. V. & Ideker, T. Mapping the multiscale structure of biological systems. Cell Syst. 12, 622–635 (2021).
doi: 10.1016/j.cels.2021.05.012
Ouyang, W. et al. Analysis of the Human Protein Atlas Image Classification competition. Nat. Methods 16, 1254–1261 (2019).
doi: 10.1038/s41592-019-0658-6
Grover, A. & Leskovec, J. node2vec: scalable feature learning for networks. In KDD ’16: Proc. 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 855–864 (2016).
Goodfellow, I., Bengio, Y., Courville, A. & Bengio, Y. Deep Learning Vol. 1 (MIT Press, 2016).
Fortunato, S. & Hric, D. Community detection in networks: a user guide. Phys. Rep. 659, 1–44 (2016).
doi: 10.1016/j.physrep.2016.09.002
Go, C. D. et al. A proximity-dependent biotinylation map of a human cell. Nature 595, 120–124 (2021)
doi: 10.1038/s41586-021-03592-2
Meyers, R. M. et al. Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779–1784 (2017).
doi: 10.1038/ng.3984
Deckert, J. et al. Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions. Mol. Cell. Biol. 26, 5528–5543 (2006).
doi: 10.1128/MCB.00582-06
Charenton, C., Wilkinson, M. E. & Nagai, K. Mechanism of 5′ splice site transfer for human spliceosome activation. Science 364, 362–367 (2019).
doi: 10.1126/science.aax3289
Yoshikatsu, Y. et al. NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing. Biochem. Biophys. Res. Commun. 464, 780–786 (2015).
doi: 10.1016/j.bbrc.2015.07.032
Chaudhuri, S. et al. Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation. RNA 13, 2224–2237 (2007).
doi: 10.1261/rna.694007
Tafforeau, L. et al. The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of pre-rRNA processing factors. Mol. Cell 51, 539–551 (2013).
doi: 10.1016/j.molcel.2013.08.011
Eppens, N. A. et al. Deletions in the S1 domain of Rrp5p cause processing at a novel site in ITS1 of yeast pre-rRNA that depends on Rex4p. Nucleic Acids Res. 30, 4222–4231 (2002).
doi: 10.1093/nar/gkf538
De Silva, D., Tu, Y.-T., Amunts, A., Fontanesi, F. & Barrientos, A. Mitochondrial ribosome assembly in health and disease. Cell Cycle 14, 2226–2250 (2015).
doi: 10.1080/15384101.2015.1053672
Blencowe, B. J. et al. The SRm160/300 splicing coactivator subunits. RNA 6, 111–120 (2000).
doi: 10.1017/S1355838200991982
The UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47, D506–D515 (2019).
doi: 10.1093/nar/gky1049
Pavan Kumar, P. et al. Phosphorylation of SATB1, a global gene regulator, acts as a molecular switch regulating its transcriptional activity in vivo. Mol. Cell 22, 231–243 (2006).
doi: 10.1016/j.molcel.2006.03.010
Pomeranz Krummel, D. A., Oubridge, C., Leung, A. K. W., Li, J. & Nagai, K. Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature 458, 475–480 (2009).
doi: 10.1038/nature07851
Fleckner, J., Zhang, M., Valcárcel, J. & Green, M. R. U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. Genes Dev. 11, 1864–1872 (1997).
doi: 10.1101/gad.11.14.1864
Van Nostrand, E. L. et al. A large-scale binding and functional map of human RNA-binding proteins. Nature 583, 711–719 (2020).
doi: 10.1038/s41586-020-2077-3
Van Nostrand, E. L. et al. Robust, cost-effective profiling of RNA binding protein targets with single-end enhanced crosslinking and immunoprecipitation (seCLIP). In mRNA Processing, Methods in Molecular Biology Vol. 1648 (ed. Shi, Y.) 177–200 (Humana Press, 2017).
Stryer, L. Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47, 819–846 (1978).
doi: 10.1146/annurev.bi.47.070178.004131
Wang, T. et al. Gene essentiality profiling reveals gene networks and synthetic lethal interactions with oncogenic Ras. Cell 168, 890–903 (2017).
doi: 10.1016/j.cell.2017.01.013
Huttlin, E. L. et al. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 184, 3022–3040 (2021).
doi: 10.1016/j.cell.2021.04.011
Williams, S. G. & Hall, K. B. Human U2B″ protein binding to snRNA stemloops. Biophys. Chem. 159, 82–89 (2011).
doi: 10.1016/j.bpc.2011.05.010
Huang, G., Liu, Z., van der Maaten, L. & Weinberger, K. Q. Densely connected convolutional networks. Preprint at https://arxiv.org/abs/1608.06993 (2016).
Nusinow, D. P. et al. Quantitative proteomics of the Cancer Cell Line Encyclopedia. Cell 180, 387–402 (2020).
doi: 10.1016/j.cell.2019.12.023

Auteurs

Yue Qin (Y)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-0496-7134

Edward L Huttlin (EL)

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-1822-1173

Casper F Winsnes (CF)

Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
ORCID: 0000-0002-0028-5865

Maya L Gosztyla (ML)

Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0003-4758-4800

Ludivine Wacheul (L)

RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium.
ORCID: 0000-0002-0443-8865

Marcus R Kelly (MR)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Steven M Blue (SM)

Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0003-0279-6690

Fan Zheng (F)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Michael Chen (M)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Leah V Schaffer (LV)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Katherine Licon (K)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Anna Bäckström (A)

Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.

Laura Pontano Vaites (LP)

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

John J Lee (JJ)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-7967-3384

Wei Ouyang (W)

Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
ORCID: 0000-0002-0291-926X

Sophie N Liu (SN)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0001-7934-8605

Tian Zhang (T)

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

Erica Silva (E)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Jisoo Park (J)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Adriana Pitea (A)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Jason F Kreisberg (JF)

Department of Medicine, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-3616-079X

Steven P Gygi (SP)

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0001-7626-0034

Jianzhu Ma (J)

Institute for Artificial Intelligence, Peking University, Beijing, China.
ORCID: 0000-0002-8236-6609

J Wade Harper (JW)

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-6944-7236

Gene W Yeo (GW)

Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-0799-6037

Denis L J Lafontaine (DLJ)

RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium.
ORCID: 0000-0001-7295-6288

Emma Lundberg (E)

Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden. emma.lundberg@scilifelab.se.
Department of Genetics, Stanford University, Stanford, CA, USA. emma.lundberg@scilifelab.se.
Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA. emma.lundberg@scilifelab.se.
ORCID: 0000-0001-7034-0850

Trey Ideker (T)

Department of Medicine, University of California San Diego, La Jolla, CA, USA. tideker@ucsd.edu.
Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA. tideker@ucsd.edu.
Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA. tideker@ucsd.edu.
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. tideker@ucsd.edu.
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. tideker@ucsd.edu.
ORCID: 0000-0002-1708-8454

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Classifications MeSH

questionsmedicales.fr › Facteurs biologiques › Antigènes › Antigènes nucléaires › A multi-scale map of cell structure fusing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › A multi-scale map of cell structure fusing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Chromosomes › A multi-scale map of cell structure fusing...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › A multi-scale map of cell structure fusing...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines nucléaires › Protéines associées à la matrice nucléaire › A multi-scale map of cell structure fusing...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéome › A multi-scale map of cell structure fusing...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN ribosomique › A multi-scale map of cell structure fusing...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Nucléoprotéines › Protéines de liaison à l'ARN › A multi-scale map of cell structure fusing...