How many human proteoforms are there
Ruedi Aebersold,Jeffrey N. Agar,I. Jonathan Amster,Mark S. Baker,Carolyn R. Bertozzi,Emily S. Boja,Catherine E. Costello,Benjamin F. Cravatt,Catherine Fenselau,Benjamin A. Garcia,Ying Ge,Jeremy Gunawardena,Ronald C. Hendrickson,Paul J. Hergenrother,Christian G. Huber,Alexander R. Ivanov,Ole N. Jensen,Michael C. Jewett,Neil L. Kelleher,Laura L. Kiessling,Nevan J. Krogan,Martin R. Larsen,Joseph A. Loo,Rachel R. Ogorzalek Loo,Emma Lundberg,Emma Lundberg,Michael J. MacCoss,Parag Mallick,Vamsi K. Mootha,Milan Mrksich,Tom W. Muir,Steven M. Patrie,James J. Pesavento,Sharon J. Pitteri,Henry Rodriguez,Alan Saghatelian,Wendy Sandoval,Hartmut Schlüter,Salvatore Sechi,Sarah A. Slavoff,Lloyd M. Smith,Michael Snyder,Paul M. Thomas,Mathias Uhlén,Jennifer E. Van Eyk,Marc Vidal,David R. Walt,Forest M. White,Evan R. Williams,Therese Wohlschlager,Vicki H. Wysocki,Nathan A. Yates,Nicolas L. Young,Bing Zhang +53 more
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TLDR
This work frames central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today, and uses this framework to assess existing data and ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?"Abstract:
Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function O read more
Citations
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Functions and mechanisms of non-histone protein acetylation
TL;DR: Recent progress is discussed in the understanding of the scope, functional diversity and mechanisms of non-histone protein acetylation, which regulates many cellular processes, such as transcription, DNA repair, signal transduction, protein folding and autophagy.
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Global view of human protein glycosylation pathways and functions
TL;DR: This work predicts that use of (single-cell) transcriptomics, genetic screens, genetic engineering of cellular glycosylation capacities and custom design of glycoprotein therapeutics are advancements that will ignite wider integration of gly cosylation in general cell biology.
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mRNAs, proteins and the emerging principles of gene expression control.
TL;DR: How large-scale comparative studies are characterizing the degree to which mRNA and protein levels correlate is discussed, and how transcriptomics and proteomics provide useful non-redundant readouts of gene expression is described.
Journal ArticleDOI
Tau PTM Profiles Identify Patient Heterogeneity and Stages of Alzheimer's Disease
Hendrik Wesseling,Waltraud Mair,Mukesh Kumar,Christoph N. Schlaffner,Shaojun Tang,Pieter Beerepoot,Benoit Fatou,Amanda J. Guise,Long Cheng,Shuko Takeda,Jan Muntel,Melissa S. Rotunno,Simon Dujardin,Peter Davies,Kenneth S. Kosik,Bruce L. Miller,Sabina Berretta,John C. Hedreen,Lea T. Grinberg,William W. Seeley,Bradley T. Hyman,Hanno Steen,Judith A. Steen +22 more
TL;DR: Although Tau PTM maps reveal heterogeneity across subjects, a subset of PTMs display high occupancy and frequency for AD, suggesting importance in disease, and unsupervised analyses indicate that PTMs occur in an ordered manner, leading to Tau aggregation.
Journal ArticleDOI
Spatial proteomics: a powerful discovery tool for cell biology.
TL;DR: Spatial proteomics improves the understanding of protein function by revealing the subcellular localizations of proteins and their movement between compartments, and ways to improve integration of spatial proteomics data are discussed.
References
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Tissue-based map of the human proteome
Mathias Uhlén,Mathias Uhlén,Linn Fagerberg,Björn M. Hallström,Cecilia Lindskog,Per Oksvold,Adil Mardinoglu,Åsa Sivertsson,Caroline Kampf,Evelina Sjöstedt,Evelina Sjöstedt,Anna Asplund,IngMarie Olsson,Karolina Edlund,Emma Lundberg,Sanjay Navani,Cristina Al-Khalili Szigyarto,Jacob Odeberg,Dijana Djureinovic,Jenny Ottosson Takanen,Sophia Hober,Tove Alm,Per-Henrik Edqvist,Holger Berling,Hanna Tegel,Jan Mulder,Johan Rockberg,Peter Nilsson,Jochen M. Schwenk,Marica Hamsten,Kalle von Feilitzen,Mattias Forsberg,Lukas Persson,Fredric Johansson,Martin Zwahlen,Gunnar von Heijne,Jens Nielsen,Jens Nielsen,Fredrik Pontén +38 more
TL;DR: In this paper, a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level.
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Translating the Histone Code
Thomas Jenuwein,C. David Allis +1 more
TL;DR: It is proposed that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.
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UniProt: the Universal Protein knowledgebase
Rolf Apweiler,Amos Marc Bairoch,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces.
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Eric T. Wang,Rickard Sandberg,Rickard Sandberg,Shujun Luo,Irina Khrebtukova,Lu Zhang,Christine Mayr,Stephen F. Kingsmore,Gary P. Schroth,Christopher B. Burge +9 more
TL;DR: An in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments yielding a digital inventory of gene and mRNA isoform expression suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.
Journal ArticleDOI
A draft map of the human proteome
Min-Sik Kim,Sneha M. Pinto,Derese Getnet,Raja Sekhar Nirujogi,Srikanth S. Manda,Raghothama Chaerkady,Anil K. Madugundu,Dhanashree S. Kelkar,Ruth Isserlin,Shobhit Jain,Joji Kurian Thomas,Babylakshmi Muthusamy,Pamela Leal-Rojas,Pamela Leal-Rojas,Praveen Kumar,Nandini A. Sahasrabuddhe,Lavanya Balakrishnan,Jayshree Advani,Bijesh George,Santosh Renuse,Lakshmi Dhevi N. Selvan,Arun H. Patil,Vishalakshi Nanjappa,Aneesha Radhakrishnan,Samarjeet Prasad,Tejaswini Subbannayya,Rajesh Raju,Manish Kumar,Sreelakshmi K. Sreenivasamurthy,Arivusudar Marimuthu,Gajanan Sathe,Sandip Chavan,Keshava K. Datta,Yashwanth Subbannayya,Apeksha Sahu,Soujanya D. Yelamanchi,Savita Jayaram,Pavithra Rajagopalan,Jyoti Sharma,Krishna R Murthy,Nazia Syed,Renu Goel,Aafaque Ahmad Khan,Sartaj Ahmad,Gourav Dey,Keshav Mudgal,Aditi Chatterjee,Tai-Chung Huang,Jun Zhong,Xinyan Wu,Patrick G. Shaw,Donald Freed,Muhammad Saddiq Zahari,Kanchan K Mukherjee,Subramanian Shankar,Anita Mahadevan,Henry H N Lam,Chris J. Mitchell,Susarla K. Shankar,Parthasarathy Satishchandra,John T. Schroeder,Ravi Sirdeshmukh,Anirban Maitra,Steven D. Leach,Charles G. Drake,Marc K. Halushka,T. S. Keshava Prasad,Ralph H. Hruban,Candace L. Kerr,Candace L. Kerr,Gary D. Bader,Christine A. Iacobuzio-Donahue,Harsha Gowda,Akhilesh Pandey +73 more
TL;DR: A draft map of the human proteome is presented using high-resolution Fourier-transform mass spectrometry to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-c coding RNAs and upstream open reading frames.
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