Abstract:
:We examined cell cycle-dependent changes in the proteome of human cells by systematically measuring protein dynamics in individual living cells. We used time-lapse microscopy to measure the dynamics of a random subset of 20 nuclear proteins, each tagged with yellow fluorescent protein (YFP) at its endogenous chromosomal location. We synchronized the cells in silico by aligning protein dynamics in each cell between consecutive divisions. We observed widespread (40%) cell-cycle dependence of nuclear protein levels and detected previously unknown cell cycle-dependent localization changes. This approach to dynamic proteomics can aid in discovery and accurate quantification of the extensive regulation of protein concentration and localization in individual living cells.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Sigal A,Milo R,Cohen A,Geva-Zatorsky N,Klein Y,Alaluf I,Swerdlin N,Perzov N,Danon T,Liron Y,Raveh T,Carpenter AE,Lahav G,Alon Udoi
10.1038/nmeth892subject
Has Abstractpub_date
2006-07-01 00:00:00pages
525-31issue
7eissn
1548-7091issn
1548-7105pii
nmeth892journal_volume
3pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract::We report attainment of subdiffraction resolution using stimulated emission depletion (STED) microscopy with GFP-labeled samples. The approximately 70 nm lateral resolution attained in this study is demonstrated by imaging GFP-labeled viruses and the endoplasmic reticulum (ER) of a mammalian cell. Our results mark the...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/nmeth922
更新日期:2006-09-01 00:00:00
abstract:: ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/s41592-018-0200-2
更新日期:2018-11-01 00:00:00
abstract::Firefly luciferase is the most widely used optical reporter for noninvasive bioluminescence imaging (BLI) in rodents. BLI relies on the ability of the injected luciferase substrate D-luciferin to access luciferase-expressing cells and tissues within the animal. Here we show that injection of mice with a synthetic luci...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2839
更新日期:2014-04-01 00:00:00
abstract::Because of ever-increasing throughput requirements of sequencing data, most existing short-read aligners have been designed to focus on speed at the expense of accuracy. The Genome Multitool (GEM) mapper can leverage string matching by filtration to search the alignment space more efficiently, simultaneously deliverin...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2221
更新日期:2012-12-01 00:00:00
abstract::We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps o...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3286
更新日期:2015-04-01 00:00:00
abstract::High-speed, large-scale three-dimensional (3D) imaging of neuronal activity poses a major challenge in neuroscience. Here we demonstrate simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain. Our technique captures the dynamic...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2964
更新日期:2014-07-01 00:00:00
abstract::Structure probing coupled with high-throughput sequencing could revolutionize our understanding of the role of RNA structure in regulation of gene expression. Despite recent technological advances, intrinsic noise and high sequence coverage requirements greatly limit the applicability of these techniques. Here we desc...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4068
更新日期:2017-01-01 00:00:00
abstract::We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scala...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth842
更新日期:2006-01-01 00:00:00
abstract::The dynamic reshaping of tissues during morphogenesis results from a combination of individual cell behaviors and collective cell rearrangements. However, a comprehensive framework to unambiguously measure and link cell behavior to tissue morphogenesis is lacking. Here we introduce such a kinematic framework, bridging...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1327
更新日期:2009-06-01 00:00:00
abstract::Spatiotemporal activity patterns in three-dimensionally organized cellular networks are fundamental to the function of the nervous system. Despite advances in functional imaging of cell populations, a method to resolve local network activity in three dimensions has been lacking. Here we introduce a three-dimensional (...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth989
更新日期:2007-01-01 00:00:00
abstract::Gene expression is extensively regulated at the levels of mRNA stability, localization and translation. However, decoding functional RNA-regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA-element selection assay (RESA), a method that selects RNA el...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4121
更新日期:2017-02-01 00:00:00
abstract::As a result of recent improvements in mass spectrometry (MS), there is increased interest in data-independent acquisition (DIA) strategies in which all peptides are systematically fragmented using wide mass-isolation windows ('multiplex fragmentation'). DIA-Umpire (http://diaumpire.sourceforge.net/), a comprehensive c...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3255
更新日期:2015-03-01 00:00:00
abstract::Despite the widespread adoption of organoids as biomimetic tissue models, methods to comprehensively analyze cell-type-specific post-translational modification (PTM) signaling networks in organoids are absent. Here, we report multivariate single-cell analysis of such networks in organoids and organoid cocultures. Simu...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-0737-8
更新日期:2020-03-01 00:00:00
abstract::Transcription activator-like effector (TALE) proteins have gained broad appeal as a platform for targeted DNA recognition, largely owing to their simple rules for design. These rules relate the base specified by a single TALE repeat to the identity of two key residues (the repeat variable diresidue, or RVD) and enable...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3330
更新日期:2015-05-01 00:00:00
abstract::Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very larg...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1699
更新日期:2011-09-11 00:00:00
abstract:: ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/s41592-018-0283-9
更新日期:2019-01-01 00:00:00
abstract::Our Patterning on Topography (PoT) printing technique enables fibronectin, laminin and other proteins to be applied to biomaterial surfaces in complex geometries that are inaccessible using traditional soft lithography techniques. Engineering combinatorial surfaces that integrate topographical and biochemical micropat...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3210
更新日期:2015-02-01 00:00:00
abstract::We applied pulse-shape analysis (PulSA) to monitor protein localization changes in mammalian cells by flow cytometry. PulSA enabled high-throughput tracking of protein aggregation, translocation from the cytoplasm to the nucleus and trafficking from the plasma membrane to the Golgi as well as stress-granule formation....
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1930
更新日期:2012-03-18 00:00:00
abstract::High spatial and temporal resolution of conditional gene expression is typically difficult to achieve in whole tissues or organisms. We synthesized two reversibly inhibited, photoactivatable ('caged') doxycycline derivatives with different membrane permeabilities for precise spatial and temporal light-controlled activ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1340
更新日期:2009-07-01 00:00:00
abstract::Plants have evolved a unique system in which the plant hormone auxin directly induces rapid degradation of the AUX/IAA family of transcription repressors by a specific form of the SCF E3 ubiquitin ligase. Other eukaryotes lack the auxin response but share the SCF degradation pathway, allowing us to transplant the auxi...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1401
更新日期:2009-12-01 00:00:00
abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Nature methods
pub_type: 已发布勘误
doi:10.1038/s41592-019-0588-3
更新日期:2019-10-01 00:00:00
abstract::Time resolution of current single-molecule fluorescence techniques is limited to milliseconds because of dye blinking and bleaching. Here we introduce a photoprotection strategy that affords microsecond resolution by combining efficient triplet quenching by oxygen and Trolox with minimized bleaching via the oxygen rad...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1553
更新日期:2011-02-01 00:00:00
abstract::The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and b...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3407
更新日期:2015-07-01 00:00:00
abstract::Gap junction channels assembled from connexin protein subunits mediate intercellular transfer of ions and metabolites. Impaired channel function is implicated in several hereditary human diseases. In particular, defective permeation of cAMP or inositol-1,4,5-trisphosphate (InsP(3)) through connexin channels is associa...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1031
更新日期:2007-04-01 00:00:00
abstract::Dissecting the relationship between genotype and phenotype is one of the central goals in developmental biology and medicine. Transcriptome analysis is a powerful strategy to connect genotype to phenotype of a cell. Here we review the history, progress, potential applications and future developments of single-cell tra...
journal_title:Nature methods
pub_type: 历史文章,杂志文章,评审
doi:10.1038/nmeth.1557
更新日期:2011-04-01 00:00:00
abstract::Glycosylation, which represents the most complex posttranslational modification (PTM) event during protein maturation, has a vital role in biological processes. Glycan biosynthesis is orchestrated by numerous glycosyltransferases, each displaying different selectivities for multiple reaction sites. The precise specifi...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1050
更新日期:2007-07-01 00:00:00
abstract::Zinc-finger nucleases (ZFNs) have enabled highly efficient gene targeting in multiple cell types and organisms. Here we describe methods for using simple ssDNA oligonucleotides in tandem with ZFNs to efficiently produce human cell lines with three distinct genetic outcomes: (i) targeted point mutation, (ii) targeted g...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1653
更新日期:2011-07-17 00:00:00
abstract::Achieving information content of satisfactory breadth and depth remains a formidable challenge for proteomics. This problem is particularly relevant to the study of primary human specimens, such as tumor biopsies, which are heterogeneous and of finite quantity. Here we present a functional proteomics strategy that uni...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth778
更新日期:2005-09-01 00:00:00
abstract::Microfluidic channels provide a means to deliver barcodes encoding spatial information to a tissue, which allows co-profiling of gene expression and proteins of interest in a spatially resolved manner. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-01043-w
更新日期:2021-01-01 00:00:00
abstract::Photoconvertible fluorescent proteins are potential tools for investigating dynamic processes in living cells and for emerging super-resolution microscopy techniques. Unfortunately, most probes in this class are hampered by oligomerization, small photon budgets or poor photostability. Here we report an EosFP variant t...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1296
更新日期:2009-02-01 00:00:00