Abstract：
:MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular resolution. We report microRNome by methylation-dependent sequencing (mime-seq), an in vivo enzymatic small-RNA-tagging approach that enables high-throughput sequencing of tissue- and cell-type-specific miRNAs in animals. The method combines cell-type-specific 3'-terminal 2'-O-methylation of animal miRNAs by a genetically encoded, plant-specific methyltransferase (HEN1), with chemoselective small-RNA cloning and high-throughput sequencing. We show that mime-seq uncovers the miRNomes of specific cells within Caenorhabditis elegans and Drosophila at unprecedented specificity and sensitivity, enabling miRNA profiling with single-cell resolution in whole animals. Mime-seq overcomes current challenges in cell-type-specific small-RNA profiling and provides novel entry points for understanding the function of miRNAs in spatially restricted physiological settings.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Alberti C,Manzenreither RA,Sowemimo I,Burkard TR,Wang J,Mahofsky K,Ameres SL,Cochella Ldoi
10.1038/nmeth.4610subject
Has Abstractpub_date
2018-04-01 00:00:00pages
283-289issue
4eissn
1548-7091issn
1548-7105pii
nmeth.4610journal_volume
15pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract：:To enhance the repertoire of molecular tools for studying malaria parasite biology, we adapted a ligand-regulatable FKBP protein destabilization domain (ddFKBP) for use in P. falciparum. We destabilized the reporter yellow fluorescent protein (YFP) and the P. falciparum protease falcipain-2 in a ligand-reversible mann...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth1132
更新日期：2007-12-01 00:00:00
abstract：:Caenorhabditis elegans is an important model organism in biology, but until now no antibiotic selection markers have been successfully demonstrated for this species. We have developed a selection system using puromycin that allows the rapid and easy isolation of large populations of transgenic worms. This approach is ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1495
更新日期：2010-09-01 00:00:00
abstract：:We must reliably map the interactomes of cellular macromolecular complexes in order to fully explore and understand biological systems. However, there are no methods to accurately predict how to capture a given macromolecular complex with its physiological binding partners. Here, we present a screening method that com...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3395
更新日期：2015-06-01 00:00:00
abstract：:Electron cryotomography is currently the only method capable of visualizing cells in three dimensions at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information, data processing is very labor intensive and the results are often limited...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0591-8
更新日期：2019-11-01 00:00:00
abstract：:The understanding of integral membrane protein (IMP) structure and function is hampered by the difficulty of handling these proteins. Aqueous solubilization, necessary for many types of biophysical analysis, generally requires a detergent to shield the large lipophilic surfaces of native IMPs. Many proteins remain dif...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1526
更新日期：2010-12-01 00:00:00
abstract：:We have developed a versatile, potent technique for imaging cells in culture and in vivo by expressing a metabolically biotinylated cell-surface receptor and visualizing it with labeled streptavidin moieties. The recombinant reporter protein, which incorporates a biotin acceptor peptide (BAP) between an N-terminal sig...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth875
更新日期：2006-05-01 00:00:00
abstract：:We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial c...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3955
更新日期：2016-09-01 00:00:00
abstract：:We report a simple and generic method for the direct transfer of protein complexes separated by native gel electrophoresis to electron microscopy grids. After transfer, sufficient material remains in the gel for identification and characterization by mass spectrometry. The method should facilitate higher-throughput si...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1840
更新日期：2012-01-08 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：:The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. We describe an improved transcriptional regulator obtained through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3312
更新日期：2015-04-01 00:00:00
abstract：:An outstanding challenge of epigenome-wide association studies (EWASs) performed in complex tissues is the identification of the specific cell type(s) responsible for the observed differential DNA methylation. Here we present a statistical algorithm called CellDMC ( https://github.com/sjczheng/EpiDISH ), which can ide...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-018-0213-x
更新日期：2018-12-01 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：:We introduce a nonintrusive method exploiting single-cell variability after cell division to validate protein localization. We found that Clp proteases, widely reported to form biologically relevant foci, were uniformly distributed in Escherichia coli cells, and that many commonly used fluorescent proteins caused seve...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1955
更新日期：2012-04-08 00:00:00
abstract：:We present a noninvasive approach to track activation of ATP-gated P2X receptors and potentially other transmitter-gated cation channels that show calcium fluxes. We genetically engineered rat P2X receptors to carry calcium sensors near the channel pore and tested this as a reporter for P2X(2) receptor opening. The me...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth1144
更新日期：2008-01-01 00:00:00
abstract：:The protein ubiquitin is an important post-translational modifier that regulates a wide variety of biological processes. In cells, ubiquitin is apportioned among distinct pools, which include a variety of free and conjugated species. Although maintenance of a dynamic and complex equilibrium among ubiquitin pools is cr...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1649
更新日期：2011-07-10 00:00:00
abstract：:Here we integrated multiphoton laser scanning microscopy and the registration of second harmonic generation images of collagen fibers to overcome difficulties in tracking stromal cell-matrix interactions for several days in live mice. We show that the matrix-modifying hormone relaxin increased tumor-associated fibrobl...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1295
更新日期：2009-02-01 00:00:00
abstract：:Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression pro...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1315
更新日期：2009-05-01 00:00:00
abstract：:We describe a statistical analysis methodology designed to minimize the impact of off-target activities upon large-scale RNA interference (RNAi) screens in mammalian cells. Application of this approach enhances reconfirmation rates and facilitates the experimental validation of new gene activities through the probabil...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth1089
更新日期：2007-10-01 00:00:00
abstract：:Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectromet...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0461-4
更新日期：2019-08-01 00:00:00
abstract：:Phenotype-based small-molecule screening is a powerful method to identify molecules that regulate cellular functions. However, such screens are generally performed in vitro under conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3992
更新日期：2016-10-01 00:00:00
abstract：:We describe a simple method for efficiently labeling cell-surface sialic acid-containing glycans on living animal cells. The method uses mild periodate oxidation to generate an aldehyde on sialic acids, followed by aniline-catalyzed oxime ligation with a suitable tag. Aniline catalysis dramatically accelerates oxime l...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1305
更新日期：2009-03-01 00:00:00
abstract：:We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic protein...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-020-0801-4
更新日期：2020-05-01 00:00:00
abstract：:Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of in...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2592
更新日期：2013-09-01 00:00:00
abstract：:We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These 'spaghetti monster' fluorescent proteins (smFPs) distributed well in neurons, notably into sm...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3365
更新日期：2015-06-01 00:00:00
abstract：:The study of protein-protein interactions by mass spectrometry is an increasingly important part of post-genomics strategies to understand protein function. A variety of mass spectrometry-based approaches allow characterization of cellular protein assemblies under near-physiological conditions and subsequent assignmen...
journal_title：Nature methods
pub_type： 杂志文章,评审
doi：10.1038/nmeth1093
更新日期：2007-10-01 00:00:00
abstract：:New methods to quantify protein kinase activities directly from complex cellular mixtures are critical for understanding biological regulatory pathways. Herein, a fluorescence-based chemosensor strategy for the direct measurement of kinase activities in crude mammalian cell lysates is described. We first designed a ne...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth747
更新日期：2005-04-01 00:00:00
abstract：:t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-018-0308-4
更新日期：2019-03-01 00:00:00
abstract：:Membrane proteins are largely underrepresented among available atomic-resolution structures. The use of detergents in protein purification procedures hinders the formation of well-ordered crystals for X-ray crystallography and leads to slower molecular tumbling, impeding the application of solution-state NMR. Solid-st...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2248
更新日期：2012-12-01 00:00:00
abstract：:RNA-guided Cas9 nucleases derived from clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have dramatically transformed our ability to edit the genomes of diverse organisms. We believe tools and techniques based on Cas9, a single unifying factor capable of colocalizing RNA, DNA and protein,...
journal_title：Nature methods
pub_type： 杂志文章,评审
doi：10.1038/nmeth.2649
更新日期：2013-10-01 00:00:00
abstract：:We developed a microarray hybridization-based method, 'comparative genome sequencing' (CGS), to find mutations in bacterial genomes and used it to study metronidazole resistance in H. pylori. CGS identified mutations in several genes, most likely affecting metronidazole activation, and produced no false positives in a...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth805
更新日期：2005-12-01 00:00:00
