Abstract:
:Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.
journal_name
Nat Communjournal_title
Nature communicationsauthors
Clark SJ,Argelaguet R,Kapourani CA,Stubbs TM,Lee HJ,Alda-Catalinas C,Krueger F,Sanguinetti G,Kelsey G,Marioni JC,Stegle O,Reik Wdoi
10.1038/s41467-018-03149-4subject
Has Abstractpub_date
2018-02-22 00:00:00pages
781issue
1issn
2041-1723pii
10.1038/s41467-018-03149-4journal_volume
9pub_type
杂志文章abstract::Oxide-ion conductors have found applications in various electrochemical devices, such as solid-oxide fuel cells, gas sensors, and separation membranes. Dion-Jacobson phases are known for their rich magnetic and electrical properties; however, there have been no reports on oxide-ion conduction in this family of materia...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-15043-z
更新日期:2020-03-06 00:00:00
abstract::Nanofabricated and nanopatterned surfaces have revealed the sensitivity of cell adhesion to nanoscale variations in the spacing of adhesive ligands such as the tripeptide arginine-glycine-aspartic acid (RGD). To date, surface characterisation and cell adhesion are often examined in two separate experiments so that the...
journal_title:Nature communications
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更新日期:2019-09-13 00:00:00
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journal_title:Nature communications
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abstract::Two-Photon Microscopy has become an invaluable tool for biological and medical research, providing high sensitivity, molecular specificity, inherent three-dimensional sub-cellular resolution and deep tissue penetration. In terms of imaging speeds, however, mechanical scanners still limit the acquisition rates to typic...
journal_title:Nature communications
pub_type: 杂志文章
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更新日期:2020-04-28 00:00:00
abstract::In 2016 the World Health Organization identified 21 countries that could eliminate malaria by 2020. Monitoring progress towards this goal requires tracking ongoing transmission. Here we develop methods that estimate individual reproduction numbers and their variation through time and space. Individual reproduction num...
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pub_type: 杂志文章
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更新日期:2018-06-26 00:00:00
abstract::Glioblastoma (GBM) is the most common primary adult brain tumor. Despite extensive efforts, the median survival for GBM patients is approximately 14 months. GBM therapy could benefit greatly from patient-specific targeted therapies that maximize treatment efficacy. Here we report a platform termed SynergySeq to identi...
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abstract::The Hamiltonian of a closed quantum system governs its complete time evolution. While Hamiltonians with time-variation in a single basis can be recovered using a variety of methods, for more general Hamiltonians the presence of non-commuting terms complicates the reconstruction. Here using a single trapped ion, we pro...
journal_title:Nature communications
pub_type: 杂志文章
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更新日期:2016-04-14 00:00:00
abstract::Antiretroviral therapy (ART) suppresses viral replication in people living with HIV. Yet, infected cells persist for decades on ART and viremia returns if ART is stopped. Persistence has been attributed to viral replication in an ART sanctuary and long-lived and/or proliferating latently infected cells. Using ecologic...
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pub_type: 杂志文章
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abstract::Many drugs bind to and activate human pregnane X receptor (hPXR) to upregulate drug-metabolizing enzymes, resulting in decreased drug efficacy and increased resistance. This suggests that hPXR antagonists have therapeutic value. Here we report that SPA70 is a potent and selective hPXR antagonist. SPA70 inhibits hPXR i...
journal_title:Nature communications
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更新日期:2017-09-29 00:00:00
abstract::Bacterial CRISPR-Cas systems comprise diverse effector endonucleases with different targeting ranges, specificities and enzymatic properties, but many of them are inactive in mammalian cells and are thus precluded from genome-editing applications. Here we show that the type II-B FnCas9 from Francisella novicida posses...
journal_title:Nature communications
pub_type: 杂志文章
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更新日期:2017-04-07 00:00:00
abstract::Homologous recombination (HR) mediates the error-free repair of DNA double-strand breaks to maintain genomic stability. Here we characterize C17orf53/MCM8IP, an OB-fold containing protein that binds ssDNA, as a DNA repair factor involved in HR. MCM8IP-deficient cells exhibit HR defects, especially in long-tract gene c...
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更新日期:2020-06-11 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 communications
pub_type: 杂志文章,已发布勘误
doi:10.1038/s41467-020-18510-9
更新日期:2020-09-08 00:00:00
abstract::Wntless transports Wnt morphogens to the cell surface and is required for Wnt secretion and morphogenic gradients formation. Recycling of endocytosed Wntless requires the sorting nexin-3 (SNX3)-retromer-dependent endosome-to-Golgi transport pathway. Here we demonstrate the essential role of SNX3-retromer assembly for ...
journal_title:Nature communications
pub_type: 杂志文章
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更新日期:2018-09-13 00:00:00
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更新日期:2019-03-20 00:00:00
abstract::Ultra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. Here we present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obt...
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更新日期:2016-06-14 00:00:00
abstract::Mutators represent a successful strategy in rapidly adapting asexual populations, but theory predicts their eventual extinction due to their unsustainably large deleterious load. While antimutator invasions have been documented experimentally, important discrepancies among studies remain currently unexplained. Here we...
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abstract::Seeded propagation of amyloid-beta (Aβ) pathology is suggested to contribute to the progression of Alzheimer's disease. Local overproduction of aggregation-prone Aβ variants could explain the focal initiation of a seeding cascade that subsequently triggers widespread pathology. Several animal models support this seedi...
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abstract::In the original version of the Supplementary Information file associated with this Article, Supplementary Fig. 18 panel b was inadvertently replaced with a duplicate of panel a. The error has now been fixed and the corrected version of the Supplementary Information PDF is available to download from the HTML version of...
journal_title:Nature communications
pub_type: 杂志文章,已发布勘误
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journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms2242
更新日期:2012-01-01 00:00:00
abstract::Chikungunya virus (CHIKV) is a globally spreading alphavirus against which there is no commercially available vaccine or therapy. Here we use a genome-wide siRNA screen to identify 156 proviral and 41 antiviral host factors affecting CHIKV replication. We analyse the cellular pathways in which human proviral genes are...
journal_title:Nature communications
pub_type: 杂志文章
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更新日期:2016-05-12 00:00:00
abstract::Temporal cloaks have aroused tremendous research interest in both optical physics and optical communications, unfolding a distinct approach to conceal temporal events from an interrogating optical field. The state-of-the-art temporal cloaks exhibit picosecond-scale and static cloaking window, owing to significantly li...
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更新日期:2019-06-20 00:00:00
abstract::A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-bi...
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abstract::Autoimmunity and macrophage recruitment into the central nervous system (CNS) are critical determinants of neuroinflammatory diseases. However, the mechanisms that drive immunological responses targeted to the CNS remain largely unknown. Here we show that fibrinogen, a central blood coagulation protein deposited in th...
journal_title:Nature communications
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更新日期:2015-09-10 00:00:00
abstract::Recently, stretchable electronics combined with wireless technology have been crucial for realizing efficient human-machine interaction. Here, we demonstrate highly stretchable transparent wireless electronics composed of Ag nanofibers coils and functional electronic components for power transfer and information commu...
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更新日期:2020-11-06 00:00:00
abstract::Application of coherent light-matter interactions has recently been extended to the ultrafast control of magnetization. An important but unrealized technique is the manipulation of magnetization vector motion to make it follow an arbitrarily designed multidimensional trajectory. Here we demonstrate a full manipulation...
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abstract::Molecules containing multiple bonds between atoms-most often in the form of olefins-are ubiquitous in nature, commerce, and science, and as such have a huge impact on everyday life. Given their prominence, over the last few decades, frequent attempts have been made to perturb the structure and reactivity of multiply-b...
journal_title:Nature communications
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更新日期:2018-03-22 00:00:00