Abstract:
:MicroRNAs (miRNAs) are critical to somatic cell reprogramming into induced pluripotent stem cells (iPSCs), however, exactly how miRNA expression changes support the transition to pluripotency requires further investigation. Here we use a murine secondary reprogramming system to sample cellular trajectories towards iPSCs or a novel pluripotent 'F-class' state and perform small RNA sequencing. We detect sweeping changes in an early and a late wave, revealing that distinct miRNA milieus characterize alternate states of pluripotency. miRNA isoform expression is common but surprisingly varies little between cell states. Referencing other omic data sets generated in parallel, we find that miRNA expression is changed through transcriptional and post-transcriptional mechanisms. miRNA transcription is commonly regulated by dynamic histone modification, while DNA methylation/demethylation consolidates these changes at multiple loci. Importantly, our results suggest that a novel subset of distinctly expressed miRNAs supports pluripotency in the F-class state, substituting for miRNAs that serve such roles in iPSCs.
journal_name
Nat Communjournal_title
Nature communicationsauthors
Clancy JL,Patel HR,Hussein SM,Tonge PD,Cloonan N,Corso AJ,Li M,Lee DS,Shin JY,Wong JJ,Bailey CG,Benevento M,Munoz J,Chuah A,Wood D,Rasko JE,Heck AJ,Grimmond SM,Rogers IM,Seo JS,Wells CA,Puri MC,Nagy A,Preissdoi
10.1038/ncomms6522subject
Has Abstractpub_date
2014-12-10 00:00:00pages
5522issn
2041-1723pii
ncomms6522journal_volume
5pub_type
杂志文章abstract::Whether and how fracture mechanics needs to be modified for small length scales and in systems of reduced dimensionality remains an open debate. Here, employing in situ transmission electron microscopy, atomic structures and dislocation dynamics in the crack tip zone of a propagating crack in two-dimensional (2D) mono...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms14116
更新日期:2017-01-18 00:00:00
abstract::Ferroelectric domain walls constitute a completely new class of sheet-like functional material. Moreover, since domain walls are generally writable, erasable and mobile, they could be useful in functionally agile devices: for example, creating and moving conducting walls could make or break electrical connections in n...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms15105
更新日期:2017-05-16 00:00:00
abstract::The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcriptome and quantitatively describe regulatory activity under diverse co...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-20153-9
更新日期:2020-12-11 00:00:00
abstract::In carrier multiplication, the absorption of a single photon results in two or more electron-hole pairs. Quantum dots are promising materials for implementing carrier multiplication principles in real-life technologies. So far, however, most of research in this area has focused on optical studies of solution samples w...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms9185
更新日期:2015-09-08 00:00:00
abstract::Human mesenchymal stromal cells (hMSCs) are a promising source for engineered cell-based therapies in which genetic engineering could enhance therapeutic efficacy and install novel cellular functions. Here, we describe an optimized Cas9-AAV6-based genome editing tool platform for site-specific mutagenesis and integrat...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-16065-3
更新日期:2020-05-18 00:00:00
abstract::One of the fundamental challenges in nanophotonics is to gain full control over nanoscale optical elements. The precise spatiotemporal arrangement determines their interactions and collective behavior. To this end, DNA nanotechnology is employed as an unprecedented tool to create nanophotonic devices with excellent sp...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-019-13444-3
更新日期:2019-11-27 00:00:00
abstract::Ryanodine receptors (RyRs) form calcium release channels located in the membranes of the sarcoplasmic and endoplasmic reticulum. RyRs play a major role in excitation-contraction coupling and other Ca(2+)-dependent signalling events, and consist of several globular domains that together form a large assembly. Here we d...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms8947
更新日期:2015-08-06 00:00:00
abstract::The analysis of whole-genome sequencing studies is challenging due to the large number of noncoding rare variants, our limited understanding of their functional effects, and the lack of natural units for testing. Here we propose a scan statistic framework, WGScan, to simultaneously detect the existence, and estimate t...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-019-11023-0
更新日期:2019-07-09 00:00:00
abstract::Stackable select devices such as the oxide p-n junction diode and the Schottky diode (one-way switch) have been proposed for non-volatile unipolar resistive switching devices; however, bidirectional select devices (or two-way switch) need to be developed for bipolar resistive switching devices. Here we report on a ful...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms3629
更新日期:2013-01-01 00:00:00
abstract::Understanding the resilience of aquatic ectothermic animals to climate warming has been hindered by the absence of experimental systems experiencing warming across relevant timescales (for example, decades). Here, we examine European perch (Perca fluviatilis, L.) from the Biotest enclosure, a unique coastal ecosystem ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms11447
更新日期:2016-05-17 00:00:00
abstract::Acute stroke causes complex, pathological, and systemic responses that have not been treatable by any single medication. In this study, using a murine transient middle cerebral artery occlusion stroke model, a novel therapeutic strategy is proposed, where blood replacement (BR) robustly reduces infarctions and improve...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-17930-x
更新日期:2020-08-25 00:00:00
abstract::Systems allowing label-free molecular detection are expected to have enormous impact on biochemical sciences. Research focuses on materials and technologies based on exploiting localized surface plasmon resonances in metallic nanostructures. The reason for this focused attention is their suitability for single-molecul...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms7150
更新日期:2015-02-02 00:00:00
abstract::In LaAlO(3)/SrTiO(3) heterointerfaces, charge carriers migrate from the LaAlO(3) to the interface in an electronic reconstruction. Magnetism has been observed in LaAlO(3)/SrTiO(3), but its relationship to the interface conductivity is unknown. Here we show that reconstruction is necessary, but not sufficient, for the ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms1931
更新日期:2012-06-26 00:00:00
abstract::Materials genomics represents a research mode for materials development, for which reliable methods for efficient materials construction are essential. Here we present a methodology for high-throughput construction of covalent organic frameworks (COFs) based on materials genomics strategy, in which a gene partition me...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-018-07720-x
更新日期:2018-12-10 00:00:00
abstract::According to quantum theory, measurements generate random outcomes, in stark contrast with classical mechanics. This raises the question of whether there could exist an extension of the theory that removes this indeterminism, as suspected by Einstein, Podolsky and Rosen. Although this has been shown to be impossible, ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms1416
更新日期:2011-08-02 00:00:00
abstract::Aneuploidy and copy-number alterations (CNAs) are a hallmark of human cancer. Although genetically engineered mouse models (GEMMs) are commonly used to model human cancer, their chromosomal landscapes remain underexplored. Here we use gene expression profiles to infer CNAs in 3,108 samples from 45 mouse models, provid...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms12160
更新日期:2016-07-04 00:00:00
abstract::In weakly spin-orbit coupled materials, the spin-selective nature of recombination can give rise to large magnetic-field effects, e.g. on the electro-luminescence of molecular semiconductors. Although silicon has weak spin-orbit coupling, observing spin-dependent recombination through magneto-electroluminescence is ch...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-017-02804-6
更新日期:2018-01-26 00:00:00
abstract::Although many animals have evolved intrinsic transparency for the purpose of concealment, the development of dynamic, that is, controllable and reversible, transparency for living human cells and tissues has remained elusive to date. Here, by drawing inspiration from the structures and functionalities of adaptive ceph...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-16151-6
更新日期:2020-06-02 00:00:00
abstract::Hydrogen spillover phenomenon is well-documented in hydrogenation catalysis but still highly disputed in hydrogen storage. Until now, the existence of hydrogen spillover through metal-organic frameworks (MOFs) remains a topic of ongoing debate and how far the split hydrogen atoms diffuse in such materials is unknown. ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-018-06269-z
更新日期:2018-09-17 00:00:00
abstract::Many-body entanglement is at the heart of the Kondo effect, which has its hallmark in quantum dots as a zero-bias conductance peak at low temperatures. It signals the emergence of a conducting singlet state formed by a localized dot degree of freedom and conduction electrons. Carbon nanotubes offer the possibility to ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms12442
更新日期:2016-08-16 00:00:00
abstract::Proteins are co-translationally inserted into the bacterial plasma membrane via the SecYEG translocon by lateral release of hydrophobic transmembrane segments into the phospholipid bilayer. The trigger for lateral opening of the translocon is not known. Here we monitor lateral opening by photo-induced electron transfe...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms6263
更新日期:2014-10-15 00:00:00
abstract::Graphyne allotropes of carbon are fascinating materials, and their electronic properties are predicted to rival those of the "wonder material" graphene. One allotrope of graphyne, having rectangular symmetry rather than hexagonal, stands out as particularly attractive, namely 6,6,12-graphyne. It is currently an insurm...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-019-11700-0
更新日期:2019-08-16 00:00:00
abstract::Environmental challenges to plants typically entail retardation of vegetative growth and delay or cessation of flowering. Here we report a link between the flowering time regulator, GIGANTEA (GI), and adaptation to salt stress that is mechanistically based on GI degradation under saline conditions, thus retarding flow...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms2357
更新日期:2013-01-01 00:00:00
abstract::As in human speech acquisition, songbird vocal learning depends on early auditory experience. During development, juvenile songbirds listen to and form auditory memories of adult tutor songs, which they use to shape their own vocalizations in later sensorimotor learning. The higher-level auditory cortex, called the ca...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms11946
更新日期:2016-06-21 00:00:00
abstract::The atypical chemokine receptor 3 (ACKR3) plays a pivotal role in directing the migration of various cellular populations and its over-expression in tumors promotes cell proliferation and invasiveness. The intracellular signaling pathways transducing ACKR3-dependent effects remain poorly characterized, an issue we add...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-18634-y
更新日期:2020-09-25 00:00:00
abstract::Identifying therapeutic targets in rare cancers remains challenging due to the paucity of established models to perform preclinical studies. As a proof-of-concept, we developed a patient-derived cancer cell line, CLF-PED-015-T, from a paediatric patient with a rare undifferentiated sarcoma. Here, we confirm that this ...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms11987
更新日期:2016-06-22 00:00:00
abstract::Recent advances in nonlinear optics have revolutionized integrated photonics, providing on-chip solutions to a wide range of new applications. Currently, state of the art integrated nonlinear photonic devices are mainly based on dielectric material platforms, such as Si3N4 and SiO2. While semiconductor materials featu...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-020-15005-5
更新日期:2020-03-12 00:00:00
abstract::Developmental plasticity describes the influence of environmental factors on phenotypic variation. An important mediator of developmental plasticity in many animals is parental care. Here, we examine the consequences of maternal care on offspring after the initial mass provisioning of brood in the small carpenter bee,...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-018-05903-0
更新日期:2018-08-27 00:00:00
abstract::Mammals have nine different homologues (ALKBH1-9) of the Escherichia coli DNA repair demethylase AlkB. ALKBH2 is a genuine DNA repair enzyme, but the in vivo function of the other ALKBH proteins has remained elusive. It was recently shown that ALKBH8 contains an additional transfer RNA (tRNA) methyltransferase domain,...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/ncomms1173
更新日期:2011-02-01 00:00:00
abstract::Regaining the function of an impaired limb is highly desirable in paralyzed individuals. One possible avenue to achieve this goal is to bridge the interrupted pathway between preserved neural structures and muscles using a brain-computer interface. Here, we demonstrate that monkeys with subcortical stroke were able to...
journal_title:Nature communications
pub_type: 杂志文章
doi:10.1038/s41467-019-12647-y
更新日期:2019-10-16 00:00:00