当前位置： SCI文献检索 > Nature Communications期刊下所有文献 > Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains.

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains.

Abstract：

:Proximity-ligation methods such as Hi-C allow us to map physical DNA-DNA interactions along the genome, and reveal its organization into topologically associating domains (TADs). As the Hi-C data accumulate, computational methods were developed for identifying domain borders in multiple cell types and organisms. Here, we present PSYCHIC, a computational approach for analyzing Hi-C data and identifying promoter-enhancer interactions. We use a unified probabilistic model to segment the genome into domains, which we then merge hierarchically and fit using a local background model, allowing us to identify over-represented DNA-DNA interactions across the genome. By analyzing the published Hi-C data sets in human and mouse, we identify hundreds of thousands of putative enhancers and their target genes, and compile an extensive genome-wide catalog of gene regulation in human and mouse. As we show, our predictions are highly enriched for ChIP-seq and DNA accessibility data, evolutionary conservation, eQTLs and other DNA-DNA interaction data.

journal_name

Nat Commun

journal_title

Nature communications

authors

Ron G,Globerson Y,Moran D,Kaplan T

doi

10.1038/s41467-017-02386-3

subject

Has Abstract

pub_date

2017-12-21 00:00:00

pages

2237

issue

1

issn

2041-1723

pii

10.1038/s41467-017-02386-3

journal_volume

8

pub_type

杂志文章

相关文献

Nature Communications文献大全
  • Desynchronized liquid crystalline network actuators with deformation reversal capability.

    abstract：:Liquid crystalline network (LCN) actuator normally deforms upon thermally or optically induced order-disorder phase transition, switching once between two shapes (shape 1 in LC phase and shape 2 in isotropic state) for each stimulation on/off cycle. Herein, we report an LCN actuator that deforms from shape 1 to shape ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-021-20938-6

    authors： Xiao YY,Jiang ZC,Hou JB,Zhao Y

    更新日期：2021-01-27 00:00:00

  • Disclosing the temperature of columnar jointing in lavas.

    abstract：:Columnar joints form by cracking during cooling-induced contraction of lava, allowing hydrothermal fluid circulation. A lack of direct observations of their formation has led to ambiguity about the temperature window of jointing and its impact on fluid flow. Here we develop a novel thermo-mechanical experiment to disc...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-03842-4

    authors： Lamur A,Lavallée Y,Iddon FE,Hornby AJ,Kendrick JE,von Aulock FW,Wadsworth FB

    更新日期：2018-04-12 00:00:00

  • Information processing using a single dynamical node as complex system.

    abstract：:Novel methods for information processing are highly desired in our information-driven society. Inspired by the brain's ability to process information, the recently introduced paradigm known as 'reservoir computing' shows that complex networks can efficiently perform computation. Here we introduce a novel architecture ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms1476

    authors： Appeltant L,Soriano MC,Van der Sande G,Danckaert J,Massar S,Dambre J,Schrauwen B,Mirasso CR,Fischer I

    更新日期：2011-09-13 00:00:00

  • Identity crisis in alchemical space drives the entropic colloidal glass transition.

    abstract：:A universally accepted explanation for why liquids sometimes vitrify rather than crystallize remains hotly pursued, despite the ubiquity of glass in our everyday lives, the utilization of the glass transition in innumerable modern technologies, and nearly a century of theoretical and experimental investigation. Among ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-07977-2

    authors： Teich EG,van Anders G,Glotzer SC

    更新日期：2019-01-08 00:00:00

  • Design of highly efficient deep-blue organic afterglow through guest sensitization and matrices rigidification.

    abstract：:Blue/deep-blue emission is crucial for organic optoelectronics but remains a formidable challenge in organic afterglow due to the difficulties in populating and stabilizing the high-energy triplet excited states. Here, a facile strategy to realize the efficient deep-blue organic afterglow is proposed via host molecule...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-18572-9

    authors： Xu S,Wang W,Li H,Zhang J,Chen R,Wang S,Zheng C,Xing G,Song C,Huang W

    更新日期：2020-09-23 00:00:00

  • High-pressure synthesis of a polyethylene/zeolite nano-composite material.

    abstract：:Meso/micro-porous solids, such as zeolites, are complex materials used in an impressive range of applications. Here we photo-polymerized ethylene using non-catalytic high-pressure techniques at 0.5-1.5 GPa under ultraviolet (351-364 nm) irradiation on a sub-nanometre scale in the channels of a pure SiO2 zeolite, silic...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2564

    authors： Santoro M,Gorelli FA,Bini R,Haines J,van der Lee A

    更新日期：2013-01-01 00:00:00

  • Potassium channel-based optogenetic silencing.

    abstract：:Optogenetics enables manipulation of biological processes with light at high spatio-temporal resolution to control the behavior of cells, networks, or even whole animals. In contrast to the performance of excitatory rhodopsins, the effectiveness of inhibitory optogenetic tools is still insufficient. Here we report a t...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-07038-8

    authors： Bernal Sierra YA,Rost BR,Pofahl M,Fernandes AM,Kopton RA,Moser S,Holtkamp D,Masala N,Beed P,Tukker JJ,Oldani S,Bönigk W,Kohl P,Baier H,Schneider-Warme F,Hegemann P,Beck H,Seifert R,Schmitz D

    更新日期：2018-11-05 00:00:00

  • Activity enhancement of cobalt catalysts by tuning metal-support interactions.

    abstract：:Interactions between metal nanoparticles and support materials can strongly influence the performance of catalysts. In particular, reducible oxidic supports can form suboxides that can decorate metal nanoparticles and enhance catalytic performance or block active sites. Therefore, tuning this metal-support interaction...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-06903-w

    authors： Hernández Mejía C,van Deelen TW,de Jong KP

    更新日期：2018-10-26 00:00:00

  • The role of water in fault lubrication.

    abstract：:The friction between two adjacent tectonic plates under shear loading may dictate seismic activities. To advance the understanding of mechanisms underlying fault strength, we investigate the frictional characteristics of calcite in an aqueous environment. By conducting single-asperity friction experiments using an ato...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-04782-9

    authors： Diao Y,Espinosa-Marzal RM

    更新日期：2018-06-13 00:00:00

  • Metallo-polyelectrolytes as a class of ionic macromolecules for functional materials.

    abstract：:The fields of soft polymers and macromolecular sciences have enjoyed a unique combination of metals and organic frameworks in the name of metallopolymers or organometallic polymers. When metallopolymers carry charged groups, they form a class of metal-containing polyelectrolytes or metallo-polyelectrolytes. This revie...

    journal_title：Nature communications

    pub_type： 杂志文章,评审

    doi：10.1038/s41467-018-06475-9

    authors： Zhu T,Sha Y,Yan J,Pageni P,Rahman MA,Yan Y,Tang C

    更新日期：2018-10-18 00:00:00

  • Two sequential cleavage reactions on cruciform DNA structures cause palindrome-mediated chromosomal translocations.

    abstract：:Gross chromosomal rearrangements (GCRs), such as translocations, deletions or inversions, are often generated by illegitimate repair between two DNA breakages at regions with nucleotide sequences that might potentially adopt a non-B DNA conformation. We previously established a plasmid-based model system that recapitu...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2595

    authors： Inagaki H,Ohye T,Kogo H,Tsutsumi M,Kato T,Tong M,Emanuel BS,Kurahashi H

    更新日期：2013-01-01 00:00:00

  • Size-dependent surface phase change of lithium iron phosphate during carbon coating.

    abstract：:Carbon coating is a simple, effective and common technique for improving the conductivity of active materials in lithium ion batteries. However, carbon coating provides a strong reducing atmosphere and many factors remain unclear concerning the interface nature and underlying interaction mechanism that occurs between ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms4415

    authors： Wang J,Yang J,Tang Y,Liu J,Zhang Y,Liang G,Gauthier M,Chen-Wiegart YC,Norouzi Banis M,Li X,Li R,Wang J,Sham TK,Sun X

    更新日期：2014-03-05 00:00:00

  • Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle.

    abstract：:The development of native-like HIV-1 envelope (Env) trimer antigens has enabled the induction of neutralizing antibody (NAb) responses against neutralization-resistant HIV-1 strains in animal models. However, NAb responses are relatively weak and narrow in specificity. Displaying antigens in a multivalent fashion on n...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-12080-1

    authors： Brouwer PJM,Antanasijevic A,Berndsen Z,Yasmeen A,Fiala B,Bijl TPL,Bontjer I,Bale JB,Sheffler W,Allen JD,Schorcht A,Burger JA,Camacho M,Ellis D,Cottrell CA,Behrens AJ,Catalano M,Del Moral-Sánchez I,Ketas TJ,LaBranche

    更新日期：2019-09-19 00:00:00

  • Synthesis of large-area multilayer hexagonal boron nitride for high material performance.

    abstract：:Although hexagonal boron nitride (h-BN) is a good candidate for gate-insulating materials by minimizing interaction from substrate, further applications to electronic devices with available two-dimensional semiconductors continue to be limited by flake size. While monolayer h-BN has been synthesized on Pt and Cu foil ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms9662

    authors： Kim SM,Hsu A,Park MH,Chae SH,Yun SJ,Lee JS,Cho DH,Fang W,Lee C,Palacios T,Dresselhaus M,Kim KK,Lee YH,Kong J

    更新日期：2015-10-28 00:00:00

  • Detection of the thietane precursor in the UVA formation of the DNA 6-4 photoadduct.

    abstract：:Notwithstanding the central biological role of the (6-4) photoadduct in the induction of skin cancer by sunlight, crucial mechanistic details about its formation have evaded characterization despite efforts spanning more than half a century. 4-Thiothymidine (4tT) has been widely used as an important model system to st...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-17333-y

    authors： Ortiz-Rodríguez LA,Reichardt C,Hoehn SJ,Jockusch S,Crespo-Hernández CE

    更新日期：2020-07-17 00:00:00

  • Relativistic electron avalanches as a thunderstorm discharge competing with lightning.

    abstract：:Gamma-ray 'glows' are long duration (seconds to tens of minutes) X-ray and gamma-ray emission coming from thunderclouds. Measurements suggest the presence of relativistic runaway electron avalanches (RREA), the same process underlying terrestrial gamma-ray flashes. Here we demonstrate that glows are relatively a commo...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms8845

    authors： Kelley NA,Smith DM,Dwyer JR,Splitt M,Lazarus S,Martinez-McKinney F,Hazelton B,Grefenstette B,Lowell A,Rassoul HK

    更新日期：2015-08-12 00:00:00

  • Transport regimes of a split gate superconducting quantum point contact in the two-dimensional LaAlO3/SrTiO3 superfluid.

    abstract：:One of the hallmark experiments of quantum transport is the observation of the quantized resistance in a point contact in GaAs/AlGaAs heterostructures. Being formed with split gate technology, these structures represent in an ideal manner equilibrium reservoirs which are connected only through a few electron mode chan...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-04657-z

    authors： Thierschmann H,Mulazimoglu E,Manca N,Goswami S,Klapwijk TM,Caviglia AD

    更新日期：2018-06-11 00:00:00

  • CLIC4 regulates apical exocytosis and renal tube luminogenesis through retromer- and actin-mediated endocytic trafficking.

    abstract：:Chloride intracellular channel 4 (CLIC4) is a mammalian homologue of EXC-4 whose mutation is associated with cystic excretory canals in nematodes. Here we show that CLIC4-null mouse embryos exhibit impaired renal tubulogenesis. In both developing and developed kidneys, CLIC4 is specifically enriched in the proximal tu...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms10412

    authors： Chou SY,Hsu KS,Otsu W,Hsu YC,Luo YC,Yeh C,Shehab SS,Chen J,Shieh V,He GA,Marean MB,Felsen D,Ding A,Poppas DP,Chuang JZ,Sung CH

    更新日期：2016-01-20 00:00:00

  • Memory phototransistors based on exponential-association photoelectric conversion law.

    abstract：:Ultraweak light detectors have wide-ranging important applications such as astronomical observation, remote sensing, laser ranging, and night vision. Current commercial ultraweak light detectors are commonly based on a photomultiplier tube or an avalanche photodiode, and they are incompatible with microelectronic devi...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-09206-w

    authors： Shao Z,Jiang T,Zhang X,Zhang X,Wu X,Xia F,Xiong S,Lee ST,Jie J

    更新日期：2019-03-20 00:00:00

  • RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.

    abstract：:The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFα mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ∼ 3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms8367

    authors： Murakawa Y,Hinz M,Mothes J,Schuetz A,Uhl M,Wyler E,Yasuda T,Mastrobuoni G,Friedel CC,Dölken L,Kempa S,Schmidt-Supprian M,Blüthgen N,Backofen R,Heinemann U,Wolf J,Scheidereit C,Landthaler M

    更新日期：2015-07-14 00:00:00

  • Optical imaging of strain in two-dimensional crystals.

    abstract：:Strain engineering is widely used in material science to tune the (opto-)electronic properties of materials and enhance the performance of devices. Two-dimensional atomic crystals are a versatile playground to study the influence of strain, as they can sustain very large deformations without breaking. Various optical ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-02830-y

    authors： Mennel L,Furchi MM,Wachter S,Paur M,Polyushkin DK,Mueller T

    更新日期：2018-02-06 00:00:00

  • PAK proteins and YAP-1 signalling downstream of integrin beta-1 in myofibroblasts promote liver fibrosis.

    abstract：:Fibrosis due to extracellular matrix (ECM) secretion from myofibroblasts complicates many chronic liver diseases causing scarring and organ failure. Integrin-dependent interaction with scar ECM promotes pro-fibrotic features. However, the pathological intracellular mechanism in liver myofibroblasts is not completely u...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms12502

    authors： Martin K,Pritchett J,Llewellyn J,Mullan AF,Athwal VS,Dobie R,Harvey E,Zeef L,Farrow S,Streuli C,Henderson NC,Friedman SL,Hanley NA,Piper Hanley K

    更新日期：2016-08-18 00:00:00

  • Secreted CLIC3 drives cancer progression through its glutathione-dependent oxidoreductase activity.

    abstract：:The secretome of cancer and stromal cells generates a microenvironment that contributes to tumour cell invasion and angiogenesis. Here we compare the secretome of human mammary normal and cancer-associated fibroblasts (CAFs). We discover that the chloride intracellular channel protein 3 (CLIC3) is an abundant componen...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms14206

    authors： Hernandez-Fernaud JR,Ruengeler E,Casazza A,Neilson LJ,Pulleine E,Santi A,Ismail S,Lilla S,Dhayade S,MacPherson IR,McNeish I,Ennis D,Ali H,Kugeratski FG,Al Khamici H,van den Biggelaar M,van den Berghe PV,Cloix C,McDona

    更新日期：2017-02-15 00:00:00

  • Publisher Correction: A downy mildew effector evades recognition by polymorphism of expression and subcellular localization.

    abstract：:The original version of this article contained an error in the author affiliations. Oliver J. Furzer was incorrectly associated with Department of Plant Sciences, College of Life Sciences, Wuhan University, 430072, Wuhan, China.This has now been corrected in the HTML version of the article. The PDF version of the arti...

    journal_title：Nature communications

    pub_type： 杂志文章,已发布勘误

    doi：10.1038/s41467-018-08095-9

    authors： Asai S,Furzer OJ,Cevik V,Kim DS,Ishaque N,Goritschnig S,Staskawicz BJ,Shirasu K,Jones JDG

    更新日期：2019-01-08 00:00:00

  • Quantum nuclear dynamics in the photophysics of diamondoids.

    abstract：:The unusual electronic properties of diamondoids, the nanoscale relatives of diamond, make them attractive for applications ranging from drug delivery to field emission displays. Identifying the fundamental origin of these properties has proven highly challenging, with even the most advanced quantum many-body calculat...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms3006

    authors： Patrick CE,Giustino F

    更新日期：2013-01-01 00:00:00

  • Freestanding three-dimensional core-shell nanoarrays for lithium-ion battery anodes.

    abstract：:Structural degradation and low conductivity of transition-metal oxides lead to severe capacity fading in lithium-ion batteries. Recent efforts to solve this issue have mainly focused on using nanocomposites or hybrids by integrating nanosized metal oxides with conducting additives. Here we design specific hierarchical...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms11774

    authors： Tan G,Wu F,Yuan Y,Chen R,Zhao T,Yao Y,Qian J,Liu J,Ye Y,Shahbazian-Yassar R,Lu J,Amine K

    更新日期：2016-06-03 00:00:00

  • Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution.

    abstract：:Biological tissues exhibit complex spatial heterogeneity that directs the functions of multicellular organisms. Quantifying protein expression is essential for elucidating processes within complex biological assemblies. Imaging mass spectrometry (IMS) is a powerful emerging tool for mapping the spatial distribution of...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-13858-z

    authors： Piehowski PD,Zhu Y,Bramer LM,Stratton KG,Zhao R,Orton DJ,Moore RJ,Yuan J,Mitchell HD,Gao Y,Webb-Robertson BM,Dey SK,Kelly RT,Burnum-Johnson KE

    更新日期：2020-01-07 00:00:00

  • Hydrogen spillover through Matryoshka-type (ZIFs@)n-1ZIFs nanocubes.

    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

    authors： Zhan G,Zeng HC

    更新日期：2018-09-17 00:00:00

  • Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS-PKS hybrid enzyme.

    abstract：:Tenuazonic acid (TeA) is a well-known mycotoxin produced by various plant pathogenic fungi. However, its biosynthetic gene has been unknown to date. Here we identify the TeA biosynthetic gene from Magnaporthe oryzae by finding two TeA-inducing conditions of a low-producing strain. We demonstrate that TeA is synthesize...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms9758

    authors： Yun CS,Motoyama T,Osada H

    更新日期：2015-10-27 00:00:00

  • Efficient hydrogen production on MoNi4 electrocatalysts with fast water dissociation kinetics.

    abstract：:Various platinum-free electrocatalysts have been explored for hydrogen evolution reaction in acidic solutions. However, in economical water-alkali electrolysers, sluggish water dissociation kinetics (Volmer step) on platinum-free electrocatalysts results in poor hydrogen-production activities. Here we report a MoNi4 e...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms15437

    authors： Zhang J,Wang T,Liu P,Liao Z,Liu S,Zhuang X,Chen M,Zschech E,Feng X

    更新日期：2017-05-17 00:00:00