Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling.

Abstract:

:ATAC-seq has become a leading technology for probing the chromatin landscape of single and aggregated cells. Distilling functional regions from ATAC-seq presents diverse analysis challenges. Methods commonly used to analyze chromatin accessibility datasets are adapted from algorithms designed to process different experimental technologies, disregarding the statistical and biological differences intrinsic to the ATAC-seq technology. Here, we present a Bayesian statistical approach that uses latent space models to better model accessible regions, termed ChromA. ChromA annotates chromatin landscape by integrating information from replicates, producing a consensus de-noised annotation of chromatin accessibility. ChromA can analyze single cell ATAC-seq data, correcting many biases generated by the sparse sampling inherent in single cell technologies. We validate ChromA on multiple technologies and biological systems, including mouse and human immune cells, establishing ChromA as a top performing general platform for mapping the chromatin landscape in different cellular populations from diverse experimental designs.

journal_name

Nat Commun

journal_title

Nature communications

authors

Gabitto MI,Rasmussen A,Wapinski O,Allaway K,Carriero N,Fishell GJ,Bonneau R

doi

10.1038/s41467-020-14497-5

subject

Has Abstract

pub_date

2020-02-06 00:00:00

pages

747

issue

1

issn

2041-1723

pii

10.1038/s41467-020-14497-5

journal_volume

11

pub_type

杂志文章
  • Observational evidence confirms modelling of the long-term integrity of CO2-reservoir caprocks.

    abstract::Storage of anthropogenic CO2 in geological formations relies on a caprock as the primary seal preventing buoyant super-critical CO2 escaping. Although natural CO2 reservoirs demonstrate that CO2 may be stored safely for millions of years, uncertainty remains in predicting how caprocks will react with CO2-bearing brine...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12268

    authors: Kampman N,Busch A,Bertier P,Snippe J,Hangx S,Pipich V,Di Z,Rother G,Harrington JF,Evans JP,Maskell A,Chapman HJ,Bickle MJ

    更新日期:2016-07-28 00:00:00

  • Reconstructing plate-motion changes in the presence of finite-rotations noise.

    abstract::Understanding lithospheric plate motions is of paramount importance to geodynamicists. Much effort is going into kinematic reconstructions featuring progressively finer temporal resolution. However, the challenge of precisely identifying ocean-floor magnetic lineations, and uncertainties in geomagnetic reversal timesc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2051

    authors: Iaffaldano G,Bodin T,Sambridge M

    更新日期:2012-01-01 00:00:00

  • Topological proximity effect in a topological insulator hybrid.

    abstract::It is well known that a topologically protected gapless state appears at an interface between a topological insulator and an ordinary insulator; however, the physics of the interface between a topological insulator and a metal has largely been left unexplored. Here we report a novel phenomenon termed topological proxi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7547

    authors: Shoman T,Takayama A,Sato T,Souma S,Takahashi T,Oguchi T,Segawa K,Ando Y

    更新日期:2015-03-12 00:00:00

  • Broadband multi-magnon relaxometry using a quantum spin sensor for high frequency ferromagnetic dynamics sensing.

    abstract::Development of sensitive local probes of magnon dynamics is essential to further understand the physical processes that govern magnon generation, propagation, scattering, and relaxation. Quantum spin sensors like the NV center in diamond have long spin lifetimes and their relaxation can be used to sense magnetic field...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19121-0

    authors: McCullian BA,Thabt AM,Gray BA,Melendez AL,Wolf MS,Safonov VL,Pelekhov DV,Bhallamudi VP,Page MR,Hammel PC

    更新日期:2020-10-16 00:00:00

  • 6mer seed toxicity in tumor suppressive microRNAs.

    abstract::Many small-interfering (si)RNAs are toxic to cancer cells through a 6mer seed sequence (positions 2-7 of the guide strand). Here we performed an siRNA screen with all 4096 6mer seeds revealing a preference for guanine in positions 1 and 2 and a high overall G or C content in the seed of the most toxic siRNAs for four ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06526-1

    authors: Gao QQ,Putzbach WE,Murmann AE,Chen S,Sarshad AA,Peter JM,Bartom ET,Hafner M,Peter ME

    更新日期:2018-10-29 00:00:00

  • Publisher Correction: An engineered human Fc domain that behaves like a pH-toggle switch for ultra-long circulation persistence.

    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: 已发布勘误

    doi:10.1038/s41467-019-13458-x

    authors: Lee CH,Kang TH,Godon O,Watanabe M,Delidakis G,Gillis CM,Sterlin D,Hardy D,Cogné M,Macdonald LE,Murphy AJ,Tu N,Lee J,McDaniel JR,Makowski E,Tessier PM,Meyer AS,Bruhns P,Georgiou G

    更新日期:2019-11-26 00:00:00

  • Manipulating Majorana zero modes on atomic rings with an external magnetic field.

    abstract::Non-Abelian quasiparticles have been predicted to exist in a variety of condensed matter systems. Their defining property is that an adiabatic braid between two of them results in a non-trivial change of the quantum state of the system. The simplest non-Abelian quasiparticles--the Majorana bound states--can occur in o...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10395

    authors: Li J,Neupert T,Bernevig BA,Yazdani A

    更新日期:2016-01-21 00:00:00

  • Correct determination of charge transfer state energy from luminescence spectra in organic solar cells.

    abstract::Generation and recombination of electrons and holes in organic solar cells occurs via charge transfer states located at the donor/acceptor interface. The energy of these charge transfer states is a crucial factor for the attainable open-circuit voltage and its correct determination is thus of utmost importance for a d...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05987-8

    authors: List M,Sarkar T,Perkhun P,Ackermann J,Luo C,Würfel U

    更新日期:2018-09-07 00:00:00

  • Onsite GTP fuelling via DYNAMO1 drives division of mitochondria and peroxisomes.

    abstract::Mitochondria and peroxisomes proliferate by division. During division, a part of their membrane is pinched off by constriction of the ring-shaped mitochondrial division (MD) and peroxisome-dividing (POD) machinery. This constriction is mediated by a dynamin-like GTPase Dnm1 that requires a large amount of GTP as an en...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07009-z

    authors: Imoto Y,Abe Y,Honsho M,Okumoto K,Ohnuma M,Kuroiwa H,Kuroiwa T,Fujiki Y

    更新日期:2018-11-06 00:00:00

  • Erratum: Observation of ultrahigh mobility surface states in a topological crystalline insulator by infrared spectroscopy.

    abstract::A correction to this article has been published and is linked from the HTML version of this article. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-017-01354-1

    authors: Wang Y,Luo G,Liu J,Sankar R,Wang NL,Chou F,Fu L,Li Z

    更新日期:2017-10-12 00:00:00

  • Conformational dynamics of the human serotonin transporter during substrate and drug binding.

    abstract::The serotonin transporter (SERT), a member of the neurotransmitter:sodium symporter family, is responsible for termination of serotonergic signaling by re-uptake of serotonin (5-HT) into the presynaptic neuron. Its key role in synaptic transmission makes it a major drug target, e.g. for the treatment of depression, an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09675-z

    authors: Möller IR,Slivacka M,Nielsen AK,Rasmussen SGF,Gether U,Loland CJ,Rand KD

    更新日期:2019-04-11 00:00:00

  • Biochemical mechanisms determine the functional compatibility of heterologous genes.

    abstract::Elucidating the factors governing the functional compatibility of horizontally transferred genes is important to understand bacterial evolution, including the emergence and spread of antibiotic resistance, and to successfully engineer biological systems. In silico efforts and work using single-gene libraries have sugg...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-02944-3

    authors: Porse A,Schou TS,Munck C,Ellabaan MMH,Sommer MOA

    更新日期:2018-02-06 00:00:00

  • Societal decisions about climate mitigation will have dramatic impacts on eutrophication in the 21st century.

    abstract::Excessive nitrogen runoff leads to degraded water quality, harming human and ecosystem health. We examine the impact of changes in land use and land management for six combinations of socioeconomic pathways and climate outcomes, and find that societal choices will substantially impact riverine total nitrogen loading (...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-08884-w

    authors: Sinha E,Michalak AM,Calvin KV,Lawrence PJ

    更新日期:2019-02-26 00:00:00

  • Highly explosive basaltic eruptions driven by CO2 exsolution.

    abstract::The most explosive basaltic scoria cone eruption yet documented (>20 km high plumes) occurred at Sunset Crater (Arizona) ca. 1085 AD by undetermined eruptive mechanisms. We present melt inclusion analysis, including bubble contents by Raman spectroscopy, yielding high total CO2 (approaching 6000 ppm) and S (~2000 ppm)...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20354-2

    authors: Allison CM,Roggensack K,Clarke AB

    更新日期:2021-01-11 00:00:00

  • An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra.

    abstract::Polyps of the cnidarian Hydra maintain their adult anatomy through two developmental organizers, the head organizer located apically and the foot organizer basally. The head organizer is made of two antagonistic cross-reacting components, an activator, driving apical differentiation and an inhibitor, preventing ectopi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-08242-2

    authors: Vogg MC,Beccari L,Iglesias Ollé L,Rampon C,Vriz S,Perruchoud C,Wenger Y,Galliot B

    更新日期:2019-01-18 00:00:00

  • Tunable plasmons in atomically thin gold nanodisks.

    abstract::The ability to modulate light at high speeds is of paramount importance for telecommunications, information processing and medical imaging technologies. This has stimulated intense efforts to master optoelectronic switching at visible and near-infrared frequencies, although coping with current computer speeds in integ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4548

    authors: Manjavacas A,García de Abajo FJ

    更新日期:2014-03-27 00:00:00

  • From protein sequence to dynamics and disorder with DynaMine.

    abstract::Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-qua...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3741

    authors: Cilia E,Pancsa R,Tompa P,Lenaerts T,Vranken WF

    更新日期:2013-01-01 00:00:00

  • Time-compressed preplay of anticipated events in human primary visual cortex.

    abstract::Perception is guided by the anticipation of future events. It has been hypothesized that this process may be implemented by pattern completion in early visual cortex, in which a stimulus sequence is recreated after only a subset of the visual input is provided. Here we test this hypothesis using ultra-fast functional ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15276

    authors: Ekman M,Kok P,de Lange FP

    更新日期:2017-05-23 00:00:00

  • GPCR-specific autoantibody signatures are associated with physiological and pathological immune homeostasis.

    abstract::Autoantibodies have been associated with autoimmune diseases. However, studies have identified autoantibodies in healthy donors (HD) who do not develop autoimmune disorders. Here we provide evidence of a network of immunoglobulin G (IgG) autoantibodies targeting G protein-coupled receptors (GPCR) in HD compared to pat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07598-9

    authors: Cabral-Marques O,Marques A,Giil LM,De Vito R,Rademacher J,Günther J,Lange T,Humrich JY,Klapa S,Schinke S,Schimke LF,Marschner G,Pitann S,Adler S,Dechend R,Müller DN,Braicu I,Sehouli J,Schulze-Forster K,Trippel T,S

    更新日期:2018-12-06 00:00:00

  • Stagnant forearc mantle wedge inferred from mapping of shear-wave anisotropy using S-net seafloor seismometers.

    abstract::Shear-wave anisotropy in Earth's mantle helps constrain the lattice-preferred orientation of anisotropic minerals due to viscous flow. Previous studies at the Japan Trench subduction zone using land-based seismic networks identified strong anisotropy in the mantle wedge, reflecting viscous flow induced by the subducti...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19541-y

    authors: Uchida N,Nakajima J,Wang K,Takagi R,Yoshida K,Nakayama T,Hino R,Okada T,Asano Y

    更新日期:2020-11-10 00:00:00

  • Loss of Asxl2 leads to myeloid malignancies in mice.

    abstract::ASXL2 is frequently mutated in acute myeloid leukaemia patients with t(8;21). However, the roles of ASXL2 in normal haematopoiesis and the pathogenesis of myeloid malignancies remain unknown. Here we show that deletion of Asxl2 in mice leads to the development of myelodysplastic syndrome (MDS)-like disease. Asxl2-/- m...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15456

    authors: Li J,He F,Zhang P,Chen S,Shi H,Sun Y,Guo Y,Yang H,Man N,Greenblatt S,Li Z,Guo Z,Zhou Y,Wang L,Morey L,Williams S,Chen X,Wang QT,Nimer SD,Yu P,Wang QF,Xu M,Yang FC

    更新日期:2017-06-08 00:00:00

  • Intracellular interleukin-32γ mediates antiviral activity of cytokines against hepatitis B virus.

    abstract::Cytokines are involved in early host defense against pathogen infections. In particular, tumor necrosis factor (TNF) and interferon-gamma (IFN-γ) have critical functions in non-cytopathic elimination of hepatitis B virus (HBV) in hepatocytes. However, the molecular mechanisms and mediator molecules are largely unknown...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05782-5

    authors: Kim DH,Park ES,Lee AR,Park S,Park YK,Ahn SH,Kang HS,Won JH,Ha YN,Jae B,Kim DS,Chung WC,Song MJ,Kim KH,Park SH,Kim SH,Kim KH

    更新日期:2018-08-16 00:00:00

  • Control of electronic conduction at an oxide heterointerface using surface polar adsorbates.

    abstract::The interface between LaAlO(3) and SrTiO(3) possesses a range of intriguing properties, notably a proposed connection between the surface state of the LaAlO(3) and the conductivity buried in the SrTiO(3). Here we study the effect of the surface adsorption of a variety of common laboratory solvents on the conductivity ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1501

    authors: Xie Y,Hikita Y,Bell C,Hwang HY

    更新日期:2011-10-11 00:00:00

  • Systemic regulation of mammalian ageing and longevity by brain sirtuins.

    abstract::Sirtuins regulate numerous important biological processes in mammals, including various age-associated pathophysiologies. However, whether sirtuins are critical to control ageing and longevity in mammals has been controversial. Recent studies have demonstrated critical roles of sirtuins in the brain, especially the hy...

    journal_title:Nature communications

    pub_type: 杂志文章,评审

    doi:10.1038/ncomms5211

    authors: Satoh A,Imai S

    更新日期:2014-06-26 00:00:00

  • Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology.

    abstract::The potential of the folic acid biosynthesis pathway as a target for the development of antibiotics has been clinically validated. However, many pathogens have developed resistance to these antibiotics, prompting a re-evaluation of potential drug targets within the pathway. The ydaH gene of Alcanivorax borkumensis enc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7874

    authors: Bolla JR,Su CC,Delmar JA,Radhakrishnan A,Kumar N,Chou TH,Long F,Rajashankar KR,Yu EW

    更新日期:2015-04-20 00:00:00

  • Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma.

    abstract::Hepatitis B virus (HBV) can integrate into the human genome, contributing to genomic instability and hepatocarcinogenesis. Here by conducting high-throughput viral integration detection and RNA sequencing, we identify 4,225 HBV integration events in tumour and adjacent non-tumour samples from 426 patients with HCC. We...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12992

    authors: Zhao LH,Liu X,Yan HX,Li WY,Zeng X,Yang Y,Zhao J,Liu SP,Zhuang XH,Lin C,Qin CJ,Zhao Y,Pan ZY,Huang G,Liu H,Zhang J,Wang RY,Yang Y,Wen W,Lv GS,Zhang HL,Wu H,Huang S,Wang MD,Tang L,Cao HZ,Wang L,Lee TL

    更新日期:2016-10-05 00:00:00

  • Two pathways regulate cortical granule translocation to prevent polyspermy in mouse oocytes.

    abstract::An egg must be fertilized by a single sperm only. To prevent polyspermy, the zona pellucida, a structure that surrounds mammalian eggs, becomes impermeable upon fertilization, preventing the entry of further sperm. The structural changes in the zona upon fertilization are driven by the exocytosis of cortical granules....

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13726

    authors: Cheeseman LP,Boulanger J,Bond LM,Schuh M

    更新日期:2016-12-19 00:00:00

  • Mapping ecologically relevant social behaviours by gene knockout in wild mice.

    abstract::The laboratory mouse serves as an important model system for studying gene, brain and behavioural interactions. Powerful methods of gene targeting have helped to decipher gene-function associations in human diseases. Yet, the laboratory mouse, obtained after decades of human-driven artificial selection, inbreeding, an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5569

    authors: Chalfin L,Dayan M,Levy DR,Austad SN,Miller RA,Iraqi FA,Dulac C,Kimchi T

    更新日期:2014-08-05 00:00:00

  • Configurable topological textures in strain graded ferroelectric nanoplates.

    abstract::Topological defects in matter behave collectively to form highly non-trivial structures called topological textures that are characterised by conserved quantities such as the winding number. Here we show that an epitaxial ferroelectric square nanoplate of bismuth ferrite subjected to a large strain gradient (as much a...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-02813-5

    authors: Kim KE,Jeong S,Chu K,Lee JH,Kim GY,Xue F,Koo TY,Chen LQ,Choi SY,Ramesh R,Yang CH

    更新日期:2018-01-26 00:00:00

  • Switching of band inversion and topological surface states by charge density wave.

    abstract::Topologically nontrivial materials host protected edge states associated with the bulk band inversion through the bulk-edge correspondence. Manipulating such edge states is highly desired for developing new functions and devices practically using their dissipation-less nature and spin-momentum locking. Here we introdu...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16290-w

    authors: Mitsuishi N,Sugita Y,Bahramy MS,Kamitani M,Sonobe T,Sakano M,Shimojima T,Takahashi H,Sakai H,Horiba K,Kumigashira H,Taguchi K,Miyamoto K,Okuda T,Ishiwata S,Motome Y,Ishizaka K

    更新日期:2020-05-18 00:00:00