An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos.

Abstract:

:Human pre-implantation embryonic development involves extensive changes in chromatin structure and transcriptional activity. Here, we report on LiCAT-seq, a technique that enables simultaneous profiling of chromatin accessibility and gene expression with ultra-low input of cells, and map the chromatin accessibility and transcriptome landscapes for human pre-implantation embryos. We observed global difference in chromatin accessibility between sperm and all stages of embryos, finding that the accessible regions in sperm tend to occur in gene-poor genomic regions. Integrative analyses between the two datasets reveals strong association between the establishment of accessible chromatin and embryonic genome activation (EGA), and uncovers transcription factors and endogenous retrovirus (ERVs) specific to EGA. In particular, a large proportion of the early activated genes and ERVs are bound by DUX4 and become accessible as early as the 2- to 4-cell stages. Our results thus offer mechanistic insights into the molecular events inherent to human pre-implantation development.

journal_name

Nat Commun

journal_title

Nature communications

authors

Liu L,Leng L,Liu C,Lu C,Yuan Y,Wu L,Gong F,Zhang S,Wei X,Wang M,Zhao L,Hu L,Wang J,Yang H,Zhu S,Chen F,Lu G,Shang Z,Lin G

doi

10.1038/s41467-018-08244-0

subject

Has Abstract

pub_date

2019-01-21 00:00:00

pages

364

issue

1

issn

2041-1723

pii

10.1038/s41467-018-08244-0

journal_volume

10

pub_type

杂志文章
  • Land-use emissions play a critical role in land-based mitigation for Paris climate targets.

    abstract::Scenarios that limit global warming to below 2 °C by 2100 assume significant land-use change to support large-scale carbon dioxide (CO2) removal from the atmosphere by afforestation/reforestation, avoided deforestation, and Biomass Energy with Carbon Capture and Storage (BECCS). The more ambitious mitigation scenarios...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05340-z

    authors: Harper AB,Powell T,Cox PM,House J,Huntingford C,Lenton TM,Sitch S,Burke E,Chadburn SE,Collins WJ,Comyn-Platt E,Daioglou V,Doelman JC,Hayman G,Robertson E,van Vuuren D,Wiltshire A,Webber CP,Bastos A,Boysen L,Ciais

    更新日期:2018-08-07 00:00:00

  • Mps1 kinase-dependent Sgo2 centromere localisation mediates cohesin protection in mouse oocyte meiosis I.

    abstract::A key feature of meiosis is the step-wise removal of cohesin, the protein complex holding sister chromatids together, first from arms in meiosis I and then from the centromere region in meiosis II. Centromeric cohesin is protected by Sgo2 from Separase-mediated cleavage, in order to maintain sister chromatids together...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00774-3

    authors: El Yakoubi W,Buffin E,Cladière D,Gryaznova Y,Berenguer I,Touati SA,Gómez R,Suja JA,van Deursen JM,Wassmann K

    更新日期:2017-09-25 00:00:00

  • Early triage of critically ill COVID-19 patients using deep learning.

    abstract::The sudden deterioration of patients with novel coronavirus disease 2019 (COVID-19) into critical illness is of major concern. It is imperative to identify these patients early. We show that a deep learning-based survival model can predict the risk of COVID-19 patients developing critical illness based on clinical cha...

    journal_title:Nature communications

    pub_type: 杂志文章,多中心研究

    doi:10.1038/s41467-020-17280-8

    authors: Liang W,Yao J,Chen A,Lv Q,Zanin M,Liu J,Wong S,Li Y,Lu J,Liang H,Chen G,Guo H,Guo J,Zhou R,Ou L,Zhou N,Chen H,Yang F,Han X,Huan W,Tang W,Guan W,Chen Z,Zhao Y,Sang L,Xu Y,Wang W,Li S,Lu L,Zhang N

    更新日期:2020-07-15 00:00:00

  • Development of human cGAS-specific small-molecule inhibitors for repression of dsDNA-triggered interferon expression.

    abstract::Cyclic GMP-AMP synthase (cGAS) is the primary sensor for aberrant intracellular dsDNA producing the cyclic dinucleotide cGAMP, a second messenger initiating cytokine production in subsets of myeloid lineage cell types. Therefore, inhibition of the enzyme cGAS may act anti-inflammatory. Here we report the discovery of ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-08620-4

    authors: Lama L,Adura C,Xie W,Tomita D,Kamei T,Kuryavyi V,Gogakos T,Steinberg JI,Miller M,Ramos-Espiritu L,Asano Y,Hashizume S,Aida J,Imaeda T,Okamoto R,Jennings AJ,Michino M,Kuroita T,Stamford A,Gao P,Meinke P,Glickman

    更新日期:2019-05-21 00:00:00

  • Human noise blindness drives suboptimal cognitive inference.

    abstract::Humans typically make near-optimal sensorimotor judgements but show systematic biases when making more cognitive judgements. Here we test the hypothesis that, while humans are sensitive to the noise present during early sensory encoding, the "optimality gap" arises because they are blind to noise introduced by later c...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09330-7

    authors: Herce Castañón S,Moran R,Ding J,Egner T,Bang D,Summerfield C

    更新日期:2019-04-12 00:00:00

  • A moiré deflectometer for antimatter.

    abstract::The precise measurement of forces is one way to obtain deep insight into the fundamental interactions present in nature. In the context of neutral antimatter, the gravitational interaction is of high interest, potentially revealing new forces that violate the weak equivalence principle. Here we report on a successful ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5538

    authors: Aghion S,Ahlén O,Amsler C,Ariga A,Ariga T,Belov AS,Berggren K,Bonomi G,Bräunig P,Bremer J,Brusa RS,Cabaret L,Canali C,Caravita R,Castelli F,Cerchiari G,Cialdi S,Comparat D,Consolati G,Derking H,Di Domizio S,Di N

    更新日期:2014-07-28 00:00:00

  • Cooperative material transport during the early stage of sintering.

    abstract::The complex transport processes contributing to sintering are not yet fully understood, partially because in-situ observations of sintering in three dimensions (3D) are very difficult. Here we report a novel experiment in which monocrystalline copper spheres are first marked with microscopic boreholes drilled using a ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1300

    authors: Grupp R,Nöthe M,Kieback B,Banhart J

    更新日期:2011-01-01 00:00:00

  • CEP63 deficiency promotes p53-dependent microcephaly and reveals a role for the centrosome in meiotic recombination.

    abstract::CEP63 is a centrosomal protein that facilitates centriole duplication and is regulated by the DNA damage response. Mutations in CEP63 cause Seckel syndrome, a human disease characterized by microcephaly and dwarfism. Here we demonstrate that Cep63-deficient mice recapitulate Seckel syndrome pathology. The attrition of...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms8676

    authors: Marjanović M,Sánchez-Huertas C,Terré B,Gómez R,Scheel JF,Pacheco S,Knobel PA,Martínez-Marchal A,Aivio S,Palenzuela L,Wolfrum U,McKinnon PJ,Suja JA,Roig I,Costanzo V,Lüders J,Stracker TH

    更新日期:2015-07-09 00:00:00

  • Sound-induced length changes in outer hair cell stereocilia.

    abstract::Hearing relies on mechanical stimulation of stereocilia bundles on the sensory cells of the inner ear. When sound hits the ear, each stereocilium pivots about a neck-like taper near their base. More than three decades of research have established that sideways deflection of stereocilia is essential for converting mech...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2100

    authors: Hakizimana P,Brownell WE,Jacob S,Fridberger A

    更新日期:2012-01-01 00:00:00

  • Controlling for the species-area effect supports constrained long-term Mesozoic terrestrial vertebrate diversification.

    abstract::Variation in the geographic spread of fossil localities strongly biases inferences about the evolution of biodiversity, due to the ubiquitous scaling of species richness with area. This obscures answers to key questions, such as how tetrapods attained their tremendous extant diversity. Here, we address this problem by...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15381

    authors: Close RA,Benson RBJ,Upchurch P,Butler RJ

    更新日期:2017-05-22 00:00:00

  • Steroidal and non-steroidal third-generation aromatase inhibitors induce pain-like symptoms via TRPA1.

    abstract::Use of aromatase inhibitors (AIs), exemestane, letrozole and anastrozole, for breast cancer therapy is associated with severe pain symptoms, the underlying mechanism of which is unknown. The electrophilic nature of AIs suggests that they may target the transient receptor potential ankyrin 1 (TRPA1) channel, a major pa...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6736

    authors: Fusi C,Materazzi S,Benemei S,Coppi E,Trevisan G,Marone IM,Minocci D,De Logu F,Tuccinardi T,Di Tommaso MR,Susini T,Moneti G,Pieraccini G,Geppetti P,Nassini R

    更新日期:2014-12-08 00:00:00

  • Solution nuclear magnetic resonance spectroscopy on a nanostructured diamond chip.

    abstract::Sensors using nitrogen-vacancy centers in diamond are a promising tool for small-volume nuclear magnetic resonance (NMR) spectroscopy, but the limited sensitivity remains a challenge. Here we show nearly two orders of magnitude improvement in concentration sensitivity over previous nitrogen-vacancy and picoliter NMR s...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00266-4

    authors: Kehayias P,Jarmola A,Mosavian N,Fescenko I,Benito FM,Laraoui A,Smits J,Bougas L,Budker D,Neumann A,Brueck SRJ,Acosta VM

    更新日期:2017-08-04 00:00:00

  • Visualization of exciton transport in ordered and disordered molecular solids.

    abstract::Transport of nanoscale energy in the form of excitons is at the core of photosynthesis and the operation of a wide range of nanostructured optoelectronic devices such as solar cells, light-emitting diodes and excitonic transistors. Of particular importance is the relationship between exciton transport and nanoscale di...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4646

    authors: Akselrod GM,Deotare PB,Thompson NJ,Lee J,Tisdale WA,Baldo MA,Menon VM,Bulović V

    更新日期:2014-04-16 00:00:00

  • Coral snakes predict the evolution of mimicry across New World snakes.

    abstract::Batesian mimicry, in which harmless species (mimics) deter predators by deceitfully imitating the warning signals of noxious species (models), generates striking cases of phenotypic convergence that are classic examples of evolution by natural selection. However, mimicry of venomous coral snakes has remained controver...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms11484

    authors: Davis Rabosky AR,Cox CL,Rabosky DL,Title PO,Holmes IA,Feldman A,McGuire JA

    更新日期:2016-05-05 00:00:00

  • Haemodynamically dependent valvulogenesis of zebrafish heart is mediated by flow-dependent expression of miR-21.

    abstract::Heartbeat is required for normal development of the heart, and perturbation of intracardiac flow leads to morphological defects resembling congenital heart diseases. These observations implicate intracardiac haemodynamics in cardiogenesis, but the signalling cascades connecting physical forces, gene expression and mor...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2978

    authors: Banjo T,Grajcarek J,Yoshino D,Osada H,Miyasaka KY,Kida YS,Ueki Y,Nagayama K,Kawakami K,Matsumoto T,Sato M,Ogura T

    更新日期:2013-01-01 00:00:00

  • Evidence for ACTN3 as a genetic modifier of Duchenne muscular dystrophy.

    abstract::Duchenne muscular dystrophy (DMD) is characterized by muscle degeneration and progressive weakness. There is considerable inter-patient variability in disease onset and progression, which can confound the results of clinical trials. Here we show that a common null polymorphism (R577X) in ACTN3 results in significantly...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14143

    authors: Hogarth MW,Houweling PJ,Thomas KC,Gordish-Dressman H,Bello L,Cooperative International Neuromuscular Research Group (CINRG).,Pegoraro E,Hoffman EP,Head SI,North KN

    更新日期:2017-01-31 00:00:00

  • Upper- and mid-mantle interaction between the Samoan plume and the Tonga-Kermadec slabs.

    abstract::Mantle plumes are thought to play a key role in transferring heat from the core-mantle boundary to the lithosphere, where it can significantly influence plate tectonics. On impinging on the lithosphere at spreading ridges or in intra-plate settings, mantle plumes may generate hotspots, large igneous provinces and henc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10799

    authors: Chang SJ,Ferreira AM,Faccenda M

    更新日期:2016-02-29 00:00:00

  • Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages.

    abstract::CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-14103-3

    authors: Siranosian BA,Tamburini FB,Sherlock G,Bhatt AS

    更新日期:2020-01-15 00:00:00

  • An engineered pathway for the biosynthesis of renewable propane.

    abstract::The deployment of next-generation renewable biofuels can be enhanced by improving their compatibility with the current infrastructure for transportation, storage and utilization. Propane, the bulk component of liquid petroleum gas, is an appealing target as it already has a global market. In addition, it is a gas unde...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5731

    authors: Kallio P,Pásztor A,Thiel K,Akhtar MK,Jones PR

    更新日期:2014-09-02 00:00:00

  • Chromatin swelling drives neutrophil extracellular trap release.

    abstract::Neutrophilic granulocytes are able to release their own DNA as neutrophil extracellular traps (NETs) to capture and eliminate pathogens. DNA expulsion (NETosis) has also been documented for other cells and organisms, thus highlighting the evolutionary conservation of this process. Moreover, dysregulated NETosis has be...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06263-5

    authors: Neubert E,Meyer D,Rocca F,Günay G,Kwaczala-Tessmann A,Grandke J,Senger-Sander S,Geisler C,Egner A,Schön MP,Erpenbeck L,Kruss S

    更新日期:2018-09-14 00:00:00

  • Trunk exoskeleton in teleosts is mesodermal in origin.

    abstract::The vertebrate mineralized skeleton is known to have first emerged as an exoskeleton that extensively covered the fossil jawless fish. The evolutionary origin of this exoskeleton has long been attributed to the emergence of the neural crest, but experimental evaluation for this is still poor. Here we determine the emb...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2643

    authors: Shimada A,Kawanishi T,Kaneko T,Yoshihara H,Yano T,Inohaya K,Kinoshita M,Kamei Y,Tamura K,Takeda H

    更新日期:2013-01-01 00:00:00

  • Changes in the regulation of cortical neurogenesis contribute to encephalization during amniote brain evolution.

    abstract::The emergence of larger brains with large numbers of neurons is an evolutionary innovation in mammals and birds. However, the corresponding changes in cortical developmental programmes during amniote evolution are poorly understood. Here we examine the cortical development of Madagascar ground geckos, and report uniqu...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3206

    authors: Nomura T,Gotoh H,Ono K

    更新日期:2013-01-01 00:00:00

  • High precision epidermal radio frequency antenna via nanofiber network for wireless stretchable multifunction electronics.

    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...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19367-8

    authors: Zhang Y,Huo Z,Wang X,Han X,Wu W,Wan B,Wang H,Zhai J,Tao J,Pan C,Wang ZL

    更新日期:2020-11-06 00:00:00

  • Variants in ELL2 influencing immunoglobulin levels associate with multiple myeloma.

    abstract::Multiple myeloma (MM) is characterized by an uninhibited, clonal growth of plasma cells. While first-degree relatives of patients with MM show an increased risk of MM, the genetic basis of inherited MM susceptibility is incompletely understood. Here we report a genome-wide association study in the Nordic region identi...

    journal_title:Nature communications

    pub_type: 杂志文章,meta分析,多中心研究

    doi:10.1038/ncomms8213

    authors: Swaminathan B,Thorleifsson G,Jöud M,Ali M,Johnsson E,Ajore R,Sulem P,Halvarsson BM,Eyjolfsson G,Haraldsdottir V,Hultman C,Ingelsson E,Kristinsson SY,Kähler AK,Lenhoff S,Masson G,Mellqvist UH,Månsson R,Nelander S,Ola

    更新日期:2015-05-26 00:00:00

  • A randomized trial evaluating virus-specific effects of a combination probiotic in children with acute gastroenteritis.

    abstract::Gastroenteritis accounts for nearly 500,000 deaths in children younger than 5 years annually. Although probiotics have been touted as having the potential to expedite diarrhea resolution, recent clinical trials question their effectiveness. A potential explanation is a shift in pathogens following the introduction of ...

    journal_title:Nature communications

    pub_type: 杂志文章,多中心研究,随机对照试验

    doi:10.1038/s41467-020-16308-3

    authors: Freedman SB,Xie J,Nettel-Aguirre A,Pang XL,Chui L,Williamson-Urquhart S,Schnadower D,Schuh S,Sherman PM,Lee BE,Gouin S,Farion KJ,Poonai N,Hurley KF,Qiu Y,Ghandi B,Lloyd C,Finkelstein Y,Pediatric Emergency Research Can

    更新日期:2020-05-21 00:00:00

  • A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay.

    abstract::Nonsense-mediated decay (NMD) eliminates transcripts with premature termination codons. Although NMD-induced loss-of-function has been shown to contribute to the genesis of particular cancers, its global functional consequence in tumours has not been characterized. Here we develop an algorithm to predict NMD and apply...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15943

    authors: Hu Z,Yau C,Ahmed AA

    更新日期:2017-06-26 00:00:00

  • A general-purpose machine-learning force field for bulk and nanostructured phosphorus.

    abstract::Elemental phosphorus is attracting growing interest across fundamental and applied fields of research. However, atomistic simulations of phosphorus have remained an outstanding challenge. Here, we show that a universally applicable force field for phosphorus can be created by machine learning (ML) from a suitably chos...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19168-z

    authors: Deringer VL,Caro MA,Csányi G

    更新日期:2020-10-29 00:00:00

  • Loss of the E3 ubiquitin ligase MKRN1 represses diet-induced metabolic syndrome through AMPK activation.

    abstract::AMP-activated protein kinase (AMPK) plays a key role in controlling energy metabolism in response to physiological and nutritional status. Although AMPK activation has been proposed as a promising molecular target for treating obesity and its related comorbidities, the use of pharmacological AMPK activators has been m...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05721-4

    authors: Lee MS,Han HJ,Han SY,Kim IY,Chae S,Lee CS,Kim SE,Yoon SG,Park JW,Kim JH,Shin S,Jeong M,Ko A,Lee HY,Oh KJ,Lee YH,Bae KH,Koo SH,Kim JW,Seong JK,Hwang D,Song J

    更新日期:2018-08-24 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

  • Archaeogenomic evidence reveals prehistoric matrilineal dynasty.

    abstract::For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14115

    authors: Kennett DJ,Plog S,George RJ,Culleton BJ,Watson AS,Skoglund P,Rohland N,Mallick S,Stewardson K,Kistler L,LeBlanc SA,Whiteley PM,Reich D,Perry GH

    更新日期:2017-02-21 00:00:00