Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation.

Abstract:

:X-chromosome inactivation (XCI), i.e., the inactivation of one of the female X chromosomes, restores equal expression of X-chromosomal genes between females and males. However, ~10% of genes show variable degrees of escape from XCI between females, although little is known about the causes of variable XCI. Using a discovery data-set of 1867 females and 1398 males and a replication sample of 3351 females, we show that genetic variation at three autosomal loci is associated with female-specific changes in X-chromosome methylation. Through cis-eQTL expression analysis, we map these loci to the genes SMCHD1/METTL4, TRIM6/HBG2, and ZSCAN9. Low-expression alleles of the loci are predominantly associated with mild hypomethylation of CpG islands near genes known to variably escape XCI, implicating the autosomal genes in variable XCI. Together, these results suggest a genetic basis for variable escape from XCI and highlight the potential of a population genomics approach to identify genes involved in XCI.

journal_name

Nat Commun

journal_title

Nature communications

authors

Luijk R,Wu H,Ward-Caviness CK,Hannon E,Carnero-Montoro E,Min JL,Mandaviya P,Müller-Nurasyid M,Mei H,van der Maarel SM,BIOS Consortium.,Relton C,Mill J,Waldenberger M,Bell JT,Jansen R,Zhernakova A,Franke L,'t Hoen PAC

doi

10.1038/s41467-018-05714-3

subject

Has Abstract

pub_date

2018-09-14 00:00:00

pages

3738

issue

1

issn

2041-1723

pii

10.1038/s41467-018-05714-3

journal_volume

9

pub_type

杂志文章
  • An unusual type of polymorphism in a liquid crystal.

    abstract::Polymorphism is a remarkable concept in chemistry, materials science, computer science, and biology. Whether it is the ability of a material to exist in two or more crystal structures, a single interface connecting to two different entities, or alternative phenotypes of an organism, polymorphism determines function an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03160-9

    authors: Li L,Salamończyk M,Shadpour S,Zhu C,Jákli A,Hegmann T

    更新日期:2018-02-19 00:00:00

  • GWAS for Interleukin-1β levels in gingival crevicular fluid identifies IL37 variants in periodontal inflammation.

    abstract::There is no agnostic GWAS evidence for the genetic control of IL-1β expression in periodontal disease. Here we report a GWAS for "high" gingival crevicular fluid IL-1β expression among 4910 European-American adults and identify association signals in the IL37 locus. rs3811046 at this locus (p = 3.3 × 10-22) is associa...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05940-9

    authors: Offenbacher S,Jiao Y,Kim SJ,Marchesan J,Moss KL,Jing L,Divaris K,Bencharit S,Agler CS,Morelli T,Zhang S,Sun L,Seaman WT,Cowley D,Barros SP,Beck JD,Munz M,Schaefer AS,North KE

    更新日期:2018-09-11 00:00:00

  • Simulation of non-Abelian gauge theories with optical lattices.

    abstract::Many phenomena occurring in strongly correlated quantum systems still await conclusive explanations. The absence of isolated free quarks in nature is an example. It is attributed to quark confinement, whose origin is not yet understood. The phase diagram for nuclear matter at general temperatures and densities, studie...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3615

    authors: Tagliacozzo L,Celi A,Orland P,Mitchell MW,Lewenstein M

    更新日期:2013-01-01 00:00:00

  • DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts.

    abstract::Genomic and phenotypic analyses indicate extensive intra- as well as intertumoral heterogeneity in primary human malignant cell populations despite their clonal origin. Cellular DNA barcoding offers a powerful and unbiased alternative to track the number and size of multiple subclones within a single human tumour xeno...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6871

    authors: Nguyen LV,Cox CL,Eirew P,Knapp DJ,Pellacani D,Kannan N,Carles A,Moksa M,Balani S,Shah S,Hirst M,Aparicio S,Eaves CJ

    更新日期:2014-12-23 00:00:00

  • Author Correction: Restoration of patterned vision with an engineered photoactivatable G protein-coupled receptor.

    abstract::Kevin J. Cao and Richard H. Kramer, who developed extended release with beta cyclodextrin, were inadvertently omitted from the author list and author contributions section of this Article. These errors have now been corrected in both the PDF and HTML versions of the Article. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-018-03585-2

    authors: Berry MH,Holt A,Levitz J,Broichhagen J,Gaub BM,Visel M,Stanley C,Aghi K,Kim YJ,Cao K,Kramer RH,Trauner D,Flannery J,Isacoff EY

    更新日期:2018-03-13 00:00:00

  • ROW1 maintains quiescent centre identity by confining WOX5 expression to specific cells.

    abstract::The quiescent centre (QC) in the Arabidopsis root apical meristem is essential for stem cell organization. Here we show that the loss of REPRESSOR OF WUSCHEL1 (ROW1), a PHD domain-containing protein, leads to QC failure, defects in cell differentiation and ectopic expression of WUSCHEL-RELATED HOMEOBOX 5 (WOX5) in cel...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7003

    authors: Zhang Y,Jiao Y,Liu Z,Zhu YX

    更新日期:2015-01-29 00:00:00

  • Multi-cohort study identifies social determinants of systemic inflammation over the life course.

    abstract::Chronic inflammation has been proposed as having a prominent role in the construction of social inequalities in health. Disentangling the effects of early life and adulthood social disadvantage on inflammation is key in elucidating biological mechanisms underlying socioeconomic disparities. Here we explore the relatio...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-08732-x

    authors: Berger E,Castagné R,Chadeau-Hyam M,Bochud M,d'Errico A,Gandini M,Karimi M,Kivimäki M,Krogh V,Marmot M,Panico S,Preisig M,Ricceri F,Sacerdote C,Steptoe A,Stringhini S,Tumino R,Vineis P,Delpierre C,Kelly-Irving M

    更新日期:2019-02-15 00:00:00

  • High-coherence electron bunches produced by femtosecond photoionization.

    abstract::With the development of ultrafast electron and X-ray sources it is becoming possible to study structural dynamics with atomic-level spatial and temporal resolution. Because of their short mean free path, electrons are particularly well suited for investigating surfaces and thin films, such as the challenging and impor...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2700

    authors: Engelen WJ,van der Heijden MA,Bakker DJ,Vredenbregt EJ,Luiten OJ

    更新日期:2013-01-01 00:00:00

  • A global strategy to mitigate the environmental impact of China's ruminant consumption boom.

    abstract::Rising demand for ruminant meat and dairy products in developing countries is expected to double anthropogenic greenhouse gas and ammonia emissions from livestock by 2050. Mitigation strategies are urgently needed to meet demand while minimizing environmental impacts. Here, we develop scenarios for mitigating emission...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06381-0

    authors: Du Y,Ge Y,Ren Y,Fan X,Pan K,Lin L,Wu X,Min Y,Meyerson LA,Heino M,Chang SX,Liu X,Mao F,Yang G,Peng C,Qu Z,Chang J,Didham RK

    更新日期:2018-10-08 00:00:00

  • Asymmetric construction of tetrahedral chiral zinc with high configurational stability and catalytic activity.

    abstract::Chiral metal complexes show promise as asymmetric catalysts and optical materials. Chiral-at-metal complexes composed of achiral ligands have expanded the versatility and applicability of chiral metal complexes, especially for octahedral and half-sandwich complexes. However, Werner-type tetrahedral complexes with a st...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20074-7

    authors: Endo K,Liu Y,Ube H,Nagata K,Shionoya M

    更新日期:2020-12-09 00:00:00

  • HuR and miR-1192 regulate myogenesis by modulating the translation of HMGB1 mRNA.

    abstract::Upon muscle injury, the high mobility group box 1 (HMGB1) protein is upregulated and secreted to initiate reparative responses. Here we show that HMGB1 controls myogenesis both in vitro and in vivo during development and after adult muscle injury. HMGB1 expression in muscle cells is regulated at the translational leve...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3388

    authors: Dormoy-Raclet V,Cammas A,Celona B,Lian XJ,van der Giessen K,Zivojnovic M,Brunelli S,Riuzzi F,Sorci G,Wilhelm BT,Di Marco S,Donato R,Bianchi ME,Gallouzi IE

    更新日期:2013-01-01 00:00:00

  • Rapid cost decrease of renewables and storage accelerates the decarbonization of China's power system.

    abstract::The costs for solar photovoltaics, wind, and battery storage have dropped markedly since 2010, however, many recent studies and reports around the world have not adequately captured such dramatic decrease. Those costs are projected to decline further in the near future, bringing new prospects for the widespread penetr...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16184-x

    authors: He G,Lin J,Sifuentes F,Liu X,Abhyankar N,Phadke A

    更新日期:2020-05-19 00:00:00

  • Insights into catalysis and regulation of non-canonical ubiquitination and deubiquitination by bacterial deamidase effectors.

    abstract::The bacterial effector MavC catalyzes non-canonical ubiquitination of host E2 enzyme UBE2N without engaging any of the conventional ubiquitination machinery, thereby abolishing UBE2N's function in forming K63-linked ubiquitin (Ub) chains and dampening NF-кB signaling. We now report the structures of MavC in complex wi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16587-w

    authors: Wang Y,Zhan Q,Wang X,Li P,Liu S,Gao G,Gao P

    更新日期:2020-06-02 00:00:00

  • Ultrafast and highly sensitive infrared photodetectors based on two-dimensional oxyselenide crystals.

    abstract::Infrared light detection and sensing is deeply embedded in modern technology and human society and its development has always been benefitting from the discovery of various photoelectric materials. The rise of two-dimensional materials, thanks to their distinct electronic structures, extreme dimensional confinement an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05874-2

    authors: Yin J,Tan Z,Hong H,Wu J,Yuan H,Liu Y,Chen C,Tan C,Yao F,Li T,Chen Y,Liu Z,Liu K,Peng H

    更新日期:2018-08-17 00:00:00

  • Crystallographic structure of a small molecule SIRT1 activator-enzyme complex.

    abstract::SIRT1, the founding member of the mammalian family of seven NAD(+)-dependent sirtuins, is composed of 747 amino acids forming a catalytic domain and extended N- and C-terminal regions. We report the design and characterization of an engineered human SIRT1 construct (mini-hSIRT1) containing the minimal structural eleme...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms8645

    authors: Dai H,Case AW,Riera TV,Considine T,Lee JE,Hamuro Y,Zhao H,Jiang Y,Sweitzer SM,Pietrak B,Schwartz B,Blum CA,Disch JS,Caldwell R,Szczepankiewicz B,Oalmann C,Yee Ng P,White BH,Casaubon R,Narayan R,Koppetsch K,Bourb

    更新日期:2015-07-02 00:00:00

  • Dominant oceanic bacteria secure phosphate using a large extracellular buffer.

    abstract::The ubiquitous SAR11 and Prochlorococcus bacteria manage to maintain a sufficient supply of phosphate in phosphate-poor surface waters of the North Atlantic subtropical gyre. Furthermore, it seems that their phosphate uptake may counter-intuitively be lower in more productive tropical waters, as if their cellular dema...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms8878

    authors: Zubkov MV,Martin AP,Hartmann M,Grob C,Scanlan DJ

    更新日期:2015-07-22 00:00:00

  • Sub-micron phase coexistence in small-molecule organic thin films revealed by infrared nano-imaging.

    abstract::Controlling the domain size and degree of crystallization in organic films is highly important for electronic applications such as organic photovoltaics, but suitable nanoscale mapping is very difficult. Here we apply infrared-spectroscopic nano-imaging to directly determine the local crystallinity of organic thin fil...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5101

    authors: Westermeier C,Cernescu A,Amarie S,Liewald C,Keilmann F,Nickel B

    更新日期:2014-06-11 00:00:00

  • Crystal structure of mammalian acid sphingomyelinase.

    abstract::Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann-Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12196

    authors: Gorelik A,Illes K,Heinz LX,Superti-Furga G,Nagar B

    更新日期:2016-07-20 00:00:00

  • D-Glucosamine supplementation extends life span of nematodes and of ageing mice.

    abstract::D-Glucosamine (GlcN) is a freely available and commonly used dietary supplement potentially promoting cartilage health in humans, which also acts as an inhibitor of glycolysis. Here we show that GlcN, independent of the hexosamine pathway, extends Caenorhabditis elegans life span by impairing glucose metabolism that a...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4563

    authors: Weimer S,Priebs J,Kuhlow D,Groth M,Priebe S,Mansfeld J,Merry TL,Dubuis S,Laube B,Pfeiffer AF,Schulz TJ,Guthke R,Platzer M,Zamboni N,Zarse K,Ristow M

    更新日期:2014-04-08 00:00:00

  • Ontogenetic asymmetry modulates population biomass production and response to harvest.

    abstract::Patterns in biomass production are determined by resource input (productivity) and trophic transfer efficiency. At fixed resource input, variation in consumer biomass production has been related to food quality, metabolic type and diversity among species. In contrast, intraspecific variation in individual body size be...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7441

    authors: Reichstein B,Persson L,De Roos AM

    更新日期:2015-03-04 00:00:00

  • The utility of serology for elimination surveillance of trachoma.

    abstract::Robust surveillance methods are needed for trachoma control and recrudescence monitoring, but existing methods have limitations. Here, we analyse data from nine trachoma-endemic populations and provide operational thresholds for interpretation of serological data in low-transmission and post-elimination settings. Anal...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07852-0

    authors: Pinsent A,Solomon AW,Bailey RL,Bid R,Cama A,Dean D,Goodhew B,Gwyn SE,Jack KR,Kandel RP,Kama M,Massae P,Macleod C,Mabey DCW,Migchelsen S,Müller A,Sandi F,Sokana O,Taoaba R,Tekeraoi R,Martin DL,White MT

    更新日期:2018-12-21 00:00:00

  • Reduced exposure to extreme precipitation from 0.5 °C less warming in global land monsoon regions.

    abstract::The Paris Agreement set a goal to keep global warming well below 2 °C and pursue efforts to limit it to 1.5 °C. Understanding how 0.5 °C less warming reduces impacts and risks is key for climate policies. Here, we show that both areal and population exposures to dangerous extreme precipitation events (e.g., once in 10...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05633-3

    authors: Zhang W,Zhou T,Zou L,Zhang L,Chen X

    更新日期:2018-08-08 00:00:00

  • Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22.

    abstract::Epilepsy is a common brain disorder throughout history. Epilepsy-related ligand-receptor complex, LGI1-ADAM22, regulates synaptic transmission and has emerged as a determinant of brain excitability, as their mutations and acquired LGI1 autoantibodies cause epileptic disorders in human. Here, we report the crystal stru...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03947-w

    authors: Yamagata A,Miyazaki Y,Yokoi N,Shigematsu H,Sato Y,Goto-Ito S,Maeda A,Goto T,Sanbo M,Hirabayashi M,Shirouzu M,Fukata Y,Fukata M,Fukai S

    更新日期:2018-04-18 00:00:00

  • Microtubule-dependent balanced cell contraction and luminal-matrix modification accelerate epithelial tube fusion.

    abstract::Connection of tubules into larger networks is the key process for the development of circulatory systems. In Drosophila development, tip cells of the tracheal system lead the migration of each branch and connect tubules by adhering to each other and simultaneously changing into a torus-shape. We show that as adhesion ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms11141

    authors: Kato K,Dong B,Wada H,Tanaka-Matakatsu M,Yagi Y,Hayashi S

    更新日期:2016-04-12 00:00:00

  • Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice.

    abstract::Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth p...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6087

    authors: Yang W,Guo Z,Huang C,Duan L,Chen G,Jiang N,Fang W,Feng H,Xie W,Lian X,Wang G,Luo Q,Zhang Q,Liu Q,Xiong L

    更新日期:2014-10-08 00:00:00

  • Effect of hydrogen on the integrity of aluminium-oxide interface at elevated temperatures.

    abstract::Hydrogen can facilitate the detachment of protective oxide layer off metals and alloys. The degradation is usually exacerbated at elevated temperatures in many industrial applications; however, its origin remains poorly understood. Here by heating hydrogenated aluminium inside an environmental transmission electron mi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14564

    authors: Li M,Xie DG,Ma E,Li J,Zhang XX,Shan ZW

    更新日期:2017-02-20 00:00:00

  • In planta study of photosynthesis and photorespiration using NADPH and NADH/NAD+ fluorescent protein sensors.

    abstract::The challenge of monitoring in planta dynamic changes of NADP(H) and NAD(H) redox states at the subcellular level is considered a major obstacle in plant bioenergetics studies. Here, we introduced two circularly permuted yellow fluorescent protein sensors, iNAP and SoNar, into Arabidopsis thaliana to monitor the dynam...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17056-0

    authors: Lim SL,Voon CP,Guan X,Yang Y,Gardeström P,Lim BL

    更新日期:2020-06-26 00:00:00

  • High-speed and on-chip graphene blackbody emitters for optical communications by remote heat transfer.

    abstract::High-speed light emitters integrated on silicon chips can enable novel architectures for silicon-based optoelectronics, such as on-chip optical interconnects, and silicon photonics. However, conventional light sources based on compound semiconductors face major challenges for their integration with a silicon-based pla...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03695-x

    authors: Miyoshi Y,Fukazawa Y,Amasaka Y,Reckmann R,Yokoi T,Ishida K,Kawahara K,Ago H,Maki H

    更新日期:2018-03-29 00:00:00

  • CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations.

    abstract::CRISPR-Cas9 is a promising technology for genome editing. Here we use Cas9 nuclease-induced double-strand break DNA (DSB) at the UROS locus to model and correct congenital erythropoietic porphyria. We demonstrate that homology-directed repair is rare compared with NHEJ pathway leading to on-target indels and causing u...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09006-2

    authors: Cullot G,Boutin J,Toutain J,Prat F,Pennamen P,Rooryck C,Teichmann M,Rousseau E,Lamrissi-Garcia I,Guyonnet-Duperat V,Bibeyran A,Lalanne M,Prouzet-Mauléon V,Turcq B,Ged C,Blouin JM,Richard E,Dabernat S,Moreau-Gaudry F,

    更新日期:2019-03-08 00:00:00

  • Prediction of the strength and timing of sunspot cycle 25 reveal decadal-scale space environmental conditions.

    abstract::The Sun's activity cycle governs the radiation, particle and magnetic flux in the heliosphere creating hazardous space weather. Decadal-scale variations define space climate and force the Earth's atmosphere. However, predicting the solar cycle is challenging. Current understanding indicates a short window for predicti...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07690-0

    authors: Bhowmik P,Nandy D

    更新日期:2018-12-06 00:00:00