The strength and pattern of natural selection on gene expression in rice.

Abstract:

:Levels of gene expression underpin organismal phenotypes1,2, but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown1,2. Here we assayed gene expression in rice (Oryza sativa)3, and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts4,5. Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions. Overall, more transcripts are conditionally neutral (2.83%) than are antagonistically pleiotropic6 (0.04%), and transcripts that display lower levels of expression and stochastic noise7-9 and higher levels of plasticity9 are under stronger selection. Selection strength was further weakly negatively associated with levels of cis-regulation and network connectivity9. Our multivariate analysis suggests that selection acts on the expression of photosynthesis genes4,5, but that the efficacy of selection is genetically constrained under drought conditions10. Drought selected for earlier flowering11,12 and a higher expression of OsMADS18 (Os07g0605200), which encodes a MADS-box transcription factor and is a known regulator of early flowering13-marking this gene as a drought-escape gene11,12. The ability to estimate selection strengths provides insights into how selection can shape molecular traits at the core of gene action.

journal_name

Nature

journal_title

Nature

authors

Groen SC,Ćalić I,Joly-Lopez Z,Platts AE,Choi JY,Natividad M,Dorph K,Mauck WM 3rd,Bracken B,Cabral CLU,Kumar A,Torres RO,Satija R,Vergara G,Henry A,Franks SJ,Purugganan MD

doi

10.1038/s41586-020-1997-2

subject

Has Abstract

pub_date

2020-02-01 00:00:00

pages

572-576

issue

7796

eissn

0028-0836

issn

1476-4687

pii

10.1038/s41586-020-1997-2

journal_volume

578

pub_type

杂志文章

相关文献

NATURE文献大全
  • Generation of prion transmission barriers by mutational control of amyloid conformations.

    abstract::Self-propagating beta-sheet-rich protein aggregates are implicated in a wide range of protein-misfolding phenomena, including amyloid diseases and prion-based inheritance. Two properties have emerged as common features of amyloids. Amyloid formation is ubiquitous: many unrelated proteins form such aggregates and even ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature01894

    authors: Chien P,DePace AH,Collins SR,Weissman JS

    更新日期:2003-08-21 00:00:00

  • Temporal integration by a slowly inactivating K+ current in hippocampal neurons.

    abstract::A central aspect of neuronal function is how each nerve cell translated synaptic input into a sequence of action potentials that carry information along the axon, coded as spike frequency. When transduction from a graded depolarizing input to spikes is studied by injecting a depolarizing current, there is often a rema...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/336379a0

    authors: Storm JF

    更新日期:1988-11-24 00:00:00

  • Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans.

    abstract::The nematode Caenorhabditis elegans is an important model for studying the genetics of ageing, with over 50 life-extension mutations known so far. However, little is known about the pathobiology of ageing in this species, limiting attempts to connect genotype with senescent phenotype. Using ultrastructural analysis an...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature01135

    authors: Herndon LA,Schmeissner PJ,Dudaronek JM,Brown PA,Listner KM,Sakano Y,Paupard MC,Hall DH,Driscoll M

    更新日期:2002-10-24 00:00:00

  • Nanotube electronics: large-scale assembly of carbon nanotubes.

    abstract::Nanoscale electronic devices made from carbon nanotubes, such as transistors and sensors, are much smaller and more versatile than those that rely on conventional microelectronic chips, but their development for mass production has been thwarted by difficulties in aligning and integrating the millions of nanotubes req...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/425036a

    authors: Rao SG,Huang L,Setyawan W,Hong S

    更新日期:2003-09-04 00:00:00

  • Distinct aspects of neuronal differentiation encoded by frequency of spontaneous Ca2+ transients.

    abstract::Stimulation of transient increases in intracellular calcium (Cai2+) activates protein kinases, regulates transcription and influences motility and morphology. Developing neurons generate spontaneous Cai2+ transients, but their role in directing neuronal differentiation and the way in which they encode information are ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/375784a0

    authors: Gu X,Spitzer NC

    更新日期:1995-06-29 00:00:00

  • More fuss about genetics and embryos.

    abstract::General alarm about genetics continues, fanned by the expectation that what may one day be possible will be a reality tomorrow. Moderation is the most urgent need, but understanding would also help. ...

    journal_title:Nature

    pub_type: 社论

    doi:10.1038/367099a0

    authors:

    更新日期:1994-01-13 00:00:00

  • Effect of natural iron fertilization on carbon sequestration in the Southern Ocean.

    abstract::The availability of iron limits primary productivity and the associated uptake of carbon over large areas of the ocean. Iron thus plays an important role in the carbon cycle, and changes in its supply to the surface ocean may have had a significant effect on atmospheric carbon dioxide concentrations over glacial-inter...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature05700

    authors: Blain S,Quéguiner B,Armand L,Belviso S,Bombled B,Bopp L,Bowie A,Brunet C,Brussaard C,Carlotti F,Christaki U,Corbière A,Durand I,Ebersbach F,Fuda JL,Garcia N,Gerringa L,Griffiths B,Guigue C,Guillerm C,Jacquet S,J

    更新日期:2007-04-26 00:00:00

  • Histone H2A.Z subunit exchange controls consolidation of recent and remote memory.

    abstract::Memory formation is a multi-stage process that initially requires cellular consolidation in the hippocampus, after which memories are downloaded to the cortex for maintenance, in a process termed systems consolidation. Epigenetic mechanisms regulate both types of consolidation, but histone variant exchange, in which c...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature13707

    authors: Zovkic IB,Paulukaitis BS,Day JJ,Etikala DM,Sweatt JD

    更新日期:2014-11-27 00:00:00

  • Regulated degradation of a class V myosin receptor directs movement of the yeast vacuole.

    abstract::Normal cellular function requires that organelles be positioned in specific locations. The direction in which molecular motors move organelles is based in part on the polarity of microtubules and actin filaments. However, this alone does not determine the intracellular destination of organelles. For example, the yeast...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature01453

    authors: Tang F,Kauffman EJ,Novak JL,Nau JJ,Catlett NL,Weisman LS

    更新日期:2003-03-06 00:00:00

  • Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups.

    abstract::The rates and routes of lethal systemic spread in breast cancer are poorly understood owing to a lack of molecularly characterized patient cohorts with long-term, detailed follow-up data. Long-term follow-up is especially important for those with oestrogen-receptor (ER)-positive breast cancers, which can recur up to t...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/s41586-019-1007-8

    authors: Rueda OM,Sammut SJ,Seoane JA,Chin SF,Caswell-Jin JL,Callari M,Batra R,Pereira B,Bruna A,Ali HR,Provenzano E,Liu B,Parisien M,Gillett C,McKinney S,Green AR,Murphy L,Purushotham A,Ellis IO,Pharoah PD,Rueda C,Apari

    更新日期:2019-03-01 00:00:00

  • Non-random segregation of sister chromosomes in Escherichia coli.

    abstract::It has long been known that the 5' to 3' polarity of DNA synthesis results in both a leading and lagging strand at all replication forks. Until now, however, there has been no evidence that leading or lagging strands are spatially organized in any way within a cell. Here we show that chromosome segregation in Escheric...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature07282

    authors: White MA,Eykelenboom JK,Lopez-Vernaza MA,Wilson E,Leach DR

    更新日期:2008-10-30 00:00:00

  • Modelling the long QT syndrome with induced pluripotent stem cells.

    abstract::The ability to generate patient-specific human induced pluripotent stem cells (iPSCs) offers a new paradigm for modelling human disease and for individualizing drug testing. Congenital long QT syndrome (LQTS) is a familial arrhythmogenic syndrome characterized by abnormal ion channel function and sudden cardiac death....

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature09747

    authors: Itzhaki I,Maizels L,Huber I,Zwi-Dantsis L,Caspi O,Winterstern A,Feldman O,Gepstein A,Arbel G,Hammerman H,Boulos M,Gepstein L

    更新日期:2011-03-10 00:00:00

  • Host-microbiota maladaptation in colorectal cancer.

    abstract::Colorectal cancer (CRC) is a heterogeneous disease of the intestinal epithelium that is characterized by the accumulation of mutations and a dysregulated immune response. Up to 90% of disease risk is thought to be due to environmental factors such as diet, which is consistent with a growing body of literature that des...

    journal_title:Nature

    pub_type: 杂志文章,评审

    doi:10.1038/s41586-020-2729-3

    authors: Janney A,Powrie F,Mann EH

    更新日期:2020-09-01 00:00:00

  • Human cyclin A is adenovirus E1A-associated protein p60 and behaves differently from cyclin B.

    abstract::CYCLINS are proteins synthesized during each cell cycle and abruptly destroyed in each mitosis. Cyclins have been implicated in the induction of mitosis and are associated with the serine-threonine protein kinase p34cdc2 as components of mitosis promoting factor (MPF). On the basis of conserved sequence motifs cyclins...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/346760a0

    authors: Pines J,Hunter T

    更新日期:1990-08-23 00:00:00

  • Background-free search for neutrinoless double-β decay of 76Ge with GERDA.

    abstract::Many extensions of the Standard Model of particle physics explain the dominance of matter over antimatter in our Universe by neutrinos being their own antiparticles. This would imply the existence of neutrinoless double-β decay, which is an extremely rare lepton-number-violating radioactive decay process whose detecti...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature21717

    authors: GERDA Collaboration.

    更新日期:2017-04-05 00:00:00

  • A role for Lin28 in primordial germ-cell development and germ-cell malignancy.

    abstract::The rarity and inaccessibility of the earliest primordial germ cells (PGCs) in the mouse embryo thwart efforts to investigate molecular mechanisms of germ-cell specification. stella (also called Dppa3) marks the rare founder population of the germ lineage. Here we differentiate mouse embryonic stem cells carrying a st...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature08210

    authors: West JA,Viswanathan SR,Yabuuchi A,Cunniff K,Takeuchi A,Park IH,Sero JE,Zhu H,Perez-Atayde A,Frazier AL,Surani MA,Daley GQ

    更新日期:2009-08-13 00:00:00

  • Mutations of two PMS homologues in hereditary nonpolyposis colon cancer.

    abstract::Hereditary nonpolyposis colorectal cancer (HNPCC) is one of man's commonest hereditary diseases. Several studies have implicated a defect in DNA mismatch repair in the pathogenesis of this disease. In particular, hMSH2 and hMLH1 homologues of the bacterial DNA mismatch repair genes mutS and mutL, respectively, were sh...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/371075a0

    authors: Nicolaides NC,Papadopoulos N,Liu B,Wei YF,Carter KC,Ruben SM,Rosen CA,Haseltine WA,Fleischmann RD,Fraser CM

    更新日期:1994-09-01 00:00:00

  • Study of allosteric communication between protomers by immunotagging.

    abstract::Ligand-induced allosteric changes in proteins are important in their cellular functions and regulation, and both concerted and sequential examples are known. The distinction has entailed elaborate analysis, however, and only a few systems have been unequivocally analysed. We have investigated the coupling between ATP ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/361749a0

    authors: Lindsley JE,Wang JC

    更新日期:1993-02-25 00:00:00

  • Computational design of ligand-binding proteins with high affinity and selectivity.

    abstract::The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition. Attempts to rationally design ligand-binding proteins have met with little success, however, and the computational d...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature12443

    authors: Tinberg CE,Khare SD,Dou J,Doyle L,Nelson JW,Schena A,Jankowski W,Kalodimos CG,Johnsson K,Stoddard BL,Baker D

    更新日期:2013-09-12 00:00:00

  • 3-A resolution structure of a protein with histone-like properties in prokaryotes.

    abstract::The 3-A structure of DNA-binding protein II, which exhibits histone-like properties in bacteria, has been determined. The molecule is dimeric and appears to bind to the phosphate backbone of DNA through two symmetry-related arms. A mechanism by which the protein induces DNA supercoiling is proposed. ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/310376a0

    authors: Tanaka I,Appelt K,Dijk J,White SW,Wilson KS

    更新日期:1984-08-02 00:00:00

  • Direct modulation of Aplysia S-K+ channels by a 12-lipoxygenase metabolite of arachidonic acid.

    abstract::Lipoxygenase metabolites of arachidonic acid have recently been shown to modulate the activity of ion channels in nerve and muscle cells. The mechanism of action of these metabolites is, however, unknown. In sensory neurons of Aplysia, the S-K- channel is under the dual modulatory control of 5-hydroxytryptamine (5-HT)...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/342553a0

    authors: Buttner N,Siegelbaum SA,Volterra A

    更新日期:1989-11-30 00:00:00

  • Postsynaptic hyperpolarization during conditioning reversibly blocks induction of long-term potentiation.

    abstract::Activity-induced changes in the efficacy of synaptic transmission between neurones are central to several prominent theories of learning. In both in vivo and in vitro preparations of the hippocampus, a conditioning high-frequency stimulus delivered to afferent fibres results in a long-term potentiation of synaptic tra...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/320529a0

    authors: Malinow R,Miller JP

    更新日期:1986-04-10 00:00:00

  • Emergence of vancomycin tolerance in Streptococcus pneumoniae.

    abstract::Streptococcus pneumoniae, the pneumococcus, is the most common cause of sepsis and meningitis. Multiple-antibiotic-resistant strains are widespread, and vancomycin is the antibiotic of last resort. Emergence of vancomycin resistance in this community-acquired bacterium would be catastrophic. Antibiotic tolerance, the ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/21202

    authors: Novak R,Henriques B,Charpentier E,Normark S,Tuomanen E

    更新日期:1999-06-10 00:00:00

  • Landscape of transcription in human cells.

    abstract::Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct out...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature11233

    authors: Djebali S,Davis CA,Merkel A,Dobin A,Lassmann T,Mortazavi A,Tanzer A,Lagarde J,Lin W,Schlesinger F,Xue C,Marinov GK,Khatun J,Williams BA,Zaleski C,Rozowsky J,Röder M,Kokocinski F,Abdelhamid RF,Alioto T,Antoshechkin

    更新日期:2012-09-06 00:00:00

  • Methanotrophic symbionts provide carbon for photosynthesis in peat bogs.

    abstract::Wetlands are the largest natural source of atmospheric methane, the second most important greenhouse gas. Methane flux to the atmosphere depends strongly on the climate; however, by far the largest part of the methane formed in wetland ecosystems is recycled and does not reach the atmosphere. The biogeochemical contro...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature03802

    authors: Raghoebarsing AA,Smolders AJ,Schmid MC,Rijpstra WI,Wolters-Arts M,Derksen J,Jetten MS,Schouten S,Sinninghe Damsté JS,Lamers LP,Roelofs JG,Op den Camp HJ,Strous M

    更新日期:2005-08-25 00:00:00

  • Extraction of a weak climatic signal by an ecosystem.

    abstract::The complexity of ecosystems can cause subtle and chaotic responses to changes in external forcing. Although ecosystems may not normally behave chaotically, sensitivity to external influences associated with nonlinearity can lead to amplification of climatic signals. Strong correlations between an El Niño index and ra...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/416629a

    authors: Taylor AH,Allen JI,Clark PA

    更新日期:2002-04-11 00:00:00

  • Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome.

    abstract::Hutchinson-Gilford progeria syndrome (HGPS) is a rare and fatal human premature ageing disease, characterized by premature arteriosclerosis and degeneration of vascular smooth muscle cells (SMCs). HGPS is caused by a single point mutation in the lamin A (LMNA) gene, resulting in the generation of progerin, a truncated...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature09879

    authors: Liu GH,Barkho BZ,Ruiz S,Diep D,Qu J,Yang SL,Panopoulos AD,Suzuki K,Kurian L,Walsh C,Thompson J,Boue S,Fung HL,Sancho-Martinez I,Zhang K,Yates J 3rd,Izpisua Belmonte JC

    更新日期:2011-04-14 00:00:00

  • Evidence for kinks in DNA folding in the nucleosome.

    abstract::The nucleosome subunit of chromatin consists of DNA folded around a histone core as a 1.8-turn left-handed solenoid. The crystal structure of the nucleosome core particle revealed that it has a dyad symmetry axis and that the minor helix groove faces outwards from the protein core. Richmond et al. noticed that the pat...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/328554a0

    authors: Hogan ME,Rooney TF,Austin RH

    更新日期:1987-08-06 00:00:00

  • Hypothalamic regulation of sleep and circadian rhythms.

    abstract::A series of findings over the past decade has begun to identify the brain circuitry and neurotransmitters that regulate our daily cycles of sleep and wakefulness. The latter depends on a network of cell groups that activate the thalamus and the cerebral cortex. A key switch in the hypothalamus shuts off this arousal s...

    journal_title:Nature

    pub_type: 杂志文章,评审

    doi:10.1038/nature04284

    authors: Saper CB,Scammell TE,Lu J

    更新日期:2005-10-27 00:00:00

  • Formation of olfactory memories mediated by nitric oxide.

    abstract::Sheep learn to recognize the odours of their lambs within two hours of giving birth, and this learning involves synaptic changes within the olfactory bulb. Specifically, mitral cells become increasingly responsive to the learned odour, which stimulates release of both glutamate and GABA (gamma-aminobutyric acid) neuro...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/41765

    authors: Kendrick KM,Guevara-Guzman R,Zorrilla J,Hinton MR,Broad KD,Mimmack M,Ohkura S

    更新日期:1997-08-14 00:00:00