The interaction landscape between transcription factors and the nucleosome.

Abstract:

:Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown. Here we systematically explore interactions between the nucleosome and 220 transcription factors representing diverse structural families. Consistent with earlier observations, we find that the majority of the studied transcription factors have less access to nucleosomal DNA than to free DNA. The motifs recovered from transcription factors bound to nucleosomal and free DNA are generally similar. However, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many transcription factors preferentially bind close to the end of nucleosomal DNA, or to periodic positions on the solvent-exposed side of the DNA. In addition, several transcription factors usually bind to nucleosomal DNA in a particular orientation. Some transcription factors specifically interact with DNA located at the dyad position at which only one DNA gyre is wound, whereas other transcription factors prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome.

journal_name

Nature

journal_title

Nature

authors

Zhu F,Farnung L,Kaasinen E,Sahu B,Yin Y,Wei B,Dodonova SO,Nitta KR,Morgunova E,Taipale M,Cramer P,Taipale J

doi

10.1038/s41586-018-0549-5

subject

Has Abstract

pub_date

2018-10-01 00:00:00

pages

76-81

issue

7725

eissn

0028-0836

issn

1476-4687

pii

10.1038/s41586-018-0549-5

journal_volume

562

pub_type

杂志文章

相关文献

NATURE文献大全
  • Entanglement of two quantum memories via fibres over dozens of kilometres.

    abstract::A quantum internet that connects remote quantum processors1,2 should enable a number of revolutionary applications such as distributed quantum computing. Its realization will rely on entanglement of remote quantum memories over long distances. Despite enormous progress3-12, at present the maximal physical separation a...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/s41586-020-1976-7

    authors: Yu Y,Ma F,Luo XY,Jing B,Sun PF,Fang RZ,Yang CW,Liu H,Zheng MY,Xie XP,Zhang WJ,You LX,Wang Z,Chen TY,Zhang Q,Bao XH,Pan JW

    更新日期:2020-02-01 00:00:00

  • Isolation of an active step I spliceosome and composition of its RNP core.

    abstract::Formation of catalytically active RNA structures within the spliceosome requires the assistance of proteins. However, little is known about the number and nature of proteins needed to establish and maintain the spliceosome's active site. Here we affinity-purified human spliceosomal C complexes and show that they catal...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature06842

    authors: Bessonov S,Anokhina M,Will CL,Urlaub H,Lührmann R

    更新日期:2008-04-17 00:00:00

  • Peripheral deletion of antigen-reactive T cells in oral tolerance.

    abstract::Oral administration of antigen is used to induce antigen-specific peripheral immune tolerance. As well as preventing systemic immune responses to ingested proteins, oral tolerance to autoantigens has also been used to suppress autoimmune diseases in animals and humans. Both active suppression and clonal anergy are sug...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/376177a0

    authors: Chen Y,Inobe J,Marks R,Gonnella P,Kuchroo VK,Weiner HL

    更新日期:1995-07-13 00:00:00

  • Structure of a human common cold virus and functional relationship to other picornaviruses.

    abstract::We report the first atomic resolution structure of an animal virus, human rhinovirus 14. It is strikingly similar to known icosahedral plant RNA viruses. Four neutralizing immunogenic regions have been identified. These, and corresponding antigenic sequences of polio and foot-and-mouth disease viruses, reside on exter...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/317145a0

    authors: Rossmann MG,Arnold E,Erickson JW,Frankenberger EA,Griffith JP,Hecht HJ,Johnson JE,Kamer G,Luo M,Mosser AG

    更新日期:1985-09-12 00:00:00

  • The crystal structure of diphtheria toxin.

    abstract::The crystal structure of the diphtheria toxin dimer at 2.5 A resolution reveals a Y-shaped molecule of three domains. The catalytic domain, called fragment A, is of the alpha + beta type. Fragment B actually consists of two domains. The transmembrane domain consists of nine alpha-helices, two pairs of which are unusua...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/357216a0

    authors: Choe S,Bennett MJ,Fujii G,Curmi PM,Kantardjieff KA,Collier RJ,Eisenberg D

    更新日期:1992-05-21 00:00:00

  • Dilute (d) coat colour mutation of DBA/2J mice is associated with the site of integration of an ecotropic MuLV genome.

    abstract::The single endogenous DBA/2J ectropic provirus segregated concordantly with the dilute (d) coat colour mutation on chromosome 9 in 53/53 DBA/2J-derived recombinant inbred mouse strains and all seven inbred and mutant strains tested that carry the d allele. Analysis of DNA from a spontaneous DBA/2J d revertant (d+2J) s...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/293370a0

    authors: Jenkins NA,Copeland NG,Taylor BA,Lee BK

    更新日期:1981-10-01 00:00:00

  • Induction and organization of Ca2+ waves by enteric neural reflexes.

    abstract::The motility of the gastrointestinal tract consists of local, non-propulsive mixing (pendular or segmental) and propulsive (peristaltic) movements. It is generally considered that mixing movements are produced by intrinsic pacemakers which generate rhythmic contractions, and peristalsis by intrinsic excitatory and inh...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/19973

    authors: Stevens RJ,Publicover NG,Smith TK

    更新日期:1999-05-06 00:00:00

  • Short alanine-based peptides may form 3(10)-helices and not alpha-helices in aqueous solution.

    abstract::Short alanine peptides, containing 16 or 17 residues, appear to form alpha-helices in aqueous solution. But the main spectroscopic analyses used on helical peptides (circular dichroism and nuclear magnetic resonance) cannot distinguish between an alpha-helix (in which the ith residue is hydrogen-bonded to residue i + ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/359653a0

    authors: Miick SM,Martinez GV,Fiori WR,Todd AP,Millhauser GL

    更新日期:1992-10-15 00:00:00

  • The background brightness of the milky way near 2500 A between lparallel= 72 degrees and 126 degrees.

    abstract::Data from a rocket experiment show details which were not known from ground-based observations. ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/226526a0

    authors: Sudbury GC,Ingham MF

    更新日期:1970-05-09 00:00:00

  • Role of spectral detail in sound-source localization.

    abstract::Sounds heard over headphones are typically perceived inside the head (internalized), unlike real sound sources which are perceived outside the head (externalized). If the acoustical waveforms from a real sound source are reproduced precisely using headphones, auditory images are appropriately externalized and localize...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/25526

    authors: Kulkarni A,Colburn HS

    更新日期:1998-12-24 00:00:00

  • DMRT1 prevents female reprogramming in the postnatal mammalian testis.

    abstract::Sex in mammals is determined in the fetal gonad by the presence or absence of the Y chromosome gene Sry, which controls whether bipotential precursor cells differentiate into testicular Sertoli cells or ovarian granulosa cells. This pivotal decision in a single gonadal cell type ultimately controls sexual differentiat...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature10239

    authors: Matson CK,Murphy MW,Sarver AL,Griswold MD,Bardwell VJ,Zarkower D

    更新日期:2011-07-20 00:00:00

  • DNA double-strand breaks activate a multi-functional genetic program in developing lymphocytes.

    abstract::DNA double-strand breaks are generated by genotoxic agents and by cellular endonucleases as intermediates of several important physiological processes. The cellular response to genotoxic DNA breaks includes the activation of transcriptional programs known primarily to regulate cell-cycle checkpoints and cell survival....

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature07392

    authors: Bredemeyer AL,Helmink BA,Innes CL,Calderon B,McGinnis LM,Mahowald GK,Gapud EJ,Walker LM,Collins JB,Weaver BK,Mandik-Nayak L,Schreiber RD,Allen PM,May MJ,Paules RS,Bassing CH,Sleckman BP

    更新日期:2008-12-11 00:00:00

  • The consequences of imperfect mixing in autocatalytic chemical and biological systems.

    abstract::When chemical reactions whose rate increases with the concentration of a product species are carried out in imperfectly mixed systems, a variety of complex behaviours can occur. These phenomena, which have relevance for biological processes as well, include chaotic and stochastic behaviour and selection of one final s...

    journal_title:Nature

    pub_type: 杂志文章,评审

    doi:10.1038/374321a0

    authors: Epstein IR

    更新日期:1995-03-23 00:00:00

  • Reassembly of shattered chromosomes in Deinococcus radiodurans.

    abstract::Dehydration or desiccation is one of the most frequent and severe challenges to living cells. The bacterium Deinococcus radiodurans is the best known extremophile among the few organisms that can survive extremely high exposures to desiccation and ionizing radiation, which shatter its genome into hundreds of short DNA...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature05160

    authors: Zahradka K,Slade D,Bailone A,Sommer S,Averbeck D,Petranovic M,Lindner AB,Radman M

    更新日期:2006-10-05 00:00:00

  • Functional asymmetry in Caenorhabditis elegans taste neurons and its computational role in chemotaxis.

    abstract::Chemotaxis in Caenorhabditis elegans, like chemotaxis in bacteria, involves a random walk biased by the time derivative of attractant concentration, but how the derivative is computed is unknown. Laser ablations have shown that the strongest deficits in chemotaxis to salts are obtained when the ASE chemosensory neuron...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature06927

    authors: Suzuki H,Thiele TR,Faumont S,Ezcurra M,Lockery SR,Schafer WR

    更新日期:2008-07-03 00:00:00

  • Decoding the development of the human hippocampus.

    abstract::The hippocampus is an important part of the limbic system in the human brain that has essential roles in spatial navigation and the consolidation of information from short-term memory to long-term memory1,2. Here we use single-cell RNA sequencing and assay for transposase-accessible chromatin using sequencing (ATAC-se...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/s41586-019-1917-5

    authors: Zhong S,Ding W,Sun L,Lu Y,Dong H,Fan X,Liu Z,Chen R,Zhang S,Ma Q,Tang F,Wu Q,Wang X

    更新日期:2020-01-01 00:00:00

  • Mimicking the alloantigenicity of proteins with chemically synthesized peptides differing in single amino acids.

    abstract::Recent studies have shown that short chemically synthesized peptides very often induce antibodies which react with the cognate sequence in the intact folded protein. Since such antibodies react with known regions of proteins, they are of predetermined specificity and offer a precision not previously possible with immu...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/306697a0

    authors: Alexander H,Johnson DA,Rosen J,Jerabek L,Green N,Weissman IL,Lerner RA

    更新日期:1983-12-15 00:00:00

  • Competition for antigen presentation in living cells involves exchange of peptides bound by class II MHC molecules.

    abstract::T cells recognize foreign proteins as peptides bound to self molecules encoded by the major histocompatibility complex (MHC). The kinetics of interaction between purified class II MHC molecules and peptides is unusual, in that the rate of association is very slow, but once formed, the complexes are extremely stable. T...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/342800a0

    authors: Adorini L,Appella E,Doria G,Cardinaux F,Nagy ZA

    更新日期:1989-12-14 00:00:00

  • Interleukin-2 stimulates association of protein kinase C with plasma membrane.

    abstract::Interleukin-2 (IL-2) is a regulatory peptide important for the growth and differentiation of antigen-specific T lymphocytes and large granular lymphocytes. Interaction of IL-2 with its specific receptor results in the promotion of S-phase progression as well as, in certain circumstances, the production and release of ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/315233a0

    authors: Farrar WL,Anderson WB

    更新日期:1985-05-16 00:00:00

  • Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia.

    abstract::Recurrent chromosomal translocations involving the mixed lineage leukaemia (MLL) gene initiate aggressive forms of leukaemia, which are often refractory to conventional therapies. Many MLL-fusion partners are members of the super elongation complex (SEC), a critical regulator of transcriptional elongation, suggesting ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature10509

    authors: Dawson MA,Prinjha RK,Dittmann A,Giotopoulos G,Bantscheff M,Chan WI,Robson SC,Chung CW,Hopf C,Savitski MM,Huthmacher C,Gudgin E,Lugo D,Beinke S,Chapman TD,Roberts EJ,Soden PE,Auger KR,Mirguet O,Doehner K,Delwel R,

    更新日期:2011-10-02 00:00:00

  • The effect of energy feedbacks on continental strength.

    abstract::The classical strength profile of continents is derived from a quasi-static view of their rheological response to stress--one that does not consider dynamic interactions between brittle and ductile layers. Such interactions result in complexities of failure in the brittle-ductile transition and the need to couple ener...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature04868

    authors: Regenauer-Lieb K,Weinberg RF,Rosenbaum G

    更新日期:2006-07-06 00:00:00

  • Maintenance and propagation of a deleterious mitochondrial genome by the mitochondrial unfolded protein response.

    abstract::Mitochondrial genomes (mitochondrial DNA, mtDNA) encode essential oxidative phosphorylation (OXPHOS) components. Because hundreds of mtDNAs exist per cell, a deletion in a single mtDNA has little impact. However, if the deletion genome is enriched, OXPHOS declines, resulting in cellular dysfunction. For example, Kearn...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature17989

    authors: Lin YF,Schulz AM,Pellegrino MW,Lu Y,Shaham S,Haynes CM

    更新日期:2016-05-19 00:00:00

  • Long-range transport in excitonic dark states in coupled quantum wells.

    abstract::During the past ten years, coupled quantum wells have emerged as a promising system for experiments on Bose condensation of excitons, with numerous theoretical and experimental studies aimed at the demonstration of this effect. One of the issues driving these studies is the possibility of long-range coherent transport...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature00940

    authors: Snoke D,Denev S,Liu Y,Pfeiffer L,West K

    更新日期:2002-08-15 00:00:00

  • An N-terminal peptide from p60src can direct myristylation and plasma membrane localization when fused to heterologous proteins.

    abstract::The src gene product, p60src, of Rous sarcoma virus (RSV) is a tyrosine-specific protein kinase which is associated with the plasma membrane of infected cells. Myristic acid is bound in an amide linkage to glycine 2 of p60src. Of the N-terminal 30 kilodaltons of p60src, only amino acids 1-14 are required for myristyla...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/314374a0

    authors: Pellman D,Garber EA,Cross FR,Hanafusa H

    更新日期:1985-03-28 00:00:00

  • Production of soluble MHC class II proteins with covalently bound single peptides.

    abstract::The alpha beta T-cell receptors (TCRs) react with complex ligands composed of peptides bound to major histocompatibility complex (MHC) proteins. In the absence of foreign antigens the peptides bound to MHC molecules come from the proteins of the host itself. Interactions between TCRs and these self-peptide-MHC ligands...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/369151a0

    authors: Kozono H,White J,Clements J,Marrack P,Kappler J

    更新日期:1994-05-12 00:00:00

  • Protease inhibitor domain encoded by an amyloid protein precursor mRNA associated with Alzheimer's disease.

    abstract::Amyloid B-protein/amyloid A4 is a peptide present in the neuritic plaques, neurofibrillary tangles and cerebrovascular deposits in patients with Alzheimer's disease and Down's syndrome (trisomy 21) and may be involved in the pathogenesis of Alzheimer's disease. Recent molecular genetic studies have indicated that amyl...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/331528a0

    authors: Tanzi RE,McClatchey AI,Lamperti ED,Villa-Komaroff L,Gusella JF,Neve RL

    更新日期:1988-02-11 00:00:00

  • Coupling of surface temperatures and atmospheric CO2 concentrations during the Palaeozoic era.

    abstract::Atmospheric carbon dioxide concentrations seem to have been several times modern levels during much of the Palaeozoic era (543-248 million years ago), but decreased during the Carboniferous period to concentrations similar to that of today. Given that carbon dioxide is a greenhouse gas, it has been proposed that surfa...

    journal_title:Nature

    pub_type: 历史文章,杂志文章

    doi:10.1038/nature06085

    authors: Came RE,Eiler JM,Veizer J,Azmy K,Brand U,Weidman CR

    更新日期:2007-09-13 00:00:00

  • Cell-type-specific asynchronous modulation of PKA by dopamine in learning.

    abstract::Reinforcement learning models postulate that neurons that release dopamine encode information about action and action outcome, and provide a teaching signal to striatal spiny projection neurons in the form of dopamine release1. Dopamine is thought to guide learning via dynamic and differential modulation of protein ki...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/s41586-020-03050-5

    authors: Lee SJ,Lodder B,Chen Y,Patriarchi T,Tian L,Sabatini BL

    更新日期:2020-12-23 00:00:00

  • The sodium channel and intracellular H+ blockage in squid axons.

    abstract::Sodium channels in plasma membranes can be blocked by a large variety of toxins and local anaesthetics. This property, however, is not confined to relatively large molecules. For instance, extracellularly applied small ions like hydrogen may also prevent the passive transport of permeant cations across open Na+ channe...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/287062a0

    authors: Wanke E,Carbone E,Testa PL

    更新日期:1980-09-04 00:00:00

  • Secreted transcription factor controls Mycobacterium tuberculosis virulence.

    abstract::Bacterial pathogens trigger specialized virulence factor secretion systems on encountering host cells. The ESX-1 protein secretion system of Mycobacterium tuberculosis-the causative agent of the human disease tuberculosis-delivers bacterial proteins into host cells during infection and is critical for virulence, but h...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature07219

    authors: Raghavan S,Manzanillo P,Chan K,Dovey C,Cox JS

    更新日期:2008-08-07 00:00:00