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
Naturejournal_title
Natureauthors
Zhu F,Farnung L,Kaasinen E,Sahu B,Yin Y,Wei B,Dodonova SO,Nitta KR,Morgunova E,Taipale M,Cramer P,Taipale Jdoi
10.1038/s41586-018-0549-5subject
Has Abstractpub_date
2018-10-01 00:00:00pages
76-81issue
7725eissn
0028-0836issn
1476-4687pii
10.1038/s41586-018-0549-5journal_volume
562pub_type
杂志文章相关文献
NATURE文献大全abstract::Bacterial toxins represent a vast reservoir of biochemical diversity that can be repurposed for biomedical applications. Such proteins include a group of predicted interbacterial toxins of the deaminase superfamily, members of which have found application in gene-editing techniques1,2. Because previously described cyt...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/s41586-020-2477-4
更新日期:2020-07-01 00:00:00
abstract::Haploids and double haploids are important resources for studying recessive traits and have large impacts on crop breeding, but natural haploids are rare in animals. Mammalian haploids are restricted to germline cells and are occasionally found in tumours with massive chromosome loss. Recent success in establishing ha...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature11435
更新日期:2012-10-18 00:00:00
abstract::The endoplasmic reticulum (ER) is the largest intracellular endomembrane system, enabling protein and lipid synthesis, ion homeostasis, quality control of newly synthesized proteins and organelle communication. Constant ER turnover and modulation is needed to meet different cellular requirements and autophagy has an i...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature14498
更新日期:2015-06-18 00:00:00
abstract::Change history: In this Letter, the received date should be 20 December 2017, instead of 27 April 2018. This has been corrected online. ...
journal_title:Nature
pub_type: 杂志文章,已发布勘误
doi:10.1038/s41586-018-0314-9
更新日期:2018-10-01 00:00:00
abstract::Topoisomerases are expressed throughout the developing and adult brain and are mutated in some individuals with autism spectrum disorder (ASD). However, how topoisomerases are mechanistically connected to ASD is unknown. Here we find that topotecan, a topoisomerase 1 (TOP1) inhibitor, dose-dependently reduces the expr...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature12504
更新日期:2013-09-05 00:00:00
abstract::Where continental plates break apart, slip along multiple normal faults provides the required space for the Earth's crust to thin and subside. After initial rifting, however, the displacement on normal faults observed at the sea floor seems not to match the inferred extension. Here we show that crustal thinning can be...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature04608
更新日期:2006-03-16 00:00:00
abstract::The cyanobacterium Prochlorococcus is the dominant oxygenic phototroph in the tropical and subtropical regions of the world's oceans. It can grow at a range of depths over which light intensities can vary by up to 4 orders of magnitude. This broad depth distribution has been hypothesized to stem from the coexistence o...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/30965
更新日期:1998-06-04 00:00:00
abstract::Nearly all protocols requiring shared quantum information--such as quantum teleportation or key distribution--rely on entanglement between distant parties. However, entanglement is difficult to characterize experimentally. All existing techniques for doing so, including entanglement witnesses or Bell inequalities, dis...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature04627
更新日期:2006-04-20 00:00:00
abstract::Mechanotransduction has an important role in physiology. Biological processes including sensing touch and sound waves require as-yet-unidentified cation channels that detect pressure. Mouse Piezo1 (MmPiezo1) and MmPiezo2 (also called Fam38a and Fam38b, respectively) induce mechanically activated cationic currents in c...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature10812
更新日期:2012-02-19 00:00:00
abstract::Pluto's tenuous nitrogen atmosphere was first detected by the imprint left on the light curve of a star that was occulted by the planet in 1985 (ref. 1), and studied more extensively during a second occultation event in 1988 (refs 2-6). These events are, however, quite rare and Pluto's atmosphere remains poorly unders...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature01766
更新日期:2003-07-10 00:00:00
abstract::The North Atlantic Oscillation (NAO) is the major source of variability in winter atmospheric circulation in the Northern Hemisphere, with large impacts on temperature, precipitation and storm tracks, and therefore also on strategic sectors such as insurance, renewable energy production, crop yields and water manageme...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature14518
更新日期:2015-07-02 00:00:00
abstract::A large impact by a comet or meteorite releases an enormous amount of energy, which evaporates, melts and fractures the surrounding rocks. Distinctive features of such impacts are 'shatter cones', deformed rocks characterized by hierarchical striated features. Although such features have been used for decades as unequ...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature00903
更新日期:2002-07-18 00:00:00
abstract::The guinea-pig (Cavia porcellus), traditionally classified as a New World hystricomorph rodent, often shows anomalous morphological and molecular features in comparison with other eutherian mammals. For example, its insulin differs from that of other mammals in anabolic and growth-promoting activities and in its capab...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/351649a0
更新日期:1991-06-20 00:00:00
abstract::Vertebrate and invertebrate digestive systems show extensive similarities in their development, cellular makeup and genetic control. The Drosophila midgut is typical: enterocytes make up the majority of the intestinal epithelial monolayer, but are interspersed with hormone-producing enteroendocrine cells. Human (and m...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature04333
更新日期:2006-01-26 00:00:00
abstract::'Hot Jupiter' extrasolar planets are expected to be tidally locked because they are close (<0.05 astronomical units, where 1 au is the average Sun-Earth distance) to their parent stars, resulting in permanent daysides and nightsides. By observing systems where the planet and star periodically eclipse each other, sever...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature05782
更新日期:2007-05-10 00:00:00
abstract::The recent decades-long decline in East African rainfall suggests that multidecadal variability is an important component of the climate of this vulnerable region. Prior work based on analysing the instrumental record implicates both Indian and Pacific ocean sea surface temperatures (SSTs) as possible drivers of East ...
journal_title:Nature
pub_type: 历史文章,杂志文章
doi:10.1038/nature11785
更新日期:2013-01-17 00:00:00
abstract::Apoptosis in the immune system is a fundamental process regulating lymphocyte maturation, receptor repertoire selection and homeostasis. Thus, death by apoptosis is as essential for the function of lymphocytes as growth and differentiation. This article focuses on death receptor-associated apoptosis and the role of CD...
journal_title:Nature
pub_type: 杂志文章,评审
doi:10.1038/35037728
更新日期:2000-10-12 00:00:00
abstract::A statute banning nuclear weapons research in Cambridge, Massachusetts, is scheduled for a referendum vote in November 1983. If passed, the act would require the city to fine or imprison violators after the ban takes effect in October 1985, and could have an impact on work done at Harvard University and the Massachus...
journal_title:Nature
pub_type: 新闻
doi:10.1038/305173a0
更新日期:1983-09-15 00:00:00
abstract::Mating and egg laying are tightly cooordinated events in the reproductive life of all oviparous females. Oviposition is typically rare in virgin females but is initiated after copulation. Here we identify the neural circuitry that links egg laying to mating status in Drosophila melanogaster. Activation of female-speci...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/s41586-020-2055-9
更新日期:2020-03-01 00:00:00
abstract::Water striders Gerridae are insects of characteristic length 1 cm and weight 10 dynes that reside on the surface of ponds, rivers, and the open ocean. Their weight is supported by the surface tension force generated by curvature of the free surface, and they propel themselves by driving their central pair of hydrophob...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature01793
更新日期:2003-08-07 00:00:00
abstract::Sensory experiences exert a powerful influence on the function and future performance of neuronal circuits in the mammalian neocortex. Restructuring of synaptic connections is believed to be one mechanism by which cortical circuits store information about the sensory world. Excitatory synaptic structures, such as dend...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature07487
更新日期:2009-01-15 00:00:00
abstract::Adenylyl cyclase is the prototypical second messenger generator. Nearly all of the eight cloned adenylyl cyclases are regulated by one or other arm of the phospholipase C pathway. Functional and ultrastructural investigations have shown that adenylyl cyclases are intimately associated with sites of calcium ion entry i...
journal_title:Nature
pub_type: 杂志文章,评审
doi:10.1038/374421a0
更新日期:1995-03-30 00:00:00
abstract::Crohn's disease is a debilitating inflammatory bowel disease (IBD) that can involve the entire digestive tract. A single-nucleotide polymorphism (SNP) encoding a missense variant in the autophagy gene ATG16L1 (rs2241880, Thr300Ala) is strongly associated with the incidence of Crohn's disease. Numerous studies have dem...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature13044
更新日期:2014-02-27 00:00:00
abstract::Pinocytosis and membrane ruffling are among the earliest and most dramatic cellular responses to stimulation by growth factors or other mitogens. The small Ras-related G proteins Rho and Rac have a regulatory role in membrane ruffling and activated Rho has been shown to stimulate pinocytosis when microinjected into Xe...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/382177a0
更新日期:1996-07-11 00:00:00
abstract::Derivatives of the yeast GCN4 transcription factor containing acidic regions of 35 to 40 amino acids fused directly to the DNA-binding domain are fully functional in vivo. High resolution deletion analysis and proteolytic mapping suggest that the activation region is a repeated structure composed of small units acting...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/333635a0
更新日期:1988-06-16 00:00:00
abstract::Planet formation theories predict that some planets may be ejected from their parent systems as result of dynamical interactions and other processes. Unbound planets can also be formed through gravitational collapse, in a way similar to that in which stars form. A handful of free-floating planetary-mass objects have b...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature23276
更新日期:2017-08-10 00:00:00
abstract::The glutamate dehydrogenase gene of Escherichia coli has been cloned into broad host-range plasmids and can complement glutamate synthase mutants of Methylophilus methylotrophus. Assimilation of ammonia via glutamate dehydrogenase is more energy-efficient than via glutamate synthase, thus the recombinant organism conv...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/287396a0
更新日期:1980-10-02 00:00:00
abstract::Volatile anaesthetics have historically been considered to act in a nonspecific manner on the central nervous system. More recent studies, however, have revealed that the receptors for inhibitory neurotransmitters such as gamma-aminobutyric acid (GABA) and glycine are sensitive to clinically relevant concentrations of...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/38738
更新日期:1997-09-25 00:00:00
abstract::Graphene oxide membranes-partially oxidized, stacked sheets of graphene-can provide ultrathin, high-flux and energy-efficient membranes for precise ionic and molecular sieving in aqueous solution. These materials have shown potential in a variety of applications, including water desalination and purification, gas and ...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/nature24044
更新日期:2017-10-19 00:00:00
abstract::Experimental and simulation studies show that small monomeric proteins fold in one kinetic step, which entails overcoming the free-energy barrier between the unfolded and the native protein through a transition state. Two models of transition state formation have been proposed: a 'nonspecific' one in which it depends ...
journal_title:Nature
pub_type: 杂志文章
doi:10.1038/379096a0
更新日期:1996-01-04 00:00:00