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1 espite the highly conserved structure of the nucleosome.
2 1 CTD serves as a nexus for signaling in the nucleosome.
3 imulated by H2B-Ub, bound to a ubiquitinated nucleosome.
4 module to bind one face of an ubiquitinated nucleosome.
5 of the LSD1/CoREST complex bound to a 191-bp nucleosome.
6 contacts of the H4 tail with a neighbouring nucleosome.
7 nucleosomes; wherein two pentamers bind to a nucleosome.
8 ption initiation/repair factor TFIIH in this nucleosome.
9 biquitinate H2B in gene bodies beyond the +1 nucleosome.
10 for subsequent deposition in the centromeric nucleosome.
11 SOX2 and its close homologue SOX11 bound to nucleosomes.
12 genes), known to harbor partially-unwrapped nucleosomes.
13 ners alter material properties of individual nucleosomes.
14 of previously deposited H3/H3.3-placeholder nucleosomes.
15 omprehensively assess how proteins recognize nucleosomes.
16 e specialized to remodel partially-unwrapped nucleosomes.
17 -molecule nanoindentation of histone variant nucleosomes.
18 sine 4 and lysine 36 of Histone H3 in nearby nucleosomes.
19 Delta mutant, particularly in the downstream nucleosomes.
20 strongly bind to a randomly chosen 0.05% of nucleosomes.
21 ting access of regulatory factors to DNA and nucleosomes.
22 vidence that PRC2 can bridge pairs of distal nucleosomes.
23 cle phases when genomic DNA is packaged into nucleosomes.
24 ichment of histone variant CENP-A-containing nucleosomes.
25 cs affect transcription through TSS-proximal nucleosomes.
26 d on stable inheritance of CENP-A containing nucleosomes.
27 se that harbor a high fraction of stacked di-nucleosomes.
28 ghly methylated cytosines relative to phased nucleosomes.
29 ng by recognizing their DNA binding sites on nucleosomes.
30 are marked by centromere protein A (CENP-A) nucleosomes.
31 pecific regulation and transcription through nucleosomes.
32 an intrinsic capacity to transcribe through nucleosomes.
33 sociation with core histone proteins to form nucleosomes.
34 of resident H3 nucleosomes with CENP-A(Cnp1) nucleosomes.
35 ew the few structural studies on native-like nucleosomes.
36 ns to manage and remodel partially-unwrapped nucleosomes.
37 meres via interacting with H4 to form stable nucleosomes.
38 H4K16ac forms large domains that control nucleosome accessibility of promoters prior to ZGA in fl
40 's chromatin associated motif (ChAM) and the nucleosome acidic patch region, which in 53BP1-expressin
41 n addition to their evolutionarily conserved nucleosome acidic patch, we identify the positively char
43 zle and show that although at low densities, nucleosomes act as barriers to cohesin diffusion, beyond
48 s a chromatin enzyme (LSD1) to function on a nucleosome and not just histones, we have determined the
49 motifs that are exposed on the surface of a nucleosome and thus access silent genes that are inacces
50 bility measurements, observe single-molecule nucleosome and transcription factor protection footprint
52 tones are epigenetic regulators that bind to nucleosomes and alter chromatin structures and dynamics.
53 by evolutionarily conserved, well-positioned nucleosomes and are frequently dysregulated in cancer.
54 ics of chromatin at the level of both single nucleosomes and arrays of nucleosomes folded into 3-dime
56 analyses, that MeCP2 directly interacts with nucleosomes and its genomic distribution correlates with
57 determinants of H2A.Z occupancy at specific nucleosomes and its relationship to transcription initia
59 lytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleoso
60 ic tissue-specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-deplet
62 cleosome, on nucleosomal DNA within adjacent nucleosomes, and DNA not associated with the DNMT3A-nucl
64 xacerbate nephritis while extinguishing anti-nucleosome antibodies, whereas Tlr9 deficiency in dendri
65 rmolecular contacts between NSD proteins and nucleosomes are altered by several recurrent cancer-asso
68 the mutational mechanisms affected by strong nucleosomes are low-fidelity replication, insufficient m
70 at the dynamics of both canonical and CENP-A nucleosomes are preserved and partitioned across the nuc
72 east Reb1 and Tbf1, and a tightly positioned nucleosome, are strong blocks to the strand displacement
73 one tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-b
74 c domains are complex structures composed of nucleosome arrays that are bound by silencing factors.
77 -dependent remodelers, that are recruited to nucleosomes at defined locations and modulate their stru
78 3K4me3 chromatin profile and hyperacetylated nucleosomes at transcription start sites establish a chr
80 DNA synthesis, the efficient disruption of a nucleosome barrier by Pif1 could lead to the futile re-r
81 with in vitro measurements suggest that the nucleosome barrier to TF binding is modulated by dynamic
83 esearch provides molecular insights into the nucleosome-based recognition and histone-modification me
87 ility chromatin domains, whereas weak or non-nucleosome binding factors are excluded from the domains
89 escribe a functional interplay between a key nucleosome binding hub and a histone modification that u
90 py we observe that both histone variants and nucleosome binding partners alter material properties of
91 important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its D
93 t DNA replication through either a Reb1 or a nucleosome block occurs only in the presence of the 5'-3
96 rotein, Hmo1, to remodel partially-unwrapped nucleosomes, but show differential reliance on these fac
97 ermine whether the kinases search for target nucleosomes by primarily moving in three dimensions thro
98 ic features that discriminate CENP-A from H3 nucleosomes by revealing that DNA end flexibility can be
102 In order to unravel the mechanisms by which nucleosomes can influence, or be altered by, DNA-binding
103 Pioneer transcription factors, which bind nucleosomes, can access the low-mobility chromatin domai
106 eosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with
109 tion of end-to-end distance) upon binding to nucleosomes, consistent with a transition to an ordered
110 ed of CTCF or cohesin, whereas disruption of nucleosome contacts alters their structural organization
114 standing how molecular interactions with the nucleosome contribute to the chromatin-opening phenomeno
116 vious crystallographic studies of the CENP-A nucleosome core particle (NCP) reconstituted with a huma
118 tructure of Homo sapiens CHD4 engaged with a nucleosome core particle in the presence of the non-hydr
120 uisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleos
121 ory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to
123 ly reduces the expression of genes with wide nucleosome-deficient regions (e.g., ribosomal protein ge
125 sibility occur without significant change in nucleosome density and represent key features of AgR loc
126 ltering the distance between heterochromatic nucleosome-depleted regions (NDRs), which is predicted t
127 s and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation(9).
128 r INO80, which explains how INO80 can define nucleosome-depleted regions in the absence of other fact
129 regions of unusually low bendability within nucleosome-depleted regions upstream of transcription st
130 ioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for c
132 acent surfaces are the primary hot-spots for nucleosome disk interactions, whereas nearly half of the
133 s have suggested that an acidic patch on the nucleosome disk may be a common site for recruitment to
134 isk interactions, whereas nearly half of the nucleosome disk participates only minimally in protein b
135 for packaging of newly synthetized DNA into nucleosomes during the S phase when their expression is
139 ibitory state that is relieved by binding to nucleosomes, enabling dimethylation of histone H3 at Lys
140 ine changes in BAF complex architecture upon nucleosome engagement and compare the structural model o
143 with both histone and DNA components of the nucleosome, explaining its essential function in demethy
146 poration, which reflects the need to remodel nucleosomes following base excision by DNA glycosylases
150 T-induced indels occur disproportionately in nucleosome-free regions, suggesting that much HT-induced
151 tuations to determine the Young's modulus of nucleosomes from all-atom molecular dynamics simulations
152 ied human canonical BAF complex bound to the nucleosome, generated using cryoelectron microscopy (cry
156 ding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution se
158 gesting that the complex may target multiple nucleosomes implying a processive deacetylase function.
161 roteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing condit
165 t domains to efficient Pol I passage through nucleosomes in the context of transcription rate and pro
170 ucleosome surface requirements of nearly 300 nucleosome interacting proteins implicated in diverse nu
171 ate sufficiently stable transcription factor-nucleosome interaction to empower cryo-electron microsco
174 that disrupt BAF subunit-subunit and subunit-nucleosome interfaces in the nucleosome-bound conformati
175 ion start site (TSS)-proximal half of the +1 nucleosome is largely independent of Rad26, likely due t
178 Significantly, eviction of the more distant nucleosomes is dependent upon the FACT histone chaperone
179 ages two nucleosomes separated by one spacer nucleosome, is a preferred low-energy configuration.
181 Nucleosome flexibility and the amplitude of nucleosome motions such as breathing and twisting are en
182 taining complex remodels partially-unwrapped nucleosomes much better than does the Rsc2-containing co
187 hanges in chromatin openness in concert with nucleosome occupancy and placement of histone modificati
190 complex to regulate histone acetylation and nucleosome occupancy in the beta-globin locus control re
191 eam of a gene with a sequence that increases nucleosome occupancy in vivo reduced readthrough transcr
192 namic changes in the chromatin state such as nucleosome occupancy influence the cold-induced AS remai
194 ription overlapping gene bodies, and reduced nucleosome occupancy particularly at the 3' ends of gene
195 yses suggest that Hap2-Ino80 destabilizes H3 nucleosomes on centromere DNA through transcription-coup
196 here that DNMT3A acts on DNA within a single nucleosome, on nucleosomal DNA within adjacent nucleosom
198 identified histones, both free and bound to nucleosomes or neutrophil extracellular traps, as Clec2d
199 remodelers that directly engage and remodel nucleosomes or transcription elongation factors that fac
200 ides a powerful new methodology for studying nucleosome organization at a previously intractable reso
201 with bare DNA, mononucleosomes, and adjacent nucleosome pairs, our data also provide direct evidence
204 Furthermore, conditions that caused poor nucleosome positioning also led to defects in both heter
205 -transcriptionally, and specific patterns of nucleosome positioning and chromatin modifications corre
206 the patterns of epigenetic modifications and nucleosome positioning are established around promoters
207 s (NDRs), which is predicted to affect local nucleosome positioning by limiting how nucleosomes can b
210 our data show that characteristic changes in nucleosome positioning modulate AS in plants in response
211 le and efficient means to generate arrays of nucleosome positioning motifs, and facilitate a high deg
212 d restoration of chromatin accessibility and nucleosome positioning near transcription start sites, a
215 DNA molecules containing a defined series of nucleosome positioning sequences are often used to recon
217 l H2A.Z accumulation coincides with improved nucleosome positioning, heightened transcription factor
218 information such as chromatin accessibility, nucleosome positioning, histone tail modifications and e
221 in-remodeling enzymes control accessibility, nucleosome positioning/occupancy, and nuclear organizati
222 addition, Micro-C provides a detailed map of nucleosome positions and localizes contact domain bounda
223 ing to natively and nondestructively measure nucleosome positions on individual chromatin fibres.
230 ure shows that COMPASS spans the face of the nucleosome, recognizing ubiquitin on one face of the nuc
231 like domain that mediates recruitment of the nucleosome remodeler Brg1 and FUS-assisted liquid-liquid
233 ltransferase (KMT1/SUV39), and components of nucleosome remodeling and deacetylase (NuRD) are part of
234 ociated protein 2 (MTA2), a component of the nucleosome remodeling and deacetylase complex (NuRD).
236 ors of transcription by interacting with the nucleosome remodeling and histone deacetylase complexes.
237 y large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a wh
238 show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly
239 equently enable other transcription factors, nucleosome remodeling complexes, and histone modifiers t
241 ed in genes encoding subunits of the SWI/SNF nucleosome-remodeling and SAGA chromatin-modifying compl
243 the transcription machinery-as well as with nucleosome remodellers and histone deacetylases-at activ
246 , Micro-C, to map chromosome architecture at nucleosome resolution in human ESCs and fibroblasts.
248 -3" bridging mode, in which PRC2 engages two nucleosomes separated by one spacer nucleosome, is a pre
249 The distribution of somatic mutations in nucleosomes shows the opposite asymmetry in NER-proficie
252 omatin characteristics including compaction, nucleosome spacing, transcription regulation, and the re
253 n parameter by studying systems with regular nucleosome spacing; second, we design systems with natur
254 iants influence chromatin properties such as nucleosome stability and the local chromatin environment
255 ositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 t
257 al that pioneer factors can directly perturb nucleosome structure and chromatin accessibility in diff
258 tone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is
261 l issues related to the determination of the nucleosome structures and review the few structural stud
267 f RNAPII accumulation overlapped with the +1 nucleosome, suggesting that upon inhibition of RNA cleav
268 zation of H2A.Z almost exclusively at the +1 nucleosome suggests that a transcription-initiation depe
271 ntegrated HIV-1 DNA, we also found NucDHS, a nucleosome that covers the DNase hypersensitive site, in
272 o study the biophysical properties of hybrid nucleosomes that are known to exist in human cancer cell
273 eosome affinity proteomics with a library of nucleosomes that disrupts all exposed histone surfaces t
274 Here, we reveal the structural dynamics of nucleosomes that mediate Oct4 binding from molecular dyn
275 uture structural studies of some native-like nucleosomes that play critical roles in chromatin functi
277 on when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interact
278 rve the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matc
279 te electrostatic interaction utilized by the nucleosome to direct RNF168 orientation towards the targ
280 r how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions durin
281 ng these length scales, from the 10 nm sized nucleosome to mitotic chromosomes, whilst jostling withi
283 nteract with the acidic patch of neighboring nucleosomes to drive short-range compaction of chromatin
287 tial affinity to repressed, H2AK119Ub-marked nucleosomes, underlying the selective targeting to polyc
289 ion with fluorescence microscopy, to monitor nucleosome unwrapping and histone localisation as a func
290 arrier to TF binding is modulated by dynamic nucleosome unwrapping governed by ATP-dependent chromati
291 cules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SI
293 bind their target 5'-GAT-3' sequences in the nucleosome when they are located in solvent accessible,
294 and forms a discrete complex with pre-formed nucleosomes; wherein two pentamers bind to a nucleosome.
299 asing the remodeler-actin interaction toward nucleosomes with the non-canonical histone H2A.Z, thereb