ライフサイエンスコーパス: chromatin

1 tone mutations, and the methylation state of chromatin.

2 role of an enhancer in the context of native chromatin.

3 active Ran coordinates ring positioning with chromatin.

4 ssion by chemically and physically modifying chromatin.

5 disassembly of all replisomes that remain on chromatin.

6 ient deacetylation of histones on endogenous chromatin.

7 specificity, activity and interactions with chromatin.

8 rual of downstream repair factors at damaged chromatin.

9 f transcription factors and local opening of chromatin.

10 e in deciding the nature of the packaging of chromatin.

11 ive complex 1 (PRC1) that catalyzes H2Aub on chromatin.

12 organized and timely opening and closing of chromatin.

13 repertoire of PRC2 binding configurations on chromatin.

14 to test concepts such as phase separation of chromatin.

15 ion event prevents condensin II release from chromatin.

16 y, through preventing the binding of TCF4 to chromatin.

17 racts with PRC2 and binds to PRC2 targets on chromatin.

18 ces of ATP-fueled active processes acting on chromatin.

19 e genomes condensed by histone proteins into chromatin.

20 The establishment of silent chromatin, a heterochromatin-like structure at HML and H

21 by combining these findings with single-cell chromatin accessibility (scATAC-seq) data, we were able

22 Leveraging a granular atlas of chromatin accessibility across 81 immune cell types, we

23 Deletion of -31CBS reduces chromatin accessibility and blocks long-range interactio

24 egrative analyses of mRNAs, miRNAs, lncRNAs, chromatin accessibility and cis-regulatory elements unco

25 l regulation in bacteria, but in eukaryotes, chromatin accessibility and energy expenditure may call

26 We applied the method to analyze paired chromatin accessibility and gene expression data from a

27 igenetic alterations on the DNA methylation, chromatin accessibility and histone modification level,

28 , supporting a causal link between decreased chromatin accessibility and photoreceptor degeneration,

29 Absence of Smarcad1 leads to changes in chromatin accessibility and significant changes in histo

30 Integrated analysis of chromatin accessibility and single-cell expression data

31 JNK/AP-1 signaling commissions chromatin accessibility and Smad3 DNA binding leading to

32 e the greatest disease-associated changes in chromatin accessibility and the strongest alteration of

33 BAF60a maintains chromatin accessibility at PPARgamma and EBF2 binding si

34 We observe widespread increases in chromatin accessibility at retrotransposons when HDACs a

35 le genes recruits TFIIIC, which alters their chromatin accessibility by direct acetylation of histone

36 rdiomyocyte response to injury by regulating chromatin accessibility changes, thereby allowing the ac

37 Through analysing associated chromatin accessibility changes, we have implicated the

38 instead results in alternative splicing and chromatin accessibility events, involving genes such as

39 ) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization,

40 Chromatin accessibility mapping is a powerful approach t

41 upstream of the DDIT4L gene and changing the chromatin accessibility of a DDIT4L enhancer.

42 Here, we perform genome-wide assessment of chromatin accessibility of the human striatum in heroin

43 Chromatin accessibility of these indirect Foxp3 targets

44 ure similar to an epithelial cell and gained chromatin accessibility sites correlated with other epit

45 CNN) could learn to infer cell type-specific chromatin accessibility solely from regulatory DNA seque

46 istal candidate Runx1 enhancer exhibits high chromatin accessibility specifically in pre-HE cells at

47 , ANP32E dramatically influences genome-wide chromatin accessibility through subtle refinement of H2A

48 Moreover, we integrated chromatin accessibility with transcriptomics to identify

49 ifying enzymes involved in promoting reduced chromatin accessibility, ameliorated light damage in our

50 ating to transcription, regulatory activity, chromatin accessibility, chromatin conformation and read

51 Using single-cell transcriptomics and chromatin accessibility, we gained a better understandin

52 S and ATAC-seq that yield coverage files for chromatin accessibility.

53 c reader proteins couple proximal stimuli to chromatin, acting at super-enhancer regulatory regions t

54 s by recruiting components of the endogenous chromatin-activating machinery, eliminating the need for

55 mal cells H3.3-G34W is incorporated into the chromatin and associates with massive epigenetic alterat

56 work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of

57 is accompanied by compaction of higher-order chromatin and hindrance of mRNPs from engaging nuclear p

58 we determined the composition of centromeric chromatin and kinetochores at distinct cell-cycle stages

59 As a consequence, both chromatin and RNA modifications could serve as novel tar

60 TOP1cc localizes to cytoplasmic chromatin and TOP1 interacts with cGAS to enhance the bi

61 n cleavage of B2 RNA, release of B2 RNA from chromatin, and activation of thermal stress genes.

62 In vivo interrogation of chromatin architecture and genome-wide RALY-binding patt

63 We use this approach to study chromatin architecture at high spatial and temporal reso

64 either their exact topology or a particular chromatin architecture, is the key factor.

65 s, which perturb gene regulation by altering chromatin architecture.

66 ver, and identify de novo cell-type-specific chromatin architectures associated with gene expression,

67 equired for the dissociation of cohesin from chromatin as cells transit through mitosis.

68 tic variants exhibiting allele-specific open chromatin (ASoC).

69 Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Z

70 ric but not catalytic inhibitors prevent the chromatin assembly of functional replisomes.

71 Fibers are then immunostained for different chromatin-associated proteins and mounted for visualizat

72 Chromatin-associated RNA (caRNA) has been proposed as a

73 arms, yet how the cell regulates nuclear and chromatin-associated RNAs after chromosome condensation

74 e imaging approach in yeast cells to measure chromatin association of individual replisome subunits,

75 These changes in chromatin at AgR loci are regulated in a locus-, lineage

76 We identified that open and active chromatin at the major translocation cluster locus might

77 comb repressive complex 2 to induce bivalent chromatin at the Wapl promoter.

78 ifferences in gene expression and accessible chromatin between progenitors and MG, primarily in neuro

79 II, coupling two-sided extrusion and stable chromatin binding by condensin II promotes compaction.

80 that LSD1 inhibition globally disrupts FOXA1 chromatin binding.

81 nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous bindi

82 An important unanswered question in chromatin biology is the extent to which long-range loop

83 sing repressive polycomb group proteins from chromatin, bound to the Stat3 C-terminal region and anta

84 Finally, chromatin-capture PCR confirmed long-range co-regulation

85 erved in fixation and reported on underlying chromatin compaction states.

86 gene silencing through localized control of chromatin compaction, 3D genome organization and the epi

87 Condensin complexes are involved in chromatin compaction, but the contribution of other chro

88 ogical significance of our annotation of the chromatin compartmental domains in single cells Hi-C mat

89 nd microtubule depolymerization and changing chromatin condensation altered volume, shape, and dry ma

90 s sensor with reporter dyes for detection of chromatin condensation and cell death, enabling studies

91 egulatory activity, chromatin accessibility, chromatin conformation and readouts from functional expe

92 Chromatin conformation capture assay revealed direct con

93 ofiled using Hi-C, a technique that combines chromatin conformation capture with high-throughput sequ

94 Chromatin-conformation capture and dCas9 mediated enhanc

95 ical layout of splicing regulation where the chromatin context progressively changes as the Pol II mo

96 the spatial genome in a manner influenced by chromatin context.

97 (2020) now uncover that when the epigenetic chromatin cycle falters, a genetically hardwired mechani

98 nt function of NuMA in choreographing proper chromatin decompaction and nuclear shape by directly ass

99 DNA-binding-deficient mutant of NuMA affects chromatin decondensation at the mitotic exit, and nuclea

100 n-histone deacetylase inhibitor that renders chromatin decondensation, significantly decreased the nu

101 This suggests that sex-specific chromatin differences may contribute to sex-specific age

102 processes, including transcription, require chromatin disassembly and reassembly mediated by histone

103 roaches can address fundamental questions on chromatin dynamics in a range of model organisms.

104 served protein involved in transcription and chromatin dynamics, yet its general in vivo requirement

105 Thus, CHD1 loss results in chromatin dysregulation, thereby establishing a state of

106 atin modification, we identified features of chromatin environments that are most likely to be affect

107 erent stages of the cell cycle and in varied chromatin environments.

108 how an accessory subunit (CoREST) enables a chromatin enzyme (LSD1) to function on a nucleosome and

109 etween different biological modalities (RNA, chromatin, etc.) can help further our understanding of t

110 DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the ma

111 id and selective loss of BBB transcripts and chromatin features, as well as a greatly reduced level o

112 ts per variant on several cell type-specific chromatin features.

113 erful in the investigation of nucleosome and chromatin fiber dynamics.

114 on, DNA repair, and epigenetic modification, chromatin forms the nexus of most nuclear processes.

115 MP-AMP synthase (cGAS) recognizing cytosolic chromatin fragments and then activating the stimulator o

116 ctional telomeres creates a preponderance of chromatin fragments in the cytosol, which leads to a pre

117 Chromatin functions are influenced by the addition, remo

118 riters, erasers, and readers, the breadth of chromatin functions associated with ubiquitin signaling

119 Histone variants expand chromatin functions in eukaryote genomes.

120 like nucleosomes that play critical roles in chromatin functions.

121 ectly inhibited Brd4 recruitment to activate chromatin globally.

122 ultiple particle tracking (MPT) technique on chromatin granules, we designed a SURF (Speeded Up Robus

123 In chromatin immunoprecipitation (ChIP) assays with low dox

124 Transcriptomic and chromatin immunoprecipitation analysis revealed that CDK

125 Herein, utilizing chromatin immunoprecipitation and direct sequencing (ChI

126 Here, we use chromatin immunoprecipitation and genome-wide expression

127 ect transcriptional target of SOX9, based on chromatin immunoprecipitation and luciferase reporter as

128 Chromatin immunoprecipitation assays confirmed direct bi

129 Oligo pull down and chromatin immunoprecipitation experiments demonstrated t

130 Silencing and chromatin immunoprecipitation experiments demonstrated t

131 Chromatin immunoprecipitation followed by next-generatio

132 Despite its popularity, chromatin immunoprecipitation followed by sequencing (Ch

133 such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (Ch

134 We further used chromatin immunoprecipitation sequencing (ChIP-seq), bul

135 ic targets in CIC-DUX4 sarcoma, we performed chromatin immunoprecipitation sequencing analysis using

136 Chromatin immunoprecipitation sequencing and RNA sequenc

137 -inducible isogenic cell lines and performed chromatin immunoprecipitation sequencing and transcripto

138 AL1 oncogene, a finding validated in vivo by chromatin immunoprecipitation sequencing of a patient-de

139 rioritized candidate SNPs were examined with chromatin immunoprecipitation sequencing, RNA sequencing

140 to attenuated DNA binding, and we show using chromatin immunoprecipitation that MftR binds directly t

141 kdown hearts at 5 weeks of age combined with chromatin immunoprecipitation with deep sequencing and f

142 Chromatin immunoprecipitation with sequencing demonstrat

143 s that express individual FXR isoforms using chromatin immunoprecipitation, followed by sequencing an

144 Biochemical, structural and integrated chromatin immunoprecipitation-sequencing-based analyses

145 d YY1 from the FCER1A promotor, evaluated by chromatin immunoprecipitation.

146 genetic variation on functional readouts of chromatin in an effort to prioritize variants in terms o

147 dentify genomic regions associated with open chromatin in Arabidopsis thaliana.

148 Mapping transposase-accessible chromatin in single cells by sequencing defined the tran

149 ally examined the state and accessibility of chromatin in the developing mouse fetus.

150 ins unknown how LSH mediates its function on chromatin in vivo.

151 es that physically organize the structure of chromatin, including promoters, enhancers and insulators

152 The dynamic organization of chromatin inside the cell nucleus plays a key role in ge

153 ganoids with gallic acid reinstated the TCF4-chromatin interaction and the hyperactivation of WNT, th

154 osts the precision and power of differential chromatin interaction detection through data augmentatio

155 identifies replicable interactions shared by chromatin interaction experiments.

156 Genome-wide chromatin interaction mapping, using Hi-C, reveals conde

157 distribution and stability of different PRC2-chromatin interaction modes are modulated by accessory s

158 y active in human tissues, showed long-range chromatin interactions and mRNA abundance associations w

159 iCorr to compare the high-resolution maps of chromatin interactions from 10 tissue or cell types with

160 transcription in cytokinesis, and long-range chromatin interactions in early G1.

161 ping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitativ

162 A-HiChIP, going from cell culture to ranking chromatin interactions within 6 d.

163 addition, promoters with increased levels of chromatin interactivity-termed super-interactive promote

164 Release from chromatin involves opening of the ring at the Smc3-Scc1

165 Our analyses suggest that chromatin is comprised of both regular and irregular sin

166 In mammals, paternal chromatin is extensively reprogrammed through the global

167 etylase activities and site-selectivities in chromatin is poorly understood.

168 in levels, RGC development and survival, and chromatin landscape effects, we show that the SE ensures

169 performing general platform for mapping the chromatin landscape in different cellular populations fr

170 The chromatin landscape of human brain cells encompasses key

171 become a leading technology for probing the chromatin landscape of single and aggregated cells.

172 e heterochromatin marks and display a primed chromatin landscape, with bivalently marked primed pluri

173 characterized transcriptional and accessible chromatin landscapes of acutely isolated mouse CNS ECs.

174 At the chromatin level, aging associates with progressive accum

175 s effect depends on increased expression and chromatin loading of PRIMPOL and is regulated by ATR act

176 talization and initiated contacts reflecting chromatin loop extrusion.

177 uester genes and regulatory elements through chromatin looping.

178 a suggest that CTCF enables the formation of chromatin loops by protecting cohesin against loop relea

179 E, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps.

180 We apply this framework to predict chromatin loops in 56 Hi-C datasets, and release the res

181 associated domains (TADs)(2,3) consisting of chromatin loops(4).

182 ZIPM method produced fine-resolution diploid chromatin maps and 3D structures and provided insights i

183 Oryza sativa) genome by integrating multiple chromatin marks, including the H2A.Z histone variant, H3

184 oteomes contain proteins involved in DNA and chromatin metabolism and in transcription, respectively.

185 or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the mo

186 recognized as a transcriptionally repressive chromatin modification but the mechanism of repression r

187 ic mutations in the JAK/STAT, MAPK, MYC, and chromatin modification pathways.

188 By leveraging ENCODE data on chromatin modification, we identified features of chroma

189 control of genes is associated with specific chromatin modifications and transcription factors.

190 cific patterns of nucleosome positioning and chromatin modifications correlate with pA site usage, ep

191 rs capable of re-writing enhancer-associated chromatin modifications, we show that enCRISPRa and enCR

192 Formation of a pluripotency-specific chromatin network is a critical event in reprogramming s

193 We model the chromatin of the affected and control cells as networks

194 ther studies of the organization of archaeal chromatin, on both the organismal and domain level.

195 interactions that either weakly attract all chromatin or strongly bind to a randomly chosen 0.05% of

196 periments provide partial information on the chromatin organization in a cell population, namely the

197 How condensin contributes to chromatin organization in interphase is less well unders

198 However, the higher-order chromatin organization in T. thermophila is still largel

199 , we investigate cell-to-cell variability of chromatin organization into topologically associating do

200 Chromatin organization is critical for cell growth, diff

201 ity of our approach to deliver insights into chromatin organization of great biological relevance.

202 ach protein introduces a unique phenotype to chromatin organization, and these structures are put int

203 n TC-NER, particularly in the context of the chromatin organization, is unclear.

204 e central players in this cell type-specific chromatin organization.

205 well as cell-type-independent principles of chromatin organization.

206 tures and provided insights into the allelic chromatin organizations and functions.

207 t the CCCTC-binding factor (CTCF), a crucial chromatin organizer, is essential for Schwann cell myeli

208 Our results show how these chromatin parameters act together to produce different-s

209 Epigenetic modifications on chromatin play important roles in regulating gene expres

210 ng the complete 3D organization of the whole chromatin polymer is an inverse problem.

211 ave achieved state of the art performance on chromatin profile prediction by using short windows of D

212 in compaction, but the contribution of other chromatin proteins, DNA sequence and histone modificatio

213 However, the annotation of the genome by chromatin proteins, histone modifications, and different

214 On the other hand, chromatin quantitative trait loci, elucidated by direct

215 The Speckled Protein (SP) family of chromatin 'readers' in humans consists of SP100, SP110,

216 B2-TOP1cc-cGAS axis that enables cytoplasmic chromatin recognition and response to immune checkpoint

217 and sufficient for cGAS-mediated cytoplasmic chromatin recognition and SASP during senescence.

218 Thus, our data characterize lineage-specific chromatin reconfiguration and a unique chromatin state f

219 these same MPCs confirm that in mobile MPCs, chromatin regions around osteogenic genes are open, wher

220 mbining the preferential methylation of open chromatin regions by DNA methyltransferases with low seq

221 Mapping open chromatin regions has emerged as a widely used tool for

222 We find that open chromatin regions in glutamatergic neurons are enriched

223 Chromatin regulates spatiotemporal gene expression durin

224 rogenesis, lipid metabolism, ubiquitination, chromatin regulation and translation.

225 F binding site (here named EACBE) in dynamic chromatin regulation is unknown.

226 to change the transcription program through chromatin regulation to rewire cellular metabolism.

227 These results unveil chromatin regulation via CoREST as central to programmin

228 factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-q

229 Ubiquitously expressed chromatin regulators modulate these networks, yet the me

230 n this review, we posit that SPs are central chromatin regulators of gene silencing that establish im

231 and both the recruitment and the ejection of chromatin regulators.

232 Here, we describe the key chromatin regulatory pathways disrupted in gliomas, deli

233 BRD4 direct association to chromatin regulatory regions of the NADPH oxidase subuni

234 The SWI/SNF chromatin remodeler family includes the BAF and PBAF com

235 vel transcriptional regulators, we show that chromatin remodeler Hmga1 is highly expressed prior to s

236 ATRX is a chromatin remodeler that forms a complex with Death doma

237 tic mechanisms (e.g., histone modifications, chromatin remodeler-associated modifications, and DNA me

238 nism is distinct from the canonical modes of chromatin remodelers that directly engage and remodel nu

239 functions with both SWI/SNF and ISWI family chromatin remodelers to allow recruitment of Pol II and

240 leosome unwrapping governed by ATP-dependent chromatin remodelers.

241 iated mutations in either causing attenuated chromatin remodeling activities.

242 ons of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered

243 the gene SMARCB1, a conserved subunit of the chromatin remodeling BAF complex, which has known contri

244 ch/sucrose non-fermentable (mSWI/SNF or BAF) chromatin remodeling complex, including its core catalyt

245 nd pathways, including HMGB1 and the SWI/SNF chromatin remodeling complex, that are SARS lineage and

246 wo mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex.

247 is response and shows how a highly conserved chromatin remodeling factor has a distinct role in anti-

248 Our study sheds light onto the role of the chromatin remodeling machinery in intestinal epithelial

249 enome is modulated by the ATP-driven SWI/SNF chromatin remodeling multiprotein complexes BAF (BRG1/BR

250 Although LSH belongs to a family of chromatin remodeling proteins, it remains unknown how LS

251 Previously, SWI/SNF chromatin remodeling was found to define the kinetics an

252 d in regulating gene expression, DNA repair, chromatin remodeling, apoptosis, and cell proliferation;

253 n is a result of a complex interplay between chromatin remodeling, transcription factors, and signali

254 s the key link between T cell activation and chromatin remodeling.

255 e show that BAF60a, a subunit of the SWI/SNF chromatin-remodeling complexes, serves an indispensable

256 ATP-dependent chromatin-remodeling enzymes control accessibility, nucl

257 g their respective DNA binding or downstream chromatin-remodeling events have shown promise in precli

258 ethyltransferase 1 (CARM1) methylates Pontin chromatin-remodeling factor under glucose starvation, an

259 sable element transcript recruits repressive chromatin remodelling activities and the de novo methyla

260 ncer biology and demonstrates that different chromatin remodelling activities are required for effici

261 ell as with constituents of the NURD and BAF chromatin remodelling complexes.

262 ATP-dependent chromatin remodelling enzymes facilitate different DNA r

263 an outlook on specialized functions such as chromatin remodelling, biomarker potential and the recen

264 ng of its bromodomains to DNA and acetylated chromatin, respectively, and BRD4S phosphorylation dimin

265 interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage

266 our work provides insights into RNA-mediated chromatin silencing.

267 of m(6)A demethylase ALKBH5 is regulated by chromatin state alteration during leukemogenesis of huma

268 wide effects of proteasome inhibition on the chromatin state and RNA Pol II transcription.

269 A.Z patterns, providing a means to reprogram chromatin state and to hone gene expression levels.

270 cific chromatin reconfiguration and a unique chromatin state for primed pluripotency.

271 Heterochromatin, a densely packed chromatin state that is transcriptionally silent, is a c

272 n-coding genes exhibit a transition from one chromatin state to another at their transcription start

273 Here we define distinct chromatin states across the rice (Oryza sativa) genome b

274 on of genomic regions marked by differential chromatin states and associated with misregulated gene e

275 y networks with nodes and edges labeled with chromatin states in human cell lines.

276 Chromatin states were differentially methylated, promote

277 th, including transcriptomes, methylomes and chromatin states.

278 romote epigenetic switching between opposing chromatin states.

279 emarkable tolerance for major disruptions in chromatin structure and reveal a role for Suv39h2 in dep

280 ing of transcription factors associated with chromatin structure around methyl-valleys.

281 ant life is accompanied by global changes in chromatin structure but only localized changes in DNA me

282 Once a permissive chromatin structure has assembled, transgene expression

283 istone post-translational modifications, and chromatin structure regulation, are critical for the int

284 ncer (Ealpha) is in an open and unmethylated chromatin structure well before activation.

285 Guided by chromatin structure, through the use of Chromosome Confo

286 gulator of cat-3 expression by affecting its chromatin structure.

287 different inheritance patterns, time scales, chromatin structures, and environmental exposures, all o

288 rix-associated, actin-dependent regulator of chromatin, subfamily D, member 2) has recently been show

289 Transcription of a chromatin template involves the concerted interaction of

290 , we study the large-scale rearrangements of chromatin that happen at different stages of the growth

291 g complexes, and histone modifiers to engage chromatin, thereby initiating the formation of an activa

292 ins bind to and modulate the conformation of chromatin, thereby regulating transcription.

293 Genomic DNA in eukaryotes is organized into chromatin through association with core histone proteins

294 Thus, our analysis shows that the ability of chromatin to pattern the cortex during the process of mi

295 Kinetochores connect centromeric chromatin to spindle microtubules during mitosis.

296 ted that Pol I-associated factors facilitate chromatin transcription, but it is unknown whether Pol I

297 RTF1, a dissociable PAF subunit critical for chromatin transcription.

298 Molecular inputs to chromatin via cellular metabolism are modifiers of the e

299 To understand the structure and function of chromatin, we must determine the structures of nucleosom

300 Despite associating with SPEN and chromatin, Xist-2kb did not robustly silence transcripti