[PDF] Top 20 Prediction of nucleosome positioning based on transcription factor binding sites.
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Prediction of nucleosome positioning based on transcription factor binding sites.
... number of studies have been performed in an attempt to determine nucleosome positioning signals at the level of TFs or transcription factor binding sites (TFBSs), ... See full document
7
Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters.
... Transcription factor binding site (TFBS) identification plays an important role in deciphering gene regulatory ...knowledge of TFBSs, one can understand molecular mechanisms of gene ... See full document
7
DNA-MATRIX: a tool for constructing transcription factor binding sites Weight matrix
... one of the major challenges in molecular biology is to understand the mechanisms of gene regulation at the level of ...area of research is very encouraging. Performance comparison of ... See full document
3
Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.
... Based on the model of AtMYB61, the molecular interactions shared between the binding sites of AtMYB61 to its targets supported in vitro binding data (Figure ...modelling ... See full document
11
Human Papillomavirus Type 18 cis-Elements Crucial for Segregation and Latency.
... the transcription factor binding sites in the URR do not play an apparent role in ...sequences of E2BSs are not identical and can differ in the internal sequences of the 6 ... See full document
24
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.
... respective binding sites, we uncover the syntax of the crosstalk among them on the genomic scale, estimating the combinatorial binding patterns (CBPs) of the ...‘‘motifs ... See full document
13
Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.
... between nucleosome preferences and both predicted and functional TFBS using the first experimentally-derived in vitro nucleosome map from murine embryonic stem cells, as well as a control in vivo ... See full document
18
A systems biology approach to transcription factor binding site prediction.
... loss of regions containing bona-fide TF biding sites. On the other hand, using non-linear pattern-discovery-based conservation improved the performance considerably and use of both ... See full document
10
Co-localization of the oncogenic transcription factor MYCN and the DNA methyl binding protein MeCP2 at genomic sites in neuroblastoma.
... expression of JUNB. Our own ChIP-chip analysis of JUNB in the Kelly cell line reveals several putative overlapping MYCN and MeCP2 binding sites around the promoter region of JUNB which ... See full document
13
Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain.
... Sequences of viable MarA binding domain variants are shown in Table 1 and sequence logos generated from these variants are shown in Figure ...Each binding domain is referenced by residues 42, 45 and ... See full document
13
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.
... If nucleosome exclusion is the primary mechanism by which Poly(dA:dT) elements exert their effect, then we might also expect these elements to show a reduced affinity for nucleosome formation in ... See full document
25
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.
... consequences on gene expression of TF binding ...genomic binding of A-P factors has changed extensively along the Drosophila tree with little effect on downstream gene ...sources ... See full document
18
Transcription factor binding sites prediction based on modified nucleosomes.
... ratio of nucleosome containing top 8 marks and three repressive histone modifications (as a control) were calculated at each position around binding sites of Sp1 (see ...Sp1 ... See full document
10
A linear model for transcription factor binding affinity prediction in protein binding microarrays.
... number of different algorithms for inferring motif models from binding-enriched unaligned sequenc- ...motifs of fixed length [21], while Van Helden et ...sequences based on ... See full document
13
A structural-based strategy for recognition of transcription factor binding sites.
... illustration of our structural based strategy for predicting TFBSs is shown in Figure ...and prediction of PWMs (refer to Supplementary Text S1,S2 and Table S1,S2 for ...power of the ... See full document
10
FACT, the Bur kinase pathway, and the histone co-repressor HirC have overlapping nucleosome-related roles in yeast transcription elongation.
... Gene transcription is constrained by the nucleosomal nature of chromosomal ...mediates transcription-linked nucleosome disassembly and also nucleosome reassembly in the wake of ... See full document
14
Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity.
... role of RcsA proposed to stabilize this interaction ...detection of dimer formation from yeast two-hybrid screening and from affinity chromatography with immobilized His-tagged ...acetylation of the ... See full document
9
Activator control of nucleosome occupancy in activation and repression of transcription.
... subject of intense ...triggers transcription, but how it does so has remained ...repression of transcription, has often been correlated with the presence of ...fraction of DNA ... See full document
12
Caracterização funcional de fatores de transcrição envolvidos na regulação do metabolismo de glicogênio de Neurospora crassa
... Based on our results, we can suggest that this transcription factor acts as a repressor of carbon metabolism, because the knocked-out strain showed loss of glycogen accumulation regulati[r] ... See full document
182
The impact of HIF1α on the Per2 circadian rhythm in renal cancer cell lines.
... mL of 106 ...min of cooling on ice between pulses using a Branson 2510 Ultrasonic Cleaner (Branson, Danbury, CT, ...g of either anti-HIF1a (dilution, 1: 500; Novus Biologicals ...elution ... See full document
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