Search results for " Nucleosome Positioning"
showing 6 items of 6 documents
A MULTI-LAYER MODEL TO STUDY GENOME-SCALE POSITIONS OF NUCLEOSOMES
2007
The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. In this paper we propose a new model (called MLM) for the identification of nucleosomes and linker regions across DNA, consisting in a thresholding technique based on cut-set conditions. For this purpose we have defined a method to generate synthetic microarray data fully inspired from the approach that has been used by Yuan et al. Results have shown a good recognition rate on synthetic data, moreover, the $MLM$ shows a good agreement with the recently published method based on Hidden Markov Model …
Sliding-end-labelling
1986
Abstract A method, termed ‘sliding-end-labelling’, has been devised to avoid a frequent artifact in nucleosome positioning by indirect end labelling, namely the appearing of DNA fragments originated by two nuclease cuts, one of them lying within the region covered by the probe. The method is applied to the nucleosome positioning in the yeast SUC2 gene for invertase.
A one class classifier for Signal identification: a biological case study
2008
The paper describes an application of a one-class KNN to identify different signal patterns embedded in a noise structured background. The problem become harder whenever only one pattern is well represented in the signal, in such cases one class classifier techniques are more indicated. The classification phase is applied after a preprocessing phase based on a Multi Layer Model (MLM) that provides a preliminary signal segmentation in an interval feature space. The one-class KNN has been tested on synthetic data that simulate microarray data for the identification of nucleosomes and linker regions across DNA. Results have shown a good recognition rate on synthetic data for nucleosome and lin…
Acetylated nucleosome assembly on telomeric DNAs
2003
Abstract The role of histone N-terminal domains on the thermodynamic stability of nucleosomes assembled on several different telomeric DNAs as well as on ‘average’ sequence DNA and on strong nucleosome positioning sequences, has been studied by competitive reconstitution. We find that histone tails hyperacetylation favors nucleosome formation, in a similar extent for all the examined sequences. On the contrary, removal of histone terminal domains by selective trypsinization causes a decrease of nucleosome stability which is smaller for telomeres compared to the other sequences examined, suggesting that telomeric sequences have only minor interactions with histone tails. Micrococcal nuclease…
A Fuzzy One Class Classifier for Multi Layer Model
2009
The paper describes an application of a fuzzy one-class classifier (FOC ) for the identification of different signal patterns embedded in a noise structured background. The classification phase is applied after a preprocessing phase based on a Multi Layer Model (MLM ) that provides a preliminary signal segmentation in an interval feature space. The FOC has been tested on synthetic and real microarray data in the specific problem of DNA nucleosome and linker regions identification. Results have shown, in both cases, a good recognition rate.
A new Multi-Layers Method to Analyze Gene Expression
2007
In the paper a new Multi-Layers approach (called Multi-Layers Model MLM) for the analysis of stochastic signals and its application to the analysis of gene expression data is presented. It consists in the generation of sub-samples from the input signal by applying a threshold technique based on cut-set optimal conditions. The MLM has been applied on synthetic and real microarray data for the identification of particular regions across DNA called nucleosomes and linkers. Nucleosomes are the fundamental repeating subunits of all eukaryotic chromatin, and their positioning provides useful information regarding the regulation of gene expression in eukaryotic cells. Results have shown a good rec…