A Multi-Layer Method to Study Genome-Scale Positions of Nucleosomes

Giosue' Lo Bosco, Vito Di Gesu', Davide Corona, Vito Di Gesù, Luca Pinello, Giosuè Lo Bosco, Guo-Cheng Yuan, Luca Pinello

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13 Citations (Scopus)

Abstract

The basic unit of eukaryotic chromatin is the nucleosome, consisting of about 150 bp of DNA wrapped arounda protein core made of histone proteins. Nucleosomes position is modulated in vivo to regulate fundamentalnuclear processes. To measure nucleosome positions on a genomic scale both theoretical and experimentalapproaches have been recently reported. We have developed a new method, Multi-Layer Model (MLM), forthe analysis of nucleosome position data obtained with microarray-based approach. The MLM is a featureextraction method in which the input data is processed by a classifier to distinguish between several kinds ofpatterns. We applied our method to simulated-synthetic and experimental nucleosome position data andfound that besides a high nucleosome recognition and a strong agreement with standard statistical methods,the MLM can identify distinct classes of nucleosomes, making it an important tool for the genome wideanalysis of nucleosome position and function. In conclusion, the MLM allows a better representation ofnucleosome position data and a significant reduction in computational time.
Original languageEnglish
Pages (from-to)140-145
Number of pages6
JournalGenomics
Volume93
Publication statusPublished - 2009

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All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Lo Bosco, G., Di Gesu', V., Corona, D., Di Gesù, V., Pinello, L., Lo Bosco, G., Yuan, G-C., & Pinello, L. (2009). A Multi-Layer Method to Study Genome-Scale Positions of Nucleosomes. Genomics, 93, 140-145.