Analysis of Nucleosome Formation Potential and Conformational Properties of Human J1-J2 and D2-D1 Type Alpha Satellite DNA
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The structure-forming function of alpha satellites in arrangement of the centromeric heterochromatin implies the presence of certain contextual and conformational signals (codes) for compacting DNA of these regions into nucleosomes and chromatin structures of higher level. However, this aspect of informational content of alpha satellite primary DNA sequences yet requires further studies. Computer analysis of nucleosome formation potential (NFP) was performed using a sample of J1-J2 and D2-D1 type alpha satellites from the human genome. A number of regions with the context favorable for several variants of nucleosome positioning were detected. Statistical analysis of DNA conformational profiles, in particular, concerning the property Wedge, demonstrates a superposition of the context-dependent and CENP-B-dependent nucleosome positionings. The corresponding software packages are available at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/ (RECON method) and http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/ (SITECON method).
Key wordsalpha satellite DNA nucleosome positioning DNA conformational properties
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