High resolution positioning of intron ends on the nucleosomes |
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Authors: | Hapala Jan Trifonov Edward N |
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Institution: | a Department of Functional Genomics and Proteomics, CEITEC and Faculty of Science, Masaryk University, Kotlarska 2, CZ-61137 Brno, Czech Republicb Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, 31905 Haifa, Israel |
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Abstract: | High resolution sequence-directed nucleosome mapping is applied to 36,000 sequences containing splice junctions, from five different species. As it has been also shown in previous studies, the junctions are found to be preferentially located within nucleosomes. Moreover, the orientation of guanine residues at the GT- and AG-ends of introns within the nucleosomes is such that the guanines are positioned nearest to the surface of histone octamers, 3 and 4 bases upstream from the local DNA pseudo-dyads passing through minor grooves oriented outwards. Since the guanine residues are the most vulnerable to spontaneous damage within the cell (primarily, depurination and oxidation) such positioning of the splice junctions minimizes the damage that is caused by free radicals and highly reactive metabolites. |
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Keywords: | BLAST Basic Local Alignment Search Tool FineStr Fine Structure &mdash nucleosome mapping program (Gabdank et al 2010b) RasTop molecular graphics program intended for the visualization of proteins nucleic acids and small molecules based on the popular Rasmol software PDB Protein Data Bank GIMP GNU Image Manipulation Program |
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