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Volume 8   Issue 1   Year 2013
Yeast Gene Elongation Efficiency Correlates with Nucleosome Formation in 5’-Untranslated Region

Matushkin Yu.G., Levitsky V.G., Sokolov V.S., Likhoshvai V.A., Orlov Yu.L.

Institute of Cytology and Genetics SB RAS; Lavrentiev ave. 10; Novosibirsk, 630090; Russia
 

Abstract. Elongation Efficiency Index (EEI) was suggested earlier to estimate gene expression efficiency by nucleotide context of coding sequence in unicellular organisms. We have analyzed association between EEI and nucleosome formation potential (NFP) in 5’ regulatory regions upstream translation initiation site (TIS) from two yeast species. Theoretical estimations of NFP based on DNA sequence were obtained by Recon method. Experimental estimation of nucleosome occupancy was obtained by high-throughput sequencing data of nucleosomal DNA in S. cerevisiae. For the sample of all genes correlation coefficient was calculated between two vectors: vector of NFP values for fixed position relative to TIS and vector of EEI values. Profiles of correlation coefficients of NFP and EEI were counted in (-600; +600) regions relative to TIS for gene sequences extracted from GenBank. We found regions of strong negative dependence between NFP and EEI for all genes as well as for 15% highly expressed genes in S. pombe (15% of EEI-highest genes). At the same time we found positive dependence between NFP and EEI for all genes and for low expressed genes in S. cerevisiae (15% of EEI-lowest genes). The association between NFP and EEI could be explained by evolutionary selection of context characteristics of nucleotide sequences for gene expression optimization.

 
Key words: translation efficiency, nucleosome formation potential, elongation efficiency index correlations, Saccharomyces cerevisiae, Schizosaccharomyces pombe.
 
Table of Contents Original Article
Math. Biol. Bioinf.
2013;8(1):248-257
doi: 10.17537/2013.8.248
published in Russian

Abstract (rus.)
Abstract (eng.)
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References

 

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