Translation efficiency in yeasts correlates with nucleosome formation in promoters

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 Saccharomyces 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 10% highly expressed genes in Schizosaccharomyces pombe (10% 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 (10% 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.

Keywords:

• translation efficiency
• nucleosome formation potential
• elongation efficiency index correlations
• Saccharomyces cerevisiae
• Schizosaccharomyces pombe

Acknowledgements

The work was supported in part by, RFBR 11-04-01888, 10-04-01310; Russian Ministry of Education and Science, contract No. 07.514.11.4003, Basic research programs of Presidium RAS No. A.II.6, B25, B27, SS-5278.2012.4. Authors are grateful to N. Clarke, D.A. Afonnikov and M.P. Ponomarenko for scientific discussion.

Notes

aLocation of region respective to translation initiation site.

bSignificance in parenthesis estimated by t-test for arcsine square root transformed proportions (Fisher & Yates, 1963).