Yeast Gene Elongation Efficiency Correlates with Nucleosome Formation in 5'-Untranslated Region

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

Matematičeskaâ biologiâ i bioinformatika, Tome 8 (2013) no. 1, pp. 248-257.

Résumé

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.

Bibliographie

[1] Grantham R., Gautier C., Gouy M., Jacobzone M., Mercier R., Nucl. Acids Res., 9 (1981), 43–74 | DOI

[2] Post L. E., Strycharz G. D., Nomura M., Lewis H., Dennis P. P., Proc. Natl. Acad. Sci. USA, 76 (1979), 1697–1701 | DOI

[3] Post L. E., Nomura M., J. Biol. Chem., 255 (1980), 4660–4666

[4] Ikemura T., Genetics and evolution of RNA polymerase, tRNA and ribosomes, eds. Osawa S., Ozeki H., Uchida H., Yura T., University of Tokyo Press, Tokyo; Elsevier/North Holland, Amsterdam, 1980, 519–523

[5] Bennetzen J. L., HallL B. D., J. Biol. Chem., 257 (1982), 3026–3031

[6] Sharp P. M., Li W. H., Nucleic Acid Res., 15 (1987), 1281–1295 | DOI

[7] Vladimirov N. V., Likhoshvai V. A., Matushkin Yu. G., “Korrelyatsiya chastot kodonov i potentsialnykh vtorichnykh struktur s effektivnostyu translyatsii mRNK v odnokletochnykh organizmakh”, Molekulyarnaya biologiya, 41:5 (2007), 843–850

[8] Richmond T. J., Widom J., Chromatin Structure and Gene Expression, 2nd edn., eds. Workman J. L., Elgin S. C., Oxford University Press, Oxford, UK, 2000, 1–23 | MR

[9] Kaplan N., Moore I. K., Fondufe-Mittendorf Y., Gossett A. J., Tillo D., Field Y., LeProust E. M., Hughes T. R., Lieb J. D., Widom J., Segal E., Nature, 458:7236 (2009), 362–366 | DOI

[10] Levitsky V. G., Nucl. Acids. Res., 32 (2004), 346–349 | DOI

[11] Segal E., Fondufe-Mittendorf Y., Chen L., Thastrom A., Field Y., Moore I. K., Wang J. P., Widom J., Nature, 442:7104 (2006), 772–778 | DOI

[12] Schones D. E., Cui K., Cuddapah S., Roh T. Y., Barski A., Wang Z., Wei G., Zhao K., Cell, 132 (2008), 887–898 | DOI

[13] Tanaka Y., Nakai K., Genome Inform., 23:1 (2009), 169–178 | DOI

[14] Goh W. S., Orlov Y., Li J., Clarke N. D., PLoS Comput Biol., 6:1 (2010), e1000649 | DOI

[15] Levitsky V. G., Katokhin A. V., Podkolodnaya O. A., Furman D. P., Kolchanov N. A., Nucl. Acids. Res., 33 (2005), 67–70

[16] Reynolds S. M., Bilmes J. A., Noble W. S., PLoS Comput Biol., 6:7 (2010), e1000834 | DOI | MR

[17] Segal E., Widom J., Trends Genet., 25:8 (2009), 335–343 | DOI

[18] Lantermann A. B., Straub T., Stålfors A., Yuan G.-C., Ekwall K., Korber P., Nat. Struct. Mol. Biol., 17:2 (2010), 251–257 | DOI