Characterization of Bovine (Bos Taurus) Imprinted Genes from Genomic to Amino Acid Attributes by Data Mining Approaches

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2019 Jun 7

PMID 31170205

Citations 4

Authors

Keyvan Karami

Saeed Zerehdaran

Ali Javadmanesh

Mohammad Mahdi Shariati

Hossein Fallahi

Affiliations

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Abstract

Genomic imprinting results in monoallelic expression of genes in mammals and flowering plants. Understanding the function of imprinted genes improves our knowledge of the regulatory processes in the genome. In this study, we have employed classification and clustering algorithms with attribute weighting to specify the unique attributes of both imprinted (monoallelic) and biallelic expressed genes. We have obtained characteristics of 22 known monoallelically expressed (imprinted) and 8 biallelic expressed genes that have been experimentally validated alongside 208 randomly selected genes in bovine (Bos taurus). Attribute weighting methods and various supervised and unsupervised algorithms in machine learning were applied. Unique characteristics were discovered and used to distinguish mono and biallelic expressed genes from each other in bovine. To obtain the accuracy of classification, 10-fold cross-validation with concerning each combination of attribute weighting (feature selection) and machine learning algorithms, was used. Our approach was able to accurately predict mono and biallelic genes using the genomics and proteomics attributes.

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References

Moore G, Ishida M, Demetriou C, Al-Olabi L, Leon L, Thomas A . The role and interaction of imprinted genes in human fetal growth. Philos Trans R Soc Lond B Biol Sci. 2015; 370(1663):20140074. PMC: 4305174. DOI: 10.1098/rstb.2014.0074. View

Chen Z, Hagen D, Wang J, Elsik C, Ji T, Siqueira L . Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing. Epigenetics. 2016; 11(7):501-16. PMC: 4939914. DOI: 10.1080/15592294.2016.1184805. View

Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal S . RNAi-mediated targeting of heterochromatin by the RITS complex. Science. 2004; 303(5658):672-6. PMC: 3244756. DOI: 10.1126/science.1093686. View

Barahimipour R, Strenkert D, Neupert J, Schroda M, Merchant S, Bock R . Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii. Plant J. 2015; 84(4):704-17. PMC: 4715772. DOI: 10.1111/tpj.13033. View

Zhou J, Troyanskaya O . Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods. 2015; 12(10):931-4. PMC: 4768299. DOI: 10.1038/nmeth.3547. View

Takagi N, Sasaki M . Preferential inactivation of the paternally derived X chromosome in the extraembryonic membranes of the mouse. Nature. 1975; 256(5519):640-2. DOI: 10.1038/256640a0. View

Luedi P, Hartemink A, Jirtle R . Genome-wide prediction of imprinted murine genes. Genome Res. 2005; 15(6):875-84. PMC: 1142478. DOI: 10.1101/gr.3303505. View

Wang X, Clark A . Using next-generation RNA sequencing to identify imprinted genes. Heredity (Edinb). 2014; 113(2):156-66. PMC: 4105452. DOI: 10.1038/hdy.2014.18. View

Martienssen R . Maintenance of heterochromatin by RNA interference of tandem repeats. Nat Genet. 2003; 35(3):213-4. DOI: 10.1038/ng1252. View

10.

Rainier S, Johnson L, Dobry C, Ping A, Grundy P, Feinberg A . Relaxation of imprinted genes in human cancer. Nature. 1993; 362(6422):747-9. DOI: 10.1038/362747a0. View

11.

Ikemura T . Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 1985; 2(1):13-34. DOI: 10.1093/oxfordjournals.molbev.a040335. View

12.

Hoki Y, Kimura N, Kanbayashi M, Amakawa Y, Ohhata T, Sasaki H . A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse. Development. 2008; 136(1):139-46. DOI: 10.1242/dev.026427. View

13.

Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T . Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol. 2001; 53(4-5):290-8. DOI: 10.1007/s002390010219. View

14.

Thai K, Ecker G . Similarity-based SIBAR descriptors for classification of chemically diverse hERG blockers. Mol Divers. 2009; 13(3):321-36. DOI: 10.1007/s11030-009-9117-0. View

15.

Feinberg A . DNA methylation, genomic imprinting and cancer. Curr Top Microbiol Immunol. 2000; 249:87-99. DOI: 10.1007/978-3-642-59696-4_6. View

16.

Wei Y, Su J, Liu H, Lv J, Wang F, Yan H . MetaImprint: an information repository of mammalian imprinted genes. Development. 2014; 141(12):2516-23. DOI: 10.1242/dev.105320. View

17.

Ogawa O, Eccles M, Szeto J, McNoe L, Yun K, Maw M . Relaxation of insulin-like growth factor II gene imprinting implicated in Wilms' tumour. Nature. 1993; 362(6422):749-51. DOI: 10.1038/362749a0. View

18.

Beiki A, Saboor S, Ebrahimi M . A new avenue for classification and prediction of olive cultivars using supervised and unsupervised algorithms. PLoS One. 2012; 7(9):e44164. PMC: 3434224. DOI: 10.1371/journal.pone.0044164. View

19.

Toyota M, Ahuja N, Herman J, Baylin S, Issa J . CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A. 1999; 96(15):8681-6. PMC: 17576. DOI: 10.1073/pnas.96.15.8681. View

20.

Hosseinzadeh F, Ebrahimi M, Goliaei B, Shamabadi N . Classification of lung cancer tumors based on structural and physicochemical properties of proteins by bioinformatics models. PLoS One. 2012; 7(7):e40017. PMC: 3400626. DOI: 10.1371/journal.pone.0040017. View