Large scale analyzes of proteins and biological network construction focusing on B chromosome studies

Author(s)

Rafael Takahiro Nakajima

• Document type: Doctoral Thesis
• Press: Botucatu. 2019-06-17.
• Institution: Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu
• Defense date: 2019-05-16
• Advisor: Cesar Martins

Abstract

The B chromosomes occur in about 2,828 species of different taxa, being heterochromatic and composed of repetitive DNA.Recently, large-scale genomic analyzes are being used to elucidate questions about supernumerary chromosomes.Cichlid fish are of great scientific interest, since many species have gone through a rapid and extensive process of adaptive radiation.In some species of the group, such as Astatotilapia latifasciata, the presence of B chromosomes was described.In this work, we characterize the profile of protein expression in specific tissues in A. latifasciata and performed a functional analysis of the presence of the B chromosome in this species of teleost, elucidating the influence that it can cause in specific metabolic pathways.In addition, we integrate these data with the RNA-Seq results of this species, and construct sub-networks of co-expression and protein-protein interaction.The Shannon entropy was also calculated, which did not show diversity in the expression of the transcripts in each library. In addition, differential expression analysis was performed on each tissue separately and the relationship between the presence of B chromosome and sex chromosome was analyzed. Among the differentially expressed transcripts, functional enrichment analysis presented processes related to the cell cycle, immune response and stress response. In relation to abundance of proteins, the up regulated transcripts and the sub-networks we identified genes like the Aurora kinase, tubulin and kinetochore protein genes that are related to cell cycle control. The results obtained, in general, did not show a great change in the protein or gene profile related to the presence of the B chromosome, although it identified putative proteins and genes for the GnRH (Gonadotropin-Releasing Hormone), cell cycle and stress pathways. However, this change in the expression profile suggests subtler and punctual regulation. Therefore, the B chromosome can actin the regulation of vital processes for the survival of the cell and facilitate its maintenance and transmission for the next generations. (AU)

• FAPESP's process: 15/11485-0 - Large-scale analysis of protein and biological networks construction focusing on B chromosome
• Grantee: Rafael Takahiro Nakajima
• Support Opportunities: Scholarships in Brazil - Doctorate