Análises em larga escala de proteínas e construção de redes biológicas com foco em estudos de cromossomos B
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Data
2019-05-16
Autores
Nakajima, Rafael Takahiro [UNESP]
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Editor
Universidade Estadual Paulista (Unesp)
Resumo
Os cromossomos B ocorrem em cerca de 2.828 espécies de diferentes táxons, sendo basicamente heterocromáticos e compostos de DNAs repetitivos. Recentemente, análises genômicas em larga escala estão sendo utilizadas para elucidar questões acerca dos cromossomos supranumerários. Os peixes ciclídeos recebem grande interesse científico, uma vez que muitas espécies passaram por um rápido e extenso processo de radiação adaptativa. Em algumas espécies do grupo, como Astatotilapia latifasciata, foi descrita a presença de cromossomos B. Neste trabalho foi caracterizado o perfil de expressão proteico em tecidos específicos na A. latifasciata e realizada análise funcional da presença do cromossomo B nesta espécie de teleósteo, elucidando a influência que este pode acarretar em vias metabólicas específicas. Além disso, esses dados foram integrados com os resultados de RNA-Seq dessa espécie, e construídas sub redes de co-expressão e interação proteína-proteína. Também foi calculada a entropia de Shannon, a qual não apresentou diversidade na expressão dos transcritos em cada biblioteca comparada. Além disso, foi analisada a expressão diferencial de RNAm em cada tecido em relação a presença do cromossomo B e ao sexo. Dentre os transcritos diferencialmente expressos, a análise de enriquecimento funcional apresentou processos relacionados ao ciclo celular, resposta imune e resposta ao estresse. Na maioria dos casos analisados entre a expressão de proteínas, os transcritos up regulated e as sub redes, apareceram os genes Aurora quinase, tubulina e proteína de cinetócoro que estão relacionados ao controle do ciclo celular. Os resultados obtidos, de forma geral, não apresentaram grande alteração no perfil proteico ou gênico relacionado a presença do cromossomo B, apesar de identificar proteínas e genes putativos para as vias do GnRH (Gonadotropin-Releasing Hormone), do ciclo celular e do estresse. Contudo, essa alteração no perfil de expressão sugere regulação mais sutil e pontual. Portanto, o cromossomo B pode atuar na regulação de processos vitais para sobrevivencia da célula e faciliatr sua manutenção e transmição para as proximas gerações.
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.
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.
Descrição
Palavras-chave
proteomica, cromossomo extra, RNA mensageiro, RNA codificante, ciclídeo africano, proteomic, extra chromosome, messenger RNA, coding RNA, African cichlids