Computational Molecular Biology 2024, Vol.14, No.5, 220-228 http://bioscipublisher.com/index.php/cmb 223 4.3 Evolution of protein interaction networks The evolution of protein interaction networks is essential for understanding the functional organization of cellular processes. Integrative multi-omics approaches have enabled the construction of comprehensive protein-protein interaction (PPI) networks by combining data from various omics sources. These networks provide a global view of the molecular interactions within a cell, revealing how proteins interact with each other and with other biomolecules. Network-based methods have been particularly effective in identifying key nodes and subnetworks that are critical for cellular function and disease progression (Randhawa and Pathania, 2020; Agamah et al., 2022). By integrating proteomics with other omics data, researchers can gain a more detailed understanding of the evolutionary changes in PPI networks and their implications for cellular function. 5 Epigenomics and Its Role in Gene Evolution 5.1 Role of DNA methylation in evolution DNA methylation is a crucial epigenetic modification that influences gene expression by adding methyl groups to DNA, typically at CpG sites. This modification can lead to gene silencing and is essential for various biological processes, including development, differentiation, and disease. In the context of evolution, DNA methylation patterns can be inherited and modified in response to environmental changes, thereby contributing to evolutionary adaptation. For instance, studies have shown that DNA methylation can capture and mediate the effects of genetic and environmental risk factors on complex diseases, highlighting its role in evolutionary processes. The progressive loss of DNA methylation in heterochromatic regions during T cell differentiation underscores its importance in cellular memory and lineage specification (Durek et al., 2016). 5.2 Evolutionary function of histone modifications Histone modifications, such as methylation, acetylation, and phosphorylation, play a pivotal role in regulating chromatin structure and gene expression. These modifications can either activate or repress gene transcription, depending on the specific histone mark and its location. The dynamic nature of histone modifications allows for rapid responses to environmental stimuli, which can be crucial for evolutionary adaptation. For example, integrative analyses of histone modifications in cancer cells have revealed distinct chromatin states associated with gene activity and inactivity, suggesting that histone modifications contribute to the regulation of gene expression in response to evolutionary pressures. Furthermore, single-cell profiling of histone modifications has identified cell-type-specific regulatory mechanisms, emphasizing the role of histone modifications in the evolution of complex tissues (Zhu et al., 2021). 5.3 Epigenetic memory and environmental adaptation 5.3.1 Mechanisms of epigenetic memory in response to environmental stimuli Epigenetic memory refers to the heritable changes in gene expression that do not involve alterations in the DNA sequence. This memory can be established through various mechanisms, including DNA methylation and histone modifications. Environmental stimuli, such as stress or changes in diet, can induce epigenetic changes that are maintained across cell divisions and potentially across generations. For instance, the epigenetic landscape of chronic lymphocytic leukemia (CLL) cells shows disease-specific patterns of DNA methylation and histone modifications, which are imprints of the cellular origin and proliferative history, indicating a form of epigenetic memory (Kulis and Martín-Subero, 2022; Mason, 2024). The integrative analysis of epigenomic data has identified regulatory elements and transcription factor networks that mediate gene deregulation in response to environmental changes. 5.3.2 Role of epigenetic inheritance in long-term adaptation Epigenetic inheritance allows for the transmission of epigenetic marks from one generation to the next, providing a mechanism for long-term adaptation to environmental changes. This form of inheritance can influence phenotypic variation and evolutionary fitness without altering the underlying genetic code. For example, DNA methylation patterns can be stably inherited and influence gene expression in offspring, thereby contributing to long-term adaptation (Teschendorff and Relton, 2017). The study of epigenetic modifications in pulmonary diseases has also highlighted the potential for epigenetic marks to serve as noninvasive biomarkers, reflecting long-term environmental exposures and their impact on disease susceptibility (Benincasa et al., 2020).
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