Exploring the relation between evolutionary gene age, gene expression and chromatin 3D structure in cancer
This repository is about gene regulation and chromatin conformation across evolutionary time project. This project explores the fascinating relationship between genes' evolutionary ages, genome properties, expression regulation, and chromatin 3D conformations. The study delves into how genes, born over billions of years of evolution, exhibit unique characteristics in terms of genome organization and function. We also investigate the impact of cell differentiation and cancer on these gene age-specific properties.
The current human genome comprises genes that emerged at various evolutionary epochs spanning 3.5 billion years. These genes have progressively evolved, accumulating new functions and contributing to the increasing sophistication of species' genomes. By studying duplication events through time, evolutionary scientists have been able to estimate the precise ages of genes within the human genome. However, the connections between genes of similar evolutionary ages, their expression patterns, and their chromatin structures remain poorly understood.
In this project, we aim to:
- Investigate whether genes with different evolutionary ages exhibit specific genome properties, expression regulations, and chromatin 3D conformations.
- Explore the relationship between gene ages and chromatin structure during the process of cell differentiation.
- Examine the effects of gene age on chromatin structure in the context of cancer.
Our research leverages data integration and network sciences, employing topological measurements to define the unique chromatin properties of genes based on their evolutionary ages. Here are some key findings:
- Gene expression and DNA methylation variability are linearly correlated with gene ages.
- Old genes associated with critical cellular functions exhibit lower variability compared to newer genes.
- Chromatin network analysis reveals that old and important genes are predominantly located at the core of the network.
- Old genes have more interactions with regulatory regions, indicating a linear link between node degrees and gene ages.
- In cancer cells, genes of unicellular origin exhibit increased interconnectivity, higher node degrees, and coreness compared to normal cells.
These findings suggest that cancer cells may revert to a more undifferentiated state based on network topology, providing valuable insights into the origins of gene regulation through natural chromatin structure formation over billions of years.
- Presentation Slides
- [Project Poster]
To get started with this project, you can clone this repository to your local machine using the following command:
git clone https://github.com/VeraPancaldiLab/Gene-Ages-Paper.git