Revealing cellular conflict role in disease and development
Conflicts are a normal part of life. Avoiding and resolving them is an important skill that we acquire early on and continue practising on an everyday basis. “Conflicts however are not only a social phenomenon among human individuals,” says ConflictResolution project coordinator Stephan Hamperl(opens in new window) from Helmholtz Munich(opens in new window) in Germany. “They can also arise inside our body, within our cells.”
Investigating transcription-replication conflicts
‘Molecular machines’ assemble on our chromosomes at distinct locations to perform their dedicated functions. The ConflictResolution project, which was funded by the European Research Council(opens in new window), was launched to investigate how two of these machines, namely transcription to read out gene information and DNA replication to duplicate the genome, are regulated and coordinated. “Research suggests that there are mechanisms in place to physically separate these two essential processes and avoid what are called transcription-replication conflicts (TRCs),” adds Hamperl. “Nevertheless, this separation is not absolute, and certain regions of the genome can be considered as hotspots where these two machineries meet frequently.” Just as mismanagement of social conflicts can lead to great harm, the same holds true for cellular conflicts. TRCs are therefore potent sources for instability, potentially contributing to cancers, ageing and neurological diseases.
Expanding the toolbox to study cellular conflicts
To better understand this phenomenon, Hamperl had previously built a reporter system for identifying specific encounters between transcription and replication machineries. In ConflictResolution, he used this technique as a starting point to investigate in more detail the impact of these collisions on DNA integrity, with the aim of identifying the protein factors necessary to resolve and overcome them. “ConflictResolution has extended our toolbox to study cellular conflicts in a breast cancer genome,” explains Hamperl. “Cancer genomes show aberrant transcription and replication profiles that can lead to unscheduled TRCs and contribute to the pathological transformation of cells.” The project established a system to map these collision sites and identify associated genetic changes in a breast cancer cell model. It also assessed in vivo the contribution of TRCs during early embryonic development, to determine their contribution to cell transformation during development and cellular differentiation.
Molecular mechanisms behind transcription and replication
A number of important breakthroughs have been made. “For example, we found a histone post-translational modification named H3K79 methylation that is deposited at TRC sites, which can help to resolve the conflict,” says Hamperl. “We also found a total of 88 new factors that are recruited to TRC sites. Among these, we were able to characterise in more detail a factor called CGG-trinucleotide repeat binding factor 1 (CGGBP1). This is a mitigator of genome-destabilising DNA structures and resulting TRCs.” Hamperl also discovered that pluripotent cells – cells that develop into many different types of cells or tissues – poorly coordinate transcription and replication mechanisms and exhibit high TRC levels. “This is a molecular feature that is lost after cellular differentiation into more specialised cell types,” he explains. “This shows that different cell types vary in their ability to cope with TRCs.” All this has helped to confirm that TRCs are a frequent, internal source of genetic and epigenetic instability, and underlined the importance of TRC resolution for cellular health. The impact of these findings could be far-reaching. “Using the analytical tools developed as part of ConflictResolution, we can start to fill in a key gap in our knowledge,” adds Hamperl. “We can now study the molecular mechanisms that coordinate transcription with replication processes and reveal the pathways through which TRCs impinge on cell function.” This could help scientists like Hamperl to better understand disease progression and ultimately lead to new therapeutic approaches.
Keywords
ConflictResolution, cells, disease, genetic, epigenetic, gene, cancers, ageing
