Chromatin conformation regulates the coordination between DNA replication and transcription [array]

Chromatin is the template for the basic processes of replication and transcription, making the maintenance of chromosomal integrity critical for cell viability. To elucidate how dividing cells respond to alterations in chromatin structure we analysed the replication initiation landscape, elongation kinetics, and timing of primary cells with altered chromatin configuration caused by the genetic ablation of the HMGB1 gene, or triple-KO in three histone H1 genes. We found that loss of chromatin compaction in H1-depleted cells alters dramatically the initiation patterns triggering the accumulation of stalled forks and DNA damage as a consequence of transcription-replication conflicts, whereas reductions in nucleosome content due to the lack of HMGB1 causes faster fork progression without perturbing the initiation landscape or fork stability. Thus, perturbations in the integrity of the chromatin template elicit a range of responses in the dynamics of DNA replication and transcription, with different consequences on replicative stress. These findings have broad implications for our understanding of how defects in chromatin structure, such as those occurring during cellular aging or in some developmental disorders or cancer, contribute to genomic instability. Replication timing has been compared between two experimental conditions: WT (control) versus H1-TKO cells. Two replicates.