Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes

Recent advances in high-throughput microscopy have paved the way to study chromosome organization at the single-molecule level and have led to a better understanding of genome organization in space and time. During development, distinct maternal and paternal contributions ensure the formation of an embryo proper, yet little is known about the organization of chromosomes inherited from mothers versus fathers. To tackle this question, we have modified single-molecule chromosome tracing to distinguish between the chromosomes of two well-studied strains of C. elegans called Bristol and Hawai'ian. We find that chromosomes from these two strains have similar folding patterns in homozygous hermaphrodites. However, crosses between Bristol and Hawai'ian animals reveal that the paternal chromosome adopts the folding parameters of the maternal chromosome in embryos. This is accomplished by an increase in the polymer step size and decompaction of the chromosome. The data indicate that factors from the mother impact chromosome folding in trans. We also characterize the degree of intermixing between homologues within the chromosome territories. Sister chromosomes overlap frequently in C. elegans embryos, but pairing between homologues is rare, suggesting that transvection is unlikely to occur. This method constitutes a powerful tool to investigate chromosome architecture from mothers and fathers.