Biochemical properties of chromatin read by SAMMY-seq: transcriptional activity and 3D compartmentalisation in one shot
In the interphase cell nucleus, chromatin has a precisely organised three-dimensional architecture that is connected to the transcriptional regulation of chromatin domains. On a large-scale, euchromatic and heterochromatic domains tend to co-localize with domains of the same type, thus constituting spatially separated active ("A") and inactive ("B") compartments, that can be mapped by genomics techniques quantifying the contact frequencies between genomic loci. However, these techniques are not sensitive to chromatin compartments relocation across subnuclear environments. Based on the rationale that chromatin domains located in the same 3D nuclear region share the same biochemical properties, we developed SAMMY-seq, a new experimental technique based on the sequential purification and sequencing of biochemically distinct chromatin fractions. With a first, already published version of this method (3f-SAMMY-seq), we were able to map constitutive heterochromatin domain dynamics when their association to the nuclear lamina is compromised. More recently, we improved SAMMY-seq resolution in characterising the position of accessible chromatin in an alternative protocol called 4f-SAMMY-seq. Through the "biochemical similarity" of genomics regions as measured by 4f-SAMMY-seq, we were also able to identify chromatin compartments and sub-compartments; they are highly reproducible across 4f-SAMMY-seq replicates and highly concordant with the ones derived from Hi-C. Analysing the regions with discordant (4f-SAMMY-seq vs Hi-C) compartment assignment, we observed that 4f-SAMMY-seq is more consistent in classifying "quiescent" chromatin state in the inactive B compartment and in assigning transcribed genes to the A compartment. Polycomb-associated states and Polycomb-dependent H3K27me3 mark also show a more clear-cut association to A compartment and A sub-compartments in 4f-SAMMY-seq compared to Hi-C. In summary, 4f-SAMMY-seq is able to precisely map the location of both euchromatic and heterochromatic domains, as well as their 3D compartmentalization, providing crucial practical advantages over state-of-the-art techniques for mapping compartments in terms of costs, versatility and scalability.