Beyond A and B Compartments: how major nuclear locales define nuclear genome  organization and function.
Models of nuclear genome organization often propose a binary division into active  versus inactive compartments yet typically overlook nuclear bodies. Here we  integrated analysis of sequencing and image-based data to compare genome  organization in four human cell types relative to three different nuclear  locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene  expression correlates mostly with nuclear speckle proximity, DNA replication  timing correlates with proximity to multiple nuclear locales. Speckle attachment  regions emerge as DNA replication initiation zones whose replication timing and  gene composition vary with their attachment frequency. Most facultative LADs  retain a partially repressed state as iLADs, despite their positioning in the  nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a  shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal  relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to  lamina. Thus, these partially repressed iLADs appear to compete with LADs for  nuclear lamina attachment with consequences for replication timing. The nuclear  organization in adherent cells is polarized with nuclear bodies and genomic  regions segregating both radially and relative to the equatorial plane. Together,  our results underscore the importance of considering genome organization relative  to nuclear locales for a more complete understanding of the spatial and  functional organization of the human genome. Overall design: Total 28 samples generated using TSA-seq in H. sapiens on condition2 - conditionE - anti-MKI67IP, input - condition2 - conditionE -  anti-MKI67IP, condition2 - conditionE - anti-SON, input - condition2 - conditionE - anti-SON, condition2 - conditionAI - anti-Lamin B1, input - condition2 - conditionAI - anti-Lamin B1. (Note: 4 Samples used in this study were excluded from this GEO series as they were already added to GEO and SRA as part of another series: GSE81553. Please find details in attached supplementary file: excluded_samples.txt)