Gonzalez, G. A. H. | Search bioRxiv

bioRxiv2025

Nonrandom interchromatin trafficking through dynamic multiphase speckle connections

Nuclear speckles (NS) enhance the expression of NS-associated genes, possibly by elevating local levels of factors involved in multiple steps of gene expression. While dozens of large NS are distributed throughout interchromatin regions, the extent to which NS components dynamically redistribute between NS to adjust to local physiological demands remains unknown. Here we used live-cell imaging of endogenous NS proteins to identify an interchromatin network of connections that functionally link NS throughout the nucleus. Over timescales ranging from tens of seconds to minutes, NS material undergoes bulk transfer through these connections. Multiphase NS-connecting structures form through the dynamic juxtapositions of multiple NS component phases. Each phase exhibits distinct yet recurrent viscoelastic dynamics, but together, they integrate into a more stable, multiphase, NS-connecting structure in an ATP-and transcription-dependent manner. Our findings reveal the existence of a cellular mechanism that facilitates coordinated inter-NS protein trafficking through multiphase connections.

cell biology↗

bioRxiv2024

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.

genomics↗