ArticleeLife2025
Major nuclear locales define nuclear genome organization and function beyond A and B compartments.
Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Mapping subcellular microenvironments using oligonucleotide-directed proximity labeling.Current opinion in chemical biology · 2026Review
- Acidic transcription factors position the genome at nuclear speckles through transcription-dependent and -independent mechanisms.Molecular cell · 2026Article
- Nuclear speckles: a fundamental layer of gene regulation.Trends in cell biology · 2026Review
- Nuclear speckle-associated perispeckle networks partition active chromatin into gene expression niches.Cell reports · 2026Article
- Embryo-scale Visual Cell Sorting reveals a conserved transcriptomic signature of nucleolar size linked to proteostasis.bioRxiv : the preprint server for biology · 2026Article
- The cytoskeleton contributes to abnormal genome-lamina interactions in LMNA-deficient cardiomyocytes.The Journal of cell biology · 2026Article
- Jointly-hic: joint decomposition of contact frequency maps captures salient features of genome architecture across tissues and development.Genome biology · 2026Article
- Decoding the functions of nuclear speckles in neurodegeneration.Trends in neurosciences · 2026Review
- LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis.Nature cell biology · 2026Article
- Hierarchical Chromatin Rewiring Orchestrates Early Transcriptional Regulation in Mouse Cerebral Cortex Following Focal Ischemia.bioRxiv : the preprint server for biology · 2026Article
- Identity rather than 3D position informs splicing of rare introns in the human genome.iScience · 2026Article
- Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures.The EMBO journal · 2025Article
- Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation.Genome research · 2025Article
- Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen.bioRxiv : the preprint server for biology · 2025Article
- The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate.Nature cell biology · 2025Article
- Aere perennius: how chromatin fidelity is maintained and lost in disease.NAR molecular medicine · 2025Review
- Toward decoding the mechanisms that shape sub-megabase-scale genome organization.Current opinion in structural biology · 2025Review
- Timed chromatin invasion during mitosis governs prototype foamy virus integration site selection and infectivity.Nucleic acids research · 2025Article
- Nuclear speckle biology: At the cross-roads of discovery and functional analysis.Current opinion in cell biology · 2024Review
- Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable localization of heterochromatin in different cell types.Communications biology · 2024Article
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Abstract
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. Although 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.
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