In mammalian nuclei, DNA regions contacting the nuclear lamina are typically silent and reside in the inactive B compartment of the genome, yet it remains unknown whether this spatial organization causally regulates gene expression or merely reflects pre-existing chromatin state. Cross-lineage comparisons of public datasets show that lamina association and A/B compartment identity contribute additively to gene expression, with lineage-specific dominance (compartment identity dominates in mesenchymal-lineage cells, lamina association elsewhere), but the direction of causality - repositioning driving transcriptional change, transcription driving repositioning, or both in tandem - remains unresolved, and the mechanism behind the lineage-specific dominance, as well as the lineage-specific coupling between histone-modification changes and lamina-association switching, remains unexplained. The lineage-specific dominance pattern and the lineage-specific histone-modification coupling are among the unresolved relationships that give the question its comparative context, and the candidate explanations the source speculates for them (nuclear geometry, lamina protein composition, or chromatin state) may inform an answer. No study yet establishes the causal direction(s); the question remains open.

Background

Chromosomes in mammalian cell nuclei are not packaged randomly. The nuclear lamina - the meshwork of lamin protein filaments lining the inner face of the nuclear envelope - anchors large stretches of transcriptionally quiet, heterochromatinized DNA. These stretches, called lamina-associated domains (LADs, typically spanning hundreds of kilobases to several megabases), are mapped genome-wide by DamID, an assay in which a lamin-fused bacterial DNA adenine methyltransferase methylates the DNA that physically contacts the lamina, leaving a readable mark. Independently, Hi-C - an assay that ligates and sequences pairs of physically proximate DNA fragments to build genome-wide contact maps - reveals that each chromosome folds into two large-scale compartments: the A compartment, gene-dense, early-replicating and transcriptionally active, and the B compartment, gene-poor, late-replicating and enriched for repressive histone modifications such as methylation of histone H3 at lysine 9 (H3K9me2/3). Because most LADs lie in the B compartment, lamina contact and compartment identity are strongly correlated - but not identical. During cell differentiation or cancer progression, roughly 20-30% of genomic regions switch compartment, and many regions also gain or lose lamina contact; the two events are only loosely coupled, producing 'incongruent' regions whose compartment identity and lamina status disagree (van Steensel and Belmont, Cell 169(5):780-791, 2017, doi:10.1016/j.cell.2017.04.022).

Comparing public DamID, Hi-C and RNA-seq datasets across cell lineages (mesenchymal, that is connective-tissue-derived, epithelial, hematopoietic and embryonic stem cells), Das, San Martin and McCord (Nucleus 14(1):2197693, 2023, doi:10.1080/19491034.2023.2197693) found that lamina association and compartment identity contribute additively rather than redundantly to a region's gene expression state. However, lineages differed in which feature dominated: in mesenchymal-lineage cells, gene expression tracked compartment identity regardless of lamina state, whereas in other lineages lamina association was the stronger correlate at discordant regions. The authors could only speculate about the cause, invoking the flat ellipsoidal geometry of mesenchymal nuclei, which may force a large fraction of the genome toward the periphery regardless of chromatin state. Relationships between histone-modification changes and lamina-association switching were likewise lineage-specific and unexplained, with epigenetic dysregulation of the cancer cell lines used flagged as a possible confounder.

The deeper question is old and general: is the nuclear periphery a cause or a consequence of transcriptional repression? Artificial-tethering and relocation experiments have given partial evidence in both directions from the outset. On one side, recruiting genes to the nuclear periphery represses some of them (Finlan et al., PLoS Genetics 4(3):e1000039, 2008, doi:10.1371/journal.pgen.1000039); certain DNA sequences drive lamina targeting and silencing (Zullo et al., Cell 149(7):1474-1487, 2012, doi:10.1016/j.cell.2012.04.035); and developmentally timed relocation of the Drosophila hunchback gene to the lamina heritably silences it and restricts neural progenitor competence (Kohwi et al., Cell 152(1-2):97-108, 2013, doi:10.1016/j.cell.2012.11.049). On the other side, a genetic locus artificially anchored to the lamina remains transcriptionally competent and inducible there (Kumaran and Spector, Journal of Cell Biology 180(1):51-65, 2008, doi:10.1083/jcb.200706060); CRISPR-mediated movement of genes into LADs represses them only when promoter-intrinsic features permit (Leemans et al., Cell 177(4):852-864.e14, 2019, doi:10.1016/j.cell.2019.03.009); and transcriptional activation can itself locally detach chromatin from the lamina (Brueckner et al., The EMBO Journal 39(6):e103159, 2020, doi:10.15252/embj.2019103159). Because nearly all available data are cross-sectional comparisons between distinct cell states, the temporal order of events - repositioning before expression change, or the reverse - is not observable, and correlation alone cannot distinguish driver from passenger. What is missing is a causal, position-specific, lineage-comparative test.

Problem Statement

The problem, as left unresolved by Das, San Martin and McCord (2023), is to determine the causal structure connecting nuclear positioning and gene regulation. Directionality: when a genomic region changes both lamina association and gene expression between cell states, does the change in lamina association (or A/B compartment identity) drive the change in gene expression, does altered transcription drive the repositioning, or do the two act in tandem - and under which genomic and cellular conditions does each direction hold? The source's lineage-specific observations give the question its comparative context and are among the relationships whose directionality remains unresolved: compartment identity dominates gene-expression associations in mesenchymal-lineage cells regardless of lamin state, while lamina association dominates in other lineages at regions where the two features are discordant, and the coupling between histone-modification changes and lamina-association switching is lineage-specific. The candidate explanations the source speculates for these observations - nuclear geometry (the flat ellipsoidal shape of mesenchymal nuclei), lamina protein composition (for example lamin A/C versus lamin B ratios), or lineage-specific chromatin state (including the epigenetic dysregulation of the cancer cell lines used) - may inform an answer; the question is the direction(s) of causality and the conditions under which each holds, not the discrimination among these candidate mechanisms or an explanation of the lineage-specific histone-modification coupling. The direction(s) of causality and the conditions under which each holds are to be compared across more than one cell lineage. Purely correlative re-description of cross-sectional comparisons between cell states does not establish the causal direction(s).

References

  1. Das P, San Martin R, McCord RP (2023). Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation. Nucleus 14(1):2197693. doi:10.1080/19491034.2023.2197693 (preprint: doi:10.1101/2022.09.12.507606). https://doi.org/10.1080/19491034.2023.2197693
  2. Li H, Playter C, Das P, McCord RP (2024). Chromosome compartmentalization: causes, changes, consequences, and conundrums. Trends in Cell Biology 34(9):707-727. doi:10.1016/j.tcb.2024.01.009. https://doi.org/10.1016/j.tcb.2024.01.009
  3. Afanasyev AY, Kim Y, Tolokh IS, Sharakhov IV, Onufriev AV (2024). The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies. Epigenetics and Chromatin 17(1):13. doi:10.1186/s13072-024-00528-8. https://doi.org/10.1186/s13072-024-00528-8
  4. Leemans C, van der Zwalm MCH, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B (2019). Promoter-intrinsic and local chromatin features determine gene repression in LADs. Cell 177(4):852-864.e14. doi:10.1016/j.cell.2019.03.009. https://doi.org/10.1016/j.cell.2019.03.009
  5. Brueckner L, Zhao PA, van Schaik T, Leemans C, Sima J, Peric-Hupkes D, Gilbert DM, van Steensel B (2020). Local rewiring of genome-nuclear lamina interactions by transcription. The EMBO Journal 39(6):e103159. doi:10.15252/embj.2019103159. https://doi.org/10.15252/embj.2019103159
  6. Finlan LE, Sproul D, Thomson I, Boyle S, Kerr E, Perry P, Ylstra B, Chubb JR, Bickmore WA (2008). Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genetics 4(3):e1000039. doi:10.1371/journal.pgen.1000039. https://doi.org/10.1371/journal.pgen.1000039
  7. Kumaran RI, Spector DL (2008). A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. The Journal of Cell Biology 180(1):51-65. doi:10.1083/jcb.200706060. https://doi.org/10.1083/jcb.200706060
  8. Zullo JM, Demarco IA, Pique-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H (2012). DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell 149(7):1474-1487. doi:10.1016/j.cell.2012.04.035. https://doi.org/10.1016/j.cell.2012.04.035
  9. van Steensel B, Belmont AS (2017). Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell 169(5):780-791. doi:10.1016/j.cell.2017.04.022. https://doi.org/10.1016/j.cell.2017.04.022
  10. Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R (2023). An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biology 24(1):16. doi:10.1186/s13059-023-02849-5. https://doi.org/10.1186/s13059-023-02849-5
  11. Kohwi M, Lupton JR, Lai SL, Miller MR, Doe CQ (2013). Developmentally regulated subnuclear genome reorganization restricts neural progenitor competence in Drosophila. Cell 152(1-2):97-108. doi:10.1016/j.cell.2012.11.049. https://doi.org/10.1016/j.cell.2012.11.049
  12. Herrera I, Fernandes JAS, Shir-Mohammadi K, Levesque J, Mattar P (2023). Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration. Cell Death and Disease 14(10):701. doi:10.1038/s41419-023-06224-x. https://doi.org/10.1038/s41419-023-06224-x
  13. Walsh PJ, Kraeutler EB, Linares-Saldana R, Wai M, Nguyen SC, Zhang S, Shah PP, Park DS, Muzaffar HA, Jain R, Joyce EF (2025). Mechanistic and epigenetic partitioning of lamina-associated chromatin revealed by a genome-wide imaging screen. bioRxiv 2025.08.13.670143. doi:10.1101/2025.08.13.670143. https://doi.org/10.1101/2025.08.13.670143
  14. Lucas T, Wang LI, Glass-Klaiber J, Quiroz E, Patra S, Molotkova N, Kohwi M (2024). Gene mobility elements mediate cell type specific genome organization and radial gene movement in vivo. bioRxiv 2024.11.30.626181. doi:10.1101/2024.11.30.626181. https://doi.org/10.1101/2024.11.30.626181
  15. Das P, San Martin R, Hong T, McCord RP (2025). Rearrangement of 3D genome organization in breast cancer epithelial to mesenchymal transition and metastasis organotropism. eLife 13:RP103697. doi:10.7554/eLife.103697. https://doi.org/10.7554/eLife.103697
  16. Martin CJ, Oser EA, Nagarajan P, Popova LV, Sunkel BD, Stanton BZ, Parthun MR (2025). Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation. Genome Research 35(9):1959-1974. doi:10.1101/gr.280380.124. https://doi.org/10.1101/gr.280380.124
  17. Ren X, Zhuang H, Zhu J, Jiang H, Zhang J, Zhang Y, Feng R, Shi R, Zhang R, Li L, Adam MS, Zhou P (2026). Bioorthogonal epigenetic anchoring of heterochromatin to the nuclear lamina reverses senescence and osteoarthritis. Journal of Advanced Research, in press. doi:10.1016/j.jare.2026.07.047. https://doi.org/10.1016/j.jare.2026.07.047
  18. Nair A, Khanna J, Kler J, Ragesh R, Sengupta K (2025). Nuclear envelope and chromatin choreography direct cellular differentiation. Nucleus 16(1):2449520. doi:10.1080/19491034.2024.2449520. https://doi.org/10.1080/19491034.2024.2449520
  19. Sun C, Zhao Y, Guo L, Qiu J, Peng Q (2025). The interplay between histone modifications and nuclear lamina in genome regulation. Journal of Genetics and Genomics 52(1):24-38. doi:10.1016/j.jgg.2024.10.005. https://doi.org/10.1016/j.jgg.2024.10.005