Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation
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The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, we generated high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells via lineage-committed neural precursor cells into terminally differentiated astrocytes. This reveals that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units and multigene regions and affects many genes that determine cellular identity. Often, genes that move away from the lamina are concomitantly activated; many others, however, remain inactive yet become unlocked for activation in a next differentiation step. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation.
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Pseudo-compartments are characterized by a gradient of epigenetic signatures.
“Analysis of RNA-seq, histone marks15 and Lamin association17 suggested pseudo-compartments are characterized by a gradient of epigenetic signatures”
From Cell-cycle dynamics of chromosomal organization at single-cell resolution (2017) · cites this paper as [17]
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Babaei, S., Akhtar, W., de Jong, J., Reinders, M., & de Ridder, J. (2015) · Nature Communications · doi:10.1038/ncomms7381 · Cited by 37 · see citing works
Self-citationNuclear actin structure regulates chromatin accessibility
Sen, B., Xie, Z., Thomas, M. D., Pattenden, S. G., Howard, S., McGrath, C., Styner, M., Uzer, G., Furey, T. S., & Rubin, J. (2024) · Nature Communications · doi:10.1038/s41467-024-48580-y · Cited by 35 · see citing works
Between form and function: the complexity of genome folding
Oudelaar, A. M., Hanssen, L. L. P., Hardison, R. C., Kassouf, M. T., Hughes, J. R., & Higgs, D. R. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx306 · Cited by 16 · see citing works
- Authors
- Peric-Hupkes, D., Meuleman, W., Pagie, L., Bruggeman, S. W. M., Solovei, I., Brugman, W., Gräf, S., Flicek, P., Kerkhoven, R. M., van Lohuizen, M., Reinders, M., Wessels, L., & van Steensel, B.
- Affiliations
- The Netherlands Cancer Institute (NL)
- Ludwig-Maximilians-Universität München (DE)
- European Bioinformatics Institute (GB)
- Delft University of Technology (NL)
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2010-05
- Volume
- 38
- Issue
- 4
- Pages
- 603-613
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC5975946
- OpenAlex
- W1984340155
- Cited by
- 1,050
- References
- 43
- Citations by year
- 2026: 39 · 2025: 53 · 2024: 52 · 2023: 46 · 2022: 79 · 2021: 65 · 2020: 75 · 2019: 97 · 2018: 68 · 2017: 81 · 2016: 71 · 2015: 90 · 2014: 58 · 2013: 70 · 2012: 50
- FWCI
- 22.78
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Wellcome Trust (062023)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- nuclear lamina, chromosome organization, 3D genome organization, mouse embryonic stem cells, astrocyte differentiation, neural progenitor cells, lineage commitment, terminal differentiation, gene expression regulation, chromatin remodeling, cell identity genes
- MeSH terms
- Animals, Astrocytes, Cell Differentiation, Drosophila, Humans, Neurons, Genome, Cell Lineage, Nuclear Lamina, Chromosome Positioning, Mice, Embryonic Stem Cells
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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