In this episode of the Epigenetics Podcast, we talked with Bas van Steensel from the Netherlands Cancer Institute about his work on characterizing chromatin at the Nuclear Lamina.
The Interview starts with discussing Bas van Steensel's significant contributions to understanding genome-nuclear lamina interactions. Bas detailed the development of the DAM-ID technique during his postdoctoral studies, which provided a novel way to map genome-wide occupancy and identify Lamina-Associated Domains (LADs). He elaborated on how LADs reveal a distinct domain architecture, often correlating with gene expression levels. This prompted an exploration of the dynamics of these domains during differentiation processes, allowing insights into how gene activation and repression are influenced by their positioning relative to the nuclear lamina.
The conversation highlighted the intricate relationship between chromatin dynamics and gene regulation, with Bas sharing compelling findings on how LADs behave during cell differentiation. The research indicated that regions moving away from the lamina often correlated with increased gene expression, revealing a complex interplay of spatial genome organization and transcriptional activity.
Additionally, we ventured into the significance of outreach and transparency in scientific research. Bas shared his philosophy regarding collaboration and the ethical responsibility of scientists to share knowledge and resources openly. He emphasized that making lab notebooks and research processes accessible can greatly enhance reproducibility and understanding in the scientific community.
Open Science Policy of our lab
Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M. B., Talhout, W., Eussen, B. H., de Klein, A., Wessels, L., de Laat, W., & van Steensel, B. (2008). Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature, 453(7197), 948–951. https://doi.org/10.1038/nature06947
Kind, J., Pagie, L., Ortabozkoyun, H., Boyle, S., de Vries, S. S., Janssen, H., Amendola, M., Nolen, L. D., Bickmore, W. A., & van Steensel, B. (2013). Single-cell dynamics of genome-nuclear lamina interactions. Cell, 153(1), 178–192. https://doi.org/10.1016/j.cell.2013.02.028
Kind, J., Pagie, L., de Vries, S. S., Nahidiazar, L., Dey, S. S., Bienko, M., Zhan, Y., Lajoie, B., de Graaf, C. A., Amendola, M., Fudenberg, G., Imakaev, M., Mirny, L. A., Jalink, K., Dekker, J., van Oudenaarden, A., & van Steensel, B. (2015). Genome-wide maps of nuclear lamina interactions in single human cells. Cell, 163(1), 134–147. https://doi.org/10.1016/j.cell.2015.08.040
Leemans, C., van der Zwalm, M. C. H., 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. https://doi.org/10.1016/j.cell.2019.03.009
van Schaik, T., Liu, N. Q., Manzo, S. G., Peric-Hupkes, D., de Wit, E., & van Steensel, B. (2022). CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. Genome biology, 23(1), 185. https://doi.org/10.1186/s13059-022-02754-3
van Steensel B. (2018). Scientific honesty and publicly shared lab notebooks: Sharing lab notebooks along with publication would increase transparency and help to improve honesty when reporting results. EMBO reports, 19(10), e46866. https://doi.org/10.15252/embr.201846866
scDamID, EpiDamID and Lamina Associated Domains (Jop Kind)
Identification of Functional Elements in the Genome (Bing Ren)
Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff)