In this episode of the Epigenetics Podcast, we caught up with Jop Kind from Hubrecht Institute to talk about his work on single cell DamID, EpiDamID, and Lamina Associated Domains (LADs).
Jop Kind started out developing single cell DamID (scDamID), based on the DamID technique. First, this technique was adapted to a microscopic readout which enabled them to follow the localisation of chromatin domains after cell division. Next, the lab expanded this technique into the NGS space and created genome-wide maps of nuclear lamina Interactions in single human cells. Since LADs are in a heterochromatic chromatin context, the lab expanded scDamID into the epigenetic space. They first combined it with a transcriptional readout. Later-on they developed EpiDamID, a method to target a diverse set of chromatin types by taking advantage of the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins.
References
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
Borsos, M., Perricone, S.M., Schauer, T. et al. Genome–lamina interactions are established de novo in the early mouse embryo. Nature 569, 729–733 (2019). https://doi.org/10.1038/s41586-019-1233-0
Markodimitraki, C. M., Rang, F. J., Rooijers, K., de Vries, S. S., Chialastri, A., de Luca, K. L., Lochs, S. J. A., Mooijman, D., Dey, S. S., & Kind, J. (2020). Simultaneous quantification of protein–DNA interactions and transcriptomes in single cells with scDam&T-seq. Nature Protocols, 15(6), 1922–1953. https://doi.org/10.1038/s41596-020-0314-8
Rang, F. J., de Luca, K. L., de Vries, S. S., Valdes-Quezada, C., Boele, E., Nguyen, P. D., Guerreiro, I., Sato, Y., Kimura, H., Bakkers, J., & Kind, J. (2022). Single-cell profiling of transcriptome and histone modifications with EpiDamID. Molecular Cell, 82(10), 1956-1970.e14. https://doi.org/10.1016/j.molcel.2022.03.009
Related Episodes
Dosage Compensation in Drosophila (Asifa Akhtar)
Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff)
Single Cell Epigenomics in Neuronal Development (Tim Petros)
Contact
Epigenetics Podcast on Twitter
Epigenetics Podcast on Instagram
Epigenetics Podcast on Mastodon
Active Motif on Twitter
Active Motif on LinkedIn
Email: podcast@activemotif.com
Using Single-Cell Multiomics to Characterize Human Developmental Hematopoiesis (Ana Cvejic)
The Impact of Sequence Variation on Transcription Factor Binding (Sven Heinz)
Comparing CUT&Tag to ENCODE ChIP-Seq in Alzheimer's Disease Samples (Sarah Marzi)
The Role of Hat1p in Chromatin Assembly (Mark Parthun)
The Impact of Paternal Diet on Offspring Metabolism (Upasna Sharma)
H3K36me3, H4K16ac and Cryptic Transcription in Ageing (Weiwei Dang)
Split-Pool Recognition of Interactions by Tag Extension (SPRITE) (Mitch Guttman)
MLL Proteins in Mixed-Lineage Leukemia (Yali Dou)
Sex-biased Imprinting and DNA Regulatory Landscapes During Reprogramming (Sam Buckberry)
BET Proteins and Their Role in Chromosome Folding and Compartmentalization (Kyle Eagen)
Epigenetic Underpinnings of Human Addiction (Francesca Telese & Jessica Zhou)
H3K79 Methylation, DOT1L, and FOXG1 in Neural Development (Tanja Vogel)
Function of Insulators in 3D Genome Folding (Maria Gambetta)
Contribution of the Estrogen Receptor to Breast Cancer Progression (Jason Carroll)
Inheritance of Transcriptional Memory by Mitotic Bookmarking (Sheila Teves)
Differential Methylated Regions in Autism Spectrum Disorders (Janine La Salle)
DNA Damage in Longevity and Ageing (Björn Schumacher)
The Impact of Chromatin Modifiers on Disease Development and Progression (Capucine van Rechem)
Long-Range Transcriptional Control by 3D Chromosome Structure (Luca Giorgetti)
Transgenerational Inheritance and Epigenetic Imprinting in Plants (Mary Gehring)
Create your
podcast in
minutes
It is Free
DNA Today: A Genetics Podcast
Museum of the Missing
Strange by Nature Podcast
Sasquatch Chronicles
Hidden Brain