Boyan Bonev

Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...

Code and data to reproduce all figures, or browse and reanalyze, is available at github.com/tanaylab/mmcortex, either separately or in a standalone docker container. You can also explore the data interactively at apps.tanaylab.com/MCV/mmcortex/. 13/14

Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...

We also show explicitly that NSC methylation has a repressive effect on IPC accessibility, and that cooperativity between proximal CREs is correlated with accessibility both in terms of sequence content and total proximal activation. 11/14

Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...

Moreover, temporally activating CREs in NSCs get compacted significantly closer over time to astrocyte- or NSC-specific TSSs, an effect not observed with IPC TSSs. 9/14

Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...

Temporally activating CREs are significant: they are enriched with astrocyte-specific CREs, and astro CREs undergo extensive demethylation within NSCs across time, in contrast to other cell type-specific CREs. 7/14

Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...

Furthermore, we were able to identify CREs with dynamic accessibility within cell types, across time. We focused on CREs that either activate/increase accessibility, or deactivate over time in NSCs. 5/14

Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...

We show that astrocyte genes in NSCs are upregulated gradually over time, not suddenly, along with erosion of NSC proliferative capacity. This erosion is also correlated with lengthening of the cell cycle, suggesting that NSC fate bias is coupled to the cell cycle. 3/14

Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...

🚨New preprint from @bonevlab.bsky.social 🚨: What are the key epigenetic mechanisms that drive species-specific gene regulation during primate neurogenesis - and how do they contribute to the evolution of the human neocortex? Here’s what we discovered 👇 www.biorxiv.org/content/10.1...

Overall, we systematically link 3D epigenome evolution to gene expression changes in the context of primate brain development. This integrative approach significantly advances our understanding of how divergent regulatory networks and epigenome dynamics contribute to human brain evolution

🚨New preprint from @bonevlab.bsky.social 🚨: What are the key epigenetic mechanisms that drive species-specific gene regulation during primate neurogenesis - and how do they contribute to the evolution of the human neocortex? Here’s what we discovered 👇 www.biorxiv.org/content/10.1...

High-resolution Hi-C revealed unexpected global shifts in 3D genome architecture in the chimpanzee and gorilla NSC, while topologically associating domains remained remarkably conserved. #3DGenome #HiC

🚨New preprint from @bonevlab.bsky.social 🚨: What are the key epigenetic mechanisms that drive species-specific gene regulation during primate neurogenesis - and how do they contribute to the evolution of the human neocortex? Here’s what we discovered 👇 www.biorxiv.org/content/10.1...

We also proposed the emergence of novel TF motifs and specific class of transposable elements - SVA, as one of the key drivers of species- and cell type-specific chromatin accessibility — linking DNA sequence to epigenome evolution.

🚨New preprint from @bonevlab.bsky.social 🚨: What are the key epigenetic mechanisms that drive species-specific gene regulation during primate neurogenesis - and how do they contribute to the evolution of the human neocortex? Here’s what we discovered 👇 www.biorxiv.org/content/10.1...

We have generated one of the most comprehensive datasets of primate epigenome evolution to date — profiling and integrating genome-wide 3D genome organization, chromatin accessibility and gene expression in human, chimpanzee, gorilla and macaque IPSC and neural stem cells (NSC).