Computational & Genomics Lab studying 3D genome function and dynamics @ Netherlands Cancer Institute

Amsterdam, Netherlands
Joined August 2016
Finally we would congratulate @jonstewart with his return to the Daily Show!
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Our results establish ZNF143/ZFP143 as a conserved transcriptional regulator of cell proliferation and differentiation by safeguarding mitochondrial activity.
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Using an in vitro embryo model revealed that ZNF143 is key for proper multicellular organism development.
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But wait, there’s more!
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Are these mitochondria still functional? Hell, no! ZNF143 loss causes mitochondrial membrane depolarization, mimicking known mitochondrial dysfunction phenotypes.
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When we did live-cell imaging of mitochondria, we found that ZNF143 depletion changes mitochondrial morphology.
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What are the consequences for the cells? Well, their proliferation and differentiation capabilities are dramatically reduced.
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We found that ZNF143 binding sites are very conserved across human and mouse. ZNF143 binds to the promoters of many nuclear-encoded mitochondrial genes and its depletion results in their rapid and specific down-regulation at transcriptional and protein levels.
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So, ZNF143 was incorrectly associated with chromatin looping for almost a decade! What is ZNF143 doing then?
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How was it then picked up as a looping factor? By re-analysis of published ZNF143 occupancy data, we found that a commonly used antibody cross-reacts with CTCF.
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Nothing! Our results show that ZNF143 has no function in chromatin looping nor on CTCF binding.
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A decade ago, ZNF143 was found to bind with CTCF and suggested to be a looping factor. To study its direct role in chromatin looping, we generated a ZNF143 degron line in mouse embryonic stem cells.
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In conclusion, we find that in MRT MYC is epigenetically upregulated by distal elements that we call RhOMEs. We show that these elements are used in a patient-specific manner, adding another layer of complexity to tumorigenesis, namely intertumoral epigenetic heterogeneity.
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