Jop Kind Group

Spatiotemporal regulation of genomic function

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Our Focus

Epigenetics plays a crucial role in the priming, consolidation and maintenance of transcriptional programs. In our lab, we develop and implement single-cell genomics methods to obtain better insight into the epigenetic mechanisms that govern cellular decision making in early mammalian development and in cancer.   

  

Specifically, we are interested to understand what the role of spatial genome positioning and epigenetics is in gene regulation during mouse development, and understand how different layers of genome organization collectively coordinate and achieve precise spatiotemporal gene expression programs. To this end, we focus on developing technologies that are capable of measuring many of such features simultaneously in single cells.   

  

Secondly, we harness the power of the single-cell technologies, developed in our group, to advance our understanding of the role of epigenetics in tumorigenesis, and, in addition, develop new strategies for improved diagnostic applications.   

About Jop Kind

My Research

Jop Kind received his PhD from the Radboud University Nijmegen in 2008 for his work on chromatin and gene expression performed at the EMBL Heidelberg. He subsequently joined the Netherlands Cancer Institute for his postdoctoral training, where he developed novel methods to study nuclear organization in individual cells. For this work he received the prestigious Antoni van Leeuwenhoek (NKI) and John Kendrew awards (EMBL). In October 2014, he established his research group at the Hubrecht Institute and became a senior group leader in 2019 and a professor of single cell epigenomics at the Radboud University in 2021. His research is supported by an ERC Starting (2016) and Consolidator grant (2021) a NWO Vidi (2016) and his group is a member of two recent consortia grants NWO-PSIDER (2021) and NWO-XL (2022).

Awards
  • 2016: Sir John Kendrew Award

  • 2015: Antoni van Leeuwenhoek Award

Key Publications
  1. Rang FJ, de Luca KL, de Vries SS, Valdes-Quezada C, Boele E, Nguyen PD, Guerreiro I, Sato Y, Kimura H, BakkersJ, Kind J. Single-cell profiling of transcriptome and histone modifications with EpiDamID. Mol Cell. May19;82(10):1956-1970.e14 (2022).

  2. Rullens PMJ, Kind J.Attach and stretch: Emerging roles for genome-lamina contacts in shaping the 3Dgenome. Curr Opin Cell Biol. Jun;70:51-57 (2021).

  3. Markodimitraki CM, Rang F, Rooijers K, de Vries SS, Chialastri A, de Luca KL, Lochs SJA, Mooijman D, Dey SS and Kind J. Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells with scDam&T. Nature Protocols 15:1922-1952 (2020).

  4. Borsos M, Perricone SM, Schauer T, Pontabry J, de Luca KL, de Vries SS, Ruiz-Morales ER, Torres- Padilla ME and Kind J. Genome-lamina interactions are established de novo in the early mouse embryo. Nature 569:729-733 (2019).

  5. Rooijers K, Markodimitraki CM, Rang F, de Vries SS, Chialastri A, de Luca KL, Mooijman D, Dey SS and Kind J. Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells. Nature Biotechnology 37:766-772 (2019).

Members

Jop Kind
Oncode Investigator
Christian Valdes    
Post Doc
Franka Rang    
PostDoc
Hidde Verhage    
PhD student
Isabel Guerreiro    
Postdoc fellow
Isabel Sierra    
Post Doc
Kim de Luca    
PhD student
Marta Moreno Gonzalez    
PhD student
Moritz Bauer    
Post Doc
Pim Rullens    
PhD Student
Robin van der Weide    
Postdoc
Samy Kefalopoulou    
PhD student
Sandra de Vries    
Technician