3D-omics

We work on the functional roles of three-dimensional (3D) chromosomal architecture. To show that 3D-chromosome folding is much more than packing of long chromosomes into tiny nuclei, we are using both, state-of-the-art molecular techniques such as Hi-C and classic genetics approaches.
Our interest focuses on the interplay of the different genome organization levels, especially the relationship between the 3D-genome and the two other organizational levels, the DNA sequence and the epigenome. We are intrigued by the possibility that 3D-chromatin folding may contain information and, hence, may exert an important biological function in both, micro-scale cellular mechanisms and, macro-scale evolution.
As for micro-scale processes, a specific 3D-chromatin structure, termed the KNOT is involved in the genome’s immune system. The KNOT is formed by tight 3D contacts among ten KNOT Entangled Elements (KEEs), which are enriched in both transposable elements and associated small RNAs. Our current research aims at investigating the underlying mechanisms required to form the KNOT. Thereby, we expect to reveal important factors regulating 3D-genome architecture.

Recent Publications

  • Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies
    Zhang, L; Cai, X; Wu, J; Liu, M; Grob, S; Cheng, F; Liang, JL; Cai, CC; Liu, ZY; Liu, B; Wang, F; Li, S; Liu, FY; Li, XM; Cheng, L; Yang, WC; Li, MH; Grossniklaus, U; Zheng, HK; Wang, XWHORTICULTURE RESEARCH, 5 10.1038/s41438-018-0071-9 AUG 15 2018
  • Technical Review: A Hitchhiker's Guide to Chromosome Conformation Capture.
    Grob S, Cavalli G.
    Methods Mol Biol. 2018;1675:233-246. 10.1007/978-1-4939-7318-7_14.
  • Plants are not so different
    Grob, Stefan
    Nat Plants. 2017 Sep;3(9):690-691. 10.1038/s41477-017-0013-9.
  • Circular Chromosome Conformation Capture in Plants.
    Grob S.
    Methods Mol Biol. 2017;1610:73-92. doi: 10.1007/978-1-4939-7003-2_6.
  • Chromosome conformation capture-based studies reveal novel features of plant nuclear architecture.
    Grob S, Grossniklaus U.
    Curr Opin Plant Biol. 36:149-157. doi: 10.1016/j.pbi.2017.03.004. Epub 2017 Apr 12. Review.
  • Chromatin Conformation Capture-Based Analysis of Nuclear Architecture.
    Grob S, Grossniklaus U.
    Methods Mol Biol. 2017;1456:15-32.
  • HiCdat: a fast and easy-to-use Hi-C data analysis tool.
    Schmid MW, Grob S, Grossniklaus U.
    BMC Bioinformatics. 2015 Sep 3;16:277. doi: 10.1186/s12859-015-0678-x.
Stefan Grob Uni Zurich

Dr. Stefan Grob
University of Zurich
Department of Plant and Microbial Biology
8008 Zurich

Tel: +41 44 644 8250

Research topics

  • Epigenetics
  • Gene silencing
  • Defense against parasitic DNA elements
  • 3D chromosome architecture
  • Genome evolution

Interdisciplinary

  • Genome evolution
  • Genome assemblies
  • Analysis of -omics data
  • Transcriptional regulation by 3D contacts, such as promoter-enhancer contacts