Function Determining Chromatin Self-Organization after Heregulin Stimulation

Duration of the project

01.02.2022. - 31.10.2022.

Countries and institutions involved in the project

Latvian Biomedical Research and Study Centre
University of Heidelberg

Aims of the project

The cell nucleus, a complex system consisting of chromatin with flexibility, proteins and RNAs exists by self‐organization thermodynamic principles. Under limited nucleus volume for 2m-long DNA, the increase of complexity and entropy requires chromatin networks and cluster formations which have not been studied under this physical lens. A working hypothesis formulated by us in 2001 lies at the base of the current project. Such supra-chromosomal networks are mediated by retrotransposons ALU and LINE1 which control molecular trafficking and DNA accessibility. Our article in 2001 has shown that the constitutive pericentromere-associated domains rearrange at certain time points after treatment of cancer cells with Heregulin, inducing differentiation; enabling a transcription avalanche starting of differentiation.

The re(organisation) of networks focusing in particular on retrotransposons during differentiation will be investigated in the breast cancer cell line MCF-7. Networks fluorescence labelled by antibodies or oligonucleotide-FISH will be subjected to confocal microscopy and single molecule localization microscopy. The topologic network dynamics will be analysed by quantitative image analysis and mathematics of point geometries (Ripley statistics). Transcription of transposons, c-FOS, nc-RNA will be correlated by qPCR to chromatin dynamics. At the symposium the obtained data and outlining hypothesis will be discussed with specialists, also useful for students.

Main activities

  1. The initial activity includes MCF-7 cell culturing, specimen preparation, antibody labelling, oligonucleotide FISH (Riga + Heidelberg).
  2. Furthermore, it is followed by ncRNA transcription analysis, qPCR, molecular biology, fluorescence microscopy and image analysis which will take place in Riga.
  3. A super-resolution single molecule localization microscopy, cluster analysis by Ripley distance frequency statistics, geometric analysis of pointillist pattern, topological analysis will be organized in the city of Heidelberg.
  4. Additionally, exchange visits to Riga and Heidelberg will be held
  5. As well as a joint publication.

Direct and indirect target groups

Direct: Undergraduate and graduate students and group members supervised by Dr. Erenpreisa and Prof. Hausmann (~ 10 people)

Indirect: Latvian students and scientists visiting the symposium (~ 20 people); scientific community reading the publication of the project results (~ 10-20 citations)