Practical Course HP-F7: Transcriptional and Translational Control of Cell Fate

Type: Practical Course with Student Seminars


Date: 8.-26. February 2021; Location: DKFZ Teaching Lab

Michaela Frye (responsible organizer contact:, Fabricio Loayza-Puch, (contact:, Moritz Mall (contact:, Duncan Odom (contact:


Stem cells differentiate into all mammalian organs during development, and remain present to maintain and replenish the tissues throughout life. Stem cells continuously maintain their population (self-renewal) while generating progeny (differentiation). Tissue-specific transcriptional and chromatin-modifying networks that define the self-renewing or differentiated cell states are now well-defined. However, how these networks interact and dynamically change to establish a new cell identity during stem cell differentiation is largely unknown. Similar to normal tissues, a tumour also contains functionally and phenotypically different cell populations. The heterogenous cell populations are not equally tumourigenic. Some cancer cells are more differentiated with a limited or no tumorigenic potential. Others, potentially even rare tumour populations, exhibit stem cell-like features that drive tumourigenesis, long-term survival, and therapy resistance. Understanding the transcriptional and translational regulatory mechanisms that govern cell fate changes is important because they offer novel therapeutic strategies to steer cell differentiation into distinct lineage, such as a tumour-initating cell into a differentiated non-tumourigenic cell for instance. Aim of this course is to provide an overview how transcriptional and translational mechanisms that govern cell fate changes can be studied.

part 1: Engineering of cell fate

Hosts/Supervisors: Bhuvaneswari Nagarajan, Sarah Grieder and Moritz Mall (contact:



The fate and function of a cell is changing during development and disease. It is even possible to "rejuvenate" adult cells by reprogramming them into embryonic-like stem cells, which in turn can be differentiated into every tissue and cell type of the human body. Scientists can also "reprogram" cells directly from one type to another, i.e. convert skin cells into neurons. These possibilities to engineer cell fate have key implications for biomedical research: (1) Skin or blood cells from patients can be converted to disease relevant cell types such as neurons to study disease and test drugs in a personalized manner. (2) Cell fate and genome engineering can be applied to generate cells or tissues to model disease or replace lost or damaged cells in patients. Here, we will engineer neuronal cells from stem cells by introducing neuron-specific transcription factors using lentiviral vectors.


  • Human embryonic stem cell culture
  • Virus production and infection
  • Neuronal cell fate programming
  • Immunofluorescence microscopy

part 2: Determining translation during cell fate decisions

Hosts/Supervisors: Daniela Avilés Huerta, Fabricio Loayza-Puch and Michaela Frye (contact:;



Until recently, the composition of the cellular proteome was thought to strictly adhere to the genetic code. However, accumulating evidence shows that cells also regulate gene expression by directly modulating protein synthesis machinery. Several cellular process can change gene-specific protein levels or produce protein quantities independent of the nuclear encoded information. (1) Ribosome or tRNA mis-decoding can cause the production of mutant proteins. (2) Optimal codon content in specific mRNAs can enhance mRNA stability and translation. (3) RNA modifications can enhance or repress protein synthesis. The uncoupling of mRNA translation from genetically encoded information generally occurs when cells undergo environmental adaptation or are stressed. For instance, tumour cells are consistently exposed to a changing and often hostile micro-environment, due to shortage of oxygen and nutrients or exposure to cancer drugs. A dependency on the protein synthesis machinery to switch cell fates, for example from a proliferating tumour cell to a quiescent tumour-initiating cell in response to chemotherapy, may represent a window of opportunity to specifically target tumour-initating or resistant cell populations.



  • Ribosome profiling
  • Quantification of de novo protein synthesis
  • FACS
  • Immunofluorescence

part 3: High efficiency genome-wide profiling in low numbers of cells

Hosts/Supervisors: Duncan Odom (contact:



Transcription factors have critical roles in the maintenance of stem cells because they determine the stem cell-specific gene expression program. Deciphering the transcriptional regulatory networks that determines the specific interaction between transcription factors and with the genome is critical for our understanding how cell fate is established and maintained. The best-characterized stem cell systems are mouse and human embryo-derived pluripotent stem cells because they can be readily cultured as self-renewing or differentiated cells in defined media and in large quantities. However, the number of tissue-specific stem cells or highly tumourigenic cells in vivo can be very low. While advanced sequencing methods now allow transcriptome profiling in single cells, determining genome-wide binding of transcription factors or chromatin remodelers in low number of cells remains challenging. Here, we will discuss the advantages and disadvantages of novel sequencing technics designed for low number of cells.



  • CUT & RUN
  • Library generation
  • A practical approach to ‘How to generate figures’ and ‘how to write manuscripts’

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