GROUP LEADER: Thomas Graf (Senior Scientist)

POSTDOCTORAL FELLOWS: Jose Luis Sardina (Juan de la Cierva), Tian Tian (Juan de la Cierva), Gregoire Stik (Marie Curie), Sergi Cuartero (CRG, joined September 2018)

PhD STUDENTS: Guillem Torcal (Severo Ochoa), Marcos Plana (FIB)

TECHNICIANS: Luisa de Andres (CRG), Clara Berenguer (Plan Nacional), Carolina Segura (ERC),

BIOINFORMATICIAN: Maria Vila (joined Feb. 2018)

SUMMARY

We study mechanisms of mammalian cell fate decisions by forced transcription factor (TF)expression to induce cell reprogramming of somatic cells. The rapid and efficient reprogramming system of B cells into induced pluripotent stem cells developed in our laboratory permitted us to explore in depth the mechanisms involved at various epigenetic levels. We found that active demethylation mediated by Tet2 occurs throughout the reprogramming process and that the enzyme can be recruited to the DNA by at least three different transcription factors. These studies further revealed that active Tet2 can be recruited in the absence of chromatin opening and that demethylation of key pluripotency TF enhancers and promoters occurs as rapid as 1 day. We also analysed reprogramming at the single cell level and compared it to transdifferentiation, showing asynchronies in the timing and path of these two processes. Deconvolution of the cell conversion trajectories predicted a heterogeneity in the starting population, that could be validated by cell sorting experiments. These revealed that Mychigh pre-B cells are fated for reprogramming while Myclow cells have a bias towards transdifferentiation, and thus that cell plasticity is cell-context dependent.

Summary of TFs recruit Tet2 to the DNA during induced cell conversions (see Sardina et al., 2018)

Fig.1

Summary of TFs recruit Tet2 to the DNA during induced cell conversions (see Sardina et al., 2018)

RESEARCH PROJECTS

  • Do lineage instructive transcription factors directly alter the 3D genome structure during reprogramming and transdifferentiation?
  • Is CTCF required for transdifferentiation induced by C/EBPa?
  • What is the role of C/EBPa in early development?

SELECTED PUBLICATIONS

Sardina JL, Collombet S, Tian T, Gómez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D and Graf T.
“Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate.”
Cell Stem Cell, 23:1-15, 2018.

Stik G and Graf T.
“Hoxb5, a Trojan horse to generate T cells.”
Nat Immunol, 19(3):210-212, 2018.

Gaidt MM, Rapino F, Graf T and Hornung V.
“Modeling Primary Human Monocytes with the Trans-Differentiation Cell Line BLaER1.”
Methods Mol Biol, 1714:57-66, 2018.

Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA and Graf T.
“Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.”
Nature Genetics, 50(2):238-249 (2018).