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1.
Proc Natl Acad Sci U S A ; 120(4): e2213810120, 2023 Jan 24.
Article in English | MEDLINE | ID: mdl-36669113

ABSTRACT

Reactivation of the inactive X chromosome is a hallmark epigenetic event during reprogramming of mouse female somatic cells to induced pluripotent stem cells (iPSCs). This involves global structural remodeling from a condensed, heterochromatic into an open, euchromatic state, thereby changing a transcriptionally inactive into an active chromosome. Despite recent advances, very little is currently known about the molecular players mediating this process and how this relates to iPSC-reprogramming in general. To gain more insight, here we perform a RNAi-based knockdown screen during iPSC-reprogramming of mouse fibroblasts. We discover factors important for X chromosome reactivation (XCR) and iPSC-reprogramming. Among those, we identify the cohesin complex member SMC1a as a key molecule with a specific function in XCR, as its knockdown greatly affects XCR without interfering with iPSC-reprogramming. Using super-resolution microscopy, we find SMC1a to be preferentially enriched on the active compared with the inactive X chromosome and that SMC1a is critical for the decompacted state of the active X. Specifically, depletion of SMC1a leads to contraction of the active X both in differentiated and in pluripotent cells, where it normally is in its most open state. In summary, we reveal cohesin as a key factor for remodeling of the X chromosome from an inactive to an active structure and that this is a critical step for XCR during iPSC-reprogramming.


Subject(s)
Induced Pluripotent Stem Cells , Female , Animals , Mice , Cellular Reprogramming , X Chromosome Inactivation/genetics , X Chromosome/genetics , Chromosome Structures , Cohesins
2.
PLoS Comput Biol ; 17(11): e1009582, 2021 11.
Article in English | MEDLINE | ID: mdl-34762642

ABSTRACT

Isogenic cells cultured together show heterogeneity in their proliferation rate. To determine the differences between fast and slow-proliferating cells, we developed a method to sort cells by proliferation rate, and performed RNA-seq on slow and fast proliferating subpopulations of pluripotent mouse embryonic stem cells (mESCs) and mouse fibroblasts. We found that slowly proliferating mESCs have a more naïve pluripotent character. We identified an evolutionarily conserved proliferation-correlated transcriptomic signature that is common to all eukaryotes: fast cells have higher expression of genes for protein synthesis and protein degradation. This signature accurately predicted growth rate in yeast and cancer cells, and identified lineage-specific proliferation dynamics during development, using C. elegans scRNA-seq data. In contrast, sorting by mitochondria membrane potential revealed a highly cell-type specific mitochondria-state related transcriptome. mESCs with hyperpolarized mitochondria are fast proliferating, while the opposite is true for fibroblasts. The mitochondrial electron transport chain inhibitor antimycin affected slow and fast subpopulations differently. While a major transcriptional-signature associated with cell-to-cell heterogeneity in proliferation is conserved, the metabolic and energetic dependency of cell proliferation is cell-type specific.


Subject(s)
Cell Lineage , Mouse Embryonic Stem Cells/cytology , Pluripotent Stem Cells/cytology , Animals , Cell Proliferation , Gene Expression Regulation, Developmental , Membrane Potential, Mitochondrial/physiology , Mice , Mouse Embryonic Stem Cells/metabolism , Pluripotent Stem Cells/metabolism , Sequence Analysis, RNA/methods , Transcriptome
3.
Nat Chem Biol ; 11(4): 280-6, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25751279

ABSTRACT

Upon binding, ligands can chaperone their protein targets by preventing them from misfolding and aggregating. Thus, an organic molecule that works as folding chaperone for a protein might be its specific ligand, and, similarly, the chaperone potential could represent an alternative readout in a molecular screening campaign toward the identification of new hits. Here we show that small molecules selected for acting as pharmacological chaperones on a misfolded mutant of the Frizzled4 (Fz4) receptor bind and modulate wild-type Fz4, representing what are to our knowledge the first organic ligands of this until-now-undruggable GPCR. The novelty and the advantages of the screening platform, the allosteric binding site addressed by these new ligands and the mechanism they use to modulate Fz4 suggest new avenues for development of inhibitors of the Wnt-ß-catenin pathway and for drug discovery.


Subject(s)
Frizzled Receptors/chemistry , Molecular Chaperones/chemistry , Allosteric Site , Amino Acid Motifs , Base Sequence , Cell Line, Tumor , Chemistry, Pharmaceutical/methods , Dose-Response Relationship, Drug , Drug Design , Glycerol/chemistry , HEK293 Cells , HeLa Cells , Humans , Ligands , Microscopy, Fluorescence , Molecular Sequence Data , Mutagenesis , Protein Binding , Protein Folding , Receptors, G-Protein-Coupled/chemistry
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