TY  - JOUR
A1  - Rosales-Alvarez, Reyna Edith
A1  - Rettkowski, Jasmin
A1  - Herman, Josip Stefan
A1  - Dumbović, Gabrijela
A1  - Cabezas-Wallscheid, Nina
A1  - Grün, Dominic
T1  - VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells
JF  - Genome Biology
N2  - Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential driving force of cellular differentiation. Utilizing single-cell RNA-sequencing, we develop VarID2 for the quantification of biological noise at single-cell resolution. VarID2 reveals enhanced nuclear versus cytoplasmic noise, and distinct regulatory modes stratified by correlation between noise, expression, and chromatin accessibility. Noise levels are minimal in murine hematopoietic stem cells (HSCs) and increase during differentiation and ageing. Differential noise identifies myeloid-biased Dlk1+ long-term HSCs in aged mice with enhanced quiescence and self-renewal capacity. VarID2 reveals noise dynamics invisible to conventional single-cell transcriptome analysis.
KW  - gene expression noise
KW  - single-cell RNA sequencing
KW  - stem cell differentiation
KW  - cell sate variability
KW  - ageing
KW  - hematopoietic stem cells
KW  - machine learning
KW  - mathematical modeling
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-358042
VL  - 24
ER  - 
TY  - JOUR
A1  - Scognamiglio, Roberta
A1  - Cabezas-Wallscheid, Nina
A1  - Thier, Marc Christian
A1  - Altamura, Sandro
A1  - Reyes, Alejandro
A1  - Prendergast, Áine M.
A1  - Baumgärtner, Daniel
A1  - Carnevalli, Larissa S.
A1  - Atzberger, Ann
A1  - Haas, Simon
A1  - von Paleske, Lisa
A1  - Boroviak, Thorsten
A1  - Wörsdörfer, Philipp
A1  - Essers, Marieke A. G.
A1  - Kloz, Ulrich
A1  - Eisenman, Robert N.
A1  - Edenhofer, Frank
A1  - Bertone, Paul
A1  - Huber, Wolfgang
A1  - van der Hoeven, Franciscus
A1  - Smith, Austin
A1  - Trumpp, Andreas
T1  - Myc depletion induces a pluripotent dormant state mimicking diapause
JF  - Cell
N2  - Mouse embryonic stem cells (ESCs) are maintained in a naive ground state of pluripotency in the presence of MEK and GSK3 inhibitors. Here, we show that ground-state ESCs express low Myc levels. Deletion of both c-myc and N-myc (dKO) or pharmacological inhibition of Myc activity strongly decreases transcription, splicing, and protein synthesis, leading to proliferation arrest. This process is reversible and occurs without affecting pluripotency, suggesting that Myc-depleted stem cells enter a state of dormancy similar to embryonic diapause. Indeed, c-Myc is depleted in diapaused blastocysts, and the differential expression signatures of dKO ESCs and diapaused epiblasts are remarkably similar. Following Myc inhibition, pre-implantation blastocysts enter biosynthetic dormancy but can progress through their normal developmental program after transfer into pseudo-pregnant recipients. Our study shows that Myc controls the biosynthetic machinery of stem cells without affecting their potency, thus regulating their entry and exit from the dormant state.
KW  - hematopoietic stem cells
KW  - leukemia inhibitory factor
KW  - c-Myc
KW  - N-Myc
KW  - gene expression
KW  - embryonic stem cells
KW  - self-renewal
KW  - protein synthesis
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-190868
VL  - 164
IS  - 4
ER  -