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Seminar May 2023

Published on 22 May 2023

Start Monday May 22nd at 4pm (Berlin/Paris time)

(3 pm London/Lisbon, 10am New-York, 7am San Francisco, 5pm Tel Aviv)

Link to the Zoom conference:

Link to the YouTube stream: Useful to check starting time in your time zone

Main Speaker: Daniel Cifuentes, Assistant professor, Department of Biochemistry, Boston University School of Medicine, Boston, USA

Title: Single-cell transcriptomics reveal two distinct modes of action of microRNAs during hematopoietic stem cell differentiation


microRNAs (miRNAs), a family of small non-coding RNAs, repress the expression of their target mRNAs. In turn, this microRNA-mediated repression is embedded in the larger framework of the transcriptional program of the cell, which regulates the expression of both the miRNA and its targets. In differentiated tissues, it was reported that miRNAs and the transcriptional program tend to work in concert to repress the expression of the target mRNAs. However, it is not known if this coherent mode of action between miRNAs and the transcriptional program is maintained in non-steady state situations like cell differentiation. Here we use single cell transcriptomics (scRNA-Seq) to analyze if miRNAs maintain a coherent mode of action with the transcriptional program during differentiation of hematopoietic stem cells in zebrafish. We demonstrate that miRNAs play a fundamental role ensuring a robust and efficient transit through the transcriptional landscape continuum of hematopoietic differentiation.

Our analysis of blood marrow from wild-type or miR-451, miR-144 and Ago2 mutant zebrafish shows that cells in the erythrocyte lineage devoid of these miRNAs display an intermediate transcriptional program and are more transcriptionally diverse that wild-type counterparts. Moreover, pseudo-time analysis demonstrates that miRNA-mediated regulation acts in concert with the transcriptional regulation of their targets in the continuum of non-steady states of differentiation occurring in hematopoiesis. However, the magnitude of microRNA-mediated repression is larger at the initial stages of differentiation. At later stages, the transcriptional program takes over the control of target mRNA expression. In both cases, we observe a coherent mode of action between miRNA and transcriptional program, as it was described for steady state situations, except that now pseudo-time analysis allows us to see that one program dominates more than other depending on how far along the differentiation path the cell is. Analysis of the Ago2 mutant fish, a proxy for a miRNA-null mutant, allows us to expand and confirm our findings to the neutrophil lineage.


Overall, our results provide a single-cell resolution view of how miRNAs reduce cell-to-cell transcriptional variability and efficiently resolve developmental transitions, highlighting the role of miRNAs as boosters rather than gate keepers of cell fate determination.

Short session speaker (8 minutes long): Viktoria Wagner

Title: Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues


Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specific ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs.

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