Characterization of cell-fate decision landscapes by estimating transcription factor dynamics

Jiménez, Sara; Schreiber, Valérie; Mercier, Reuben; Gradwohl, Gérard; Molina, Nacho

doi:10.1016/j.crmeth.2023.100512

Cited by 2 publications

(1 citation statement)

References 82 publications

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“…One of the strengths of SinCMat lies in its ability to predict functional maturation TFs from only the information on the target cell type without requiring any additional input. Nonetheless, we compared its performance with FateCompass, a tool that computes TF activity over time ( Jiménez et al., 2023 ), by using time-series datasets of maturing cells/organs. Interestingly, our results unveiled that TF activity over the cell maturation time course does not correlate with the concept of functional cell maturation considered in this study, supporting the need for a model that takes into account the co-binding property of ITFs/STFs.…”

Section: Resultsmentioning

confidence: 99%

SinCMat: A single-cell-based method for predicting functional maturation transcription factors

Barvaux,

Okawa,

del Sol

2024

Stem Cell Reports

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Section: Resultsmentioning

confidence: 99%

SinCMat: A single-cell-based method for predicting functional maturation transcription factors

Barvaux,

Okawa,

del Sol

2024

Stem Cell Reports

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Synergistic DNA and RNA binding of the Hox transcription factor Ultrabithorax coordinates splicing and shapesin vivohomeotic functions

Blanco,

Xiang,

Boumpas

et al. 2024

Preprint

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The dual interaction of many transcription factors (TFs) with both DNA and RNA is an underexplored issue that could fundamentally reshape our understanding of gene regulation. We address this central issue by investigating the RNA binding activity of the Drosophila Hox TF Ultrabithorax (Ubx) in alternative splicing and morphogenesis. Relying on molecular and genetic interactions, we uncover a homodimerization-dependent mechanism by which Ubx regulates splicing. Notably, this mechanism enables the decoupling of Ubx-DNA and -RNA binding activity in splicing. We identify a critical residue for Ubx-RNA binding and demonstrate the essential role of Ubx-RNA binding ability for its homeotic functions. Overall, we uncover a unique mechanism for Ubx-mediated splicing and underscore the critical contribution of synergistic DNA/RNA binding for its morphogenetic functions. These findings advance our understanding of co-transcriptional regulation and highlight the significance of TF-DNA/RNA synergistic function in shaping gene regulatory networks in living organisms.

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Characterization of cell-fate decision landscapes by estimating transcription factor dynamics

Cited by 2 publications

References 82 publications

SinCMat: A single-cell-based method for predicting functional maturation transcription factors

SinCMat: A single-cell-based method for predicting functional maturation transcription factors

Synergistic DNA and RNA binding of the Hox transcription factor Ultrabithorax coordinates splicing and shapesin vivohomeotic functions

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