Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors.
Cell Syst
; 15(5): 462-474.e5, 2024 May 15.
Article
en En
| MEDLINE
| ID: mdl-38754366
ABSTRACT
Single-cell expression dynamics, from differentiation trajectories or RNA velocity, have the potential to reveal causal links between transcription factors (TFs) and their target genes in gene regulatory networks (GRNs). However, existing methods either overlook these expression dynamics or necessitate that cells be ordered along a linear pseudotemporal axis, which is incompatible with branching trajectories. We introduce Velorama, an approach to causal GRN inference that represents single-cell differentiation dynamics as a directed acyclic graph of cells, constructed from pseudotime or RNA velocity measurements. Additionally, Velorama enables the estimation of the speed at which TFs influence target genes. Applying Velorama, we uncover evidence that the speed of a TF's interactions is tied to its regulatory function. For human corticogenesis, we find that slow TFs are linked to gliomas, while fast TFs are associated with neuropsychiatric diseases. We expect Velorama to become a critical part of the RNA velocity toolkit for investigating the causal drivers of differentiation and disease.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Factores de Transcripción
/
ARN
/
Diferenciación Celular
/
Redes Reguladoras de Genes
Límite:
Humans
Idioma:
En
Revista:
Cell Syst
Año:
2024
Tipo del documento:
Article