SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

By C. González-Blas, S. De Winter, Gert J. Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, S. Poovathingal, J. Wouters, S. Aibar, S. Aerts. bioRxiv, 2022

562 citations recorded by the source corpus.

SCENIC+ is a comprehensive toolbox for inferring and analyzing enhancer-driven gene regulatory networks using single-cell multiomic data. Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/abe9998e249e33005981b23b97929dddb246b288

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In Molecular Biology

1. R. Argelaguet
2. J. Sáez-Rodríguez
3. Zhiliang Bai
4. Rong Fan
5. Alev Baysoy
6. Rahul Satija
7. Fabian J Theis

Citations in the corpus

• Gene regulatory network inference in the era of single-cell multi-omics (2023, methodology): “ANANSE 84 , sc-compReg 85 and SCENIC+ 67 build Box 1”
• The technological landscape and applications of single-cell multi-omics (2023, background): “include SCENIC+ 176 , functional inference of gene regulation (FigR) 177 , and probabilistic multimodal models for integrated regulatory analysis (MIRA) 178 , which model joint variation across paired transcriptomic and scATAC-seq measurements to link enhancers to genes and to identify…”