acorde unravels functionally interpretable networks of isoform co-usage from single cell data

Angeles Arzalluz-Luque, Pedro Salguero, Sonia Tarazona () and Ana Conesa ()
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Angeles Arzalluz-Luque: Universitat Politècnica de València
Pedro Salguero: Universitat Politècnica de València
Sonia Tarazona: Universitat Politècnica de València
Ana Conesa: Spanish National Research Council

Nature Communications, 2022, vol. 13, issue 1, 1-18

Abstract: Abstract Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to modulate isoform expression within genes and contribute to cell-type identity. However, the extent to which alternative isoforms establish co-expression networks that may be relevant in cellular function has not been explored yet. Here, we present acorde, a pipeline that successfully leverages bulk long reads and single-cell data to confidently detect alternative isoform co-expression relationships. To achieve this, we develop and validate percentile correlations, an innovative approach that overcomes data sparsity and yields accurate co-expression estimates from single-cell data. Next, acorde uses correlations to cluster co-expressed isoforms into a network, unraveling cell type-specific alternative isoform usage patterns. By selecting same-gene isoforms between these clusters, we subsequently detect and characterize genes with co-differential isoform usage (coDIU) across cell types. Finally, we predict functional elements from long read-defined isoforms and provide insight into biological processes, motifs, and domains potentially controlled by the coordination of post-transcriptional regulation. The code for acorde is available at https://github.com/ConesaLab/acorde .

Date: 2022
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DOI: 10.1038/s41467-022-29497-w

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