More than 600 distinct skeletal muscles constitute up to 40% of the total mass of the human body. They differ in anatomical position, origin, and function, but the diversity of muscle molecular phenotypes remains poorly explored.
Here, we present FANTOMUS, a large-scale molecular atlas of human skeletal muscles. To construct FANTOMUS, we performed cap analysis of gene expression (CAGE-Seq) using 222 autopsy samples of 75 skeletal muscles from 4 individuals, complemented by 22 matched proteomes obtained with mass spectrometry. As a result, we identified 37001 transcribed regulatory elements (TREs), including promoters of 18329 genes, and estimated the abundance of 1804 protein groups encompassing 1895 proteins.
Differential expression analysis revealed that more than 80% of genes and proteins are non-uniformly expressed across different muscles, with the most distinct molecular profiles found in extraocular muscles, tongue, and diaphragm. In particular, we observed a significant differential expression of FKRP, whose mutations cause dystroglycanopathy, between the leg muscles having different susceptibility to this disease.
Next, we performed motif activity response analysis of FANTOMUS CAGE-Seq data and detected motifs of hundreds of transcription factors with tissue-specific activity. Finally, by analyzing the allelic imbalance of CAGE-Seq reads, we discovered 6653 allele-specific single-nucleotide variants marking TREs with allele-specific activity. These SNPs often coincided with eQTLs and muscle-related GWAS SNPs, including muscle volume.
All in all, we created a detailed resource of transcriptomic and proteomic molecular profiles of diverse human skeletal muscles, facilitating further studies of gene regulation and heritable pathologies of these tissues: https://fantomus.autosome.org.

Co-authors: Daniil Popov, Oleg Gusev, Ivan Kulakovskiy