274-OR: Population-Scale Single-Nucleus Skeletal Muscle Chromatin Dynamics and Nucleosome Positioning in the Context of Type 2 Diabetes

Motivation: Insulin resistance in skeletal muscle plays a central role in the development of type 2 diabetes (T2D). T2D genome-wide association studies (GWAS) have nominated > 600 signals potentially linked to cell type-specific regulatory processes, with most lying in the non-coding region. Studying the genetic regulation of local chromatin patterns in muscle fibers can provide mechanistic insights into T2D GWAS hits. Here, we employ population-scale single-nucleus ATAC-sequencing (snATAC) to better understand T2D mechanisms.

Methods: Leveraging snATAC profiles from 281 individuals, we used statistical models to infer nucleosome positioning and nucleosome-free regions (NFR). We then combined genetic variation with chromatin accessibility patterns to identify cis-quantitative trait loci (QTL) for both NFR (nfrQTL) and nucleosome positioning (nucQTL) globally and at T2D-related trait GWAS signals.

Results: We identified 14,417 nfrQTLs and 19,265 nucQTLs (5% FDR) in type 1 muscle fibers. NfrQTLs were significantly enriched to overlap T2D and fasting insulin signals (P < 0.005). Colocalization analyses revealed that 5,890 pairs of nfr- and nucQTLs contained shared causal variants. Furthermore, mediation analyses revealed that at 765 pairs of colocalized nfr&nucQTLs, genetic variant(s) regulated the nucleosome positioning through NFRs and 65 pairs with the reverse direction (5% FDR). Notably, 25 nfrQTLs colocalized with T2D GWAS signals. Interestingly, signals at FARSA and PLEKHA1 colocalized with both nfr- and nucQTLs, and the nfrQTLs were causal on the nucQTLs. These findings imply that genetic variants in these GWAS signals regulate the NFR's position, which subsequently influences nucleosome positioning.

Conclusion: These results provide single-nucleus resolution mechanistic hypotheses for local chromatin dynamics in skeletal muscle, providing significant insights into T2D therapeutic strategies involving NFRs.