Integrative multi-omics uncovers skeletal muscle enhancer programming of cardiorespiratory fitness

This repository contains the processed data for the manuscript entitled, "Integrative multi-omics shows skeletal muscle enhancers encode cardiorespiratory fitness." These files include results from RNA-Seq, ATAC-Seq, and CUT&Tag data generated from analysis of skeletal muscle tissue collected from HCR/LCR gastrocnemius. All genomic coordinates are based on the rn7 rat reference genome. A description of all included files is provided below, categorized by analysis type.

HCR/LCR Analysis

Differential Analysis

These files with the prefix deseq-results_ contain the DESeq output for the HCR/LCR differential analysis. Positive Log2FoldChange values are associated with HCR up features, and negative with LCR up features. 

deseq-results_H3K27me3.txt

deseq-results_H3K27ac.txt

deseq-results_H3K4me1.txt

deseq-results_H3K4me3.txt

deseq-results_H3K36me3.txt

deseq-results_ATACSeq.txt

deseq-results_RNASeq.txt

pathway-enrichment_RNA-Enrich.txtDifferential gene expression pathway enrichment (RNA-Enrich) results.

Nearest-TSS Pathway Enrichment

pathway-enrichment_ChIP-Enrich-nearest-tss.txtPathway results from all epigenomic trials, when peaks were annotated to the gene with the nearest transcription start site.

pathway-enrichment_Figure2F_clustered-results.txtGene sets included in the heatmap that shows the reduced pathways in comparison to RNA-Seq and additional epigenomic modalities. This table includes representative cluster-to-child term pairs. These results were used to generate Figure 2F in the manuscript.

Peak-to-Gene Correlation Analysis

Pk2Gene-links_significant-results.txtSignificant correlation links generated from the peak-to-peak-to-gene framework. These links are used to identify target genes of epigenomic peaks of interest.

pathway-enrichment_ranked-gsea_Pk2G-link-ranked-by-correlation-significance.txtPathway enrichment results probing Pk2G target genes of differential peaks, ranked by the significance of their correlation with the peak. The analysis was carried out four separate times for each direction of change (HCR up & LCR up), and Pk2G direction of relationship (positive & negative). These results were used to generate Figure 3C in the manuscript. This file includes the representative cluster information included in the figure.

Motif Enrichment

reference-ensembl-gene-info.txtThis file contains information about genes that are expressed in the HCR/LCR skeletal muscle including 1:1 Ensembl-to-gene symbol matching used in this paper. Additional details include extended gene names, and details regarding transcription factor status and family assignments based on the Animal Transcription Factor Database v4, as described in the manuscript. This file is provided to facilitate replication of the Ensembl-gene symbol pairing used in the analyses and background of transcription factor classification used to guide the motif enrichment analysis.

reference-motif-metadata.txtReference table for motifs used in this analysis, including internal IDs used between files within this repo (motif_id, dir_name), the source database identifying information to allow for motif lookup externally (data_source, altname), and motif information (ensembl, symbol).

fst_hcr-lcr.txtFST values calculated from the reference allele frequencies of each line, provided in the “HCR” and “LCR” columns. This information was used as an inclusion criteria for the allele-specific motif enrichment criteria.

differential-motif-enrichment_global.txt

pathway-enrichment_over-representation_global-differential-motif_region-gene-input.txtRegion -> target gene pairs used for pathway enrichment input for the comparison of HCR up vs LCR up regions.

pathway-enrichment_over-representation_global-differential-motif.txtOver-representation analysis of Pk2G targets of peaks that contribute to the differential motif enrichment when comparing HCR up peaks to LCR up peaks, stratified by motif, modality, direction of change between HCR/LCR, and direction of relationship with the target gene. These results were used to generate Figure 4C-D in the manuscript, in which only gene sets included in that heatmap are provided in this table (FDR < 0.05 in at least one trial where > 1 gene resulted in the pathway).

differential-motif-enrichment_allele-specific.txtdifferential_motif-enrichment_allele-specific_disrupted-motifs.txt

pathway-enrichment_over-representation_broken-motif.txtOver-representation analysis of Pk2G targets of peaks containing broken motifs. These results were used to generate Figure 5H.

Validation Study in F2 Population

f2_caQTL.txtSignificant results from caQTL analysis (most significant variant-feature relationship returns FDR < 0.05), including variants with an LD r^2 > 0.5 to the most significant variant for each eGene or caVariant. Due to LD, there may be multiple variants that return the same strength and significance of relationship with the feature. The effect allele is designated as the HCR dominant allele, if that variant is present in the HCR/LCR analysis. The LD_r2 column provides the r^2 value of the remaining variants to the variant that is most significantly related to the feature. The af column is the allele frequency of the effect allele. The beta column is the strength and direction of relationship between the allele and gene expression or chromatin accessibility. The p_wald_rank column indicates the dense rank order of variant significance for each feature. The variant(s) with the most significant relationship with the feature have a p_wald_rank == 1. Additional column definitions:

variant_id: chromosome:position of variant

af: allele frequency

se: beta standard error

logl_H1: Log likelihood under the alternative hypothesis (doesn't seem to be defined in manual, but mentioned in this GitHub issue: https://github.com/genetics-statistics/GEMMA/issues/81)

l_remle: Restricted maximum likelihood estimate for lambda

p_wald: p value (nominal p-value, i.e. no multiple correction of any kind)

gene_id: ATAC peak

f2_eQTL.txtF2 eQTL results with the same preparation and column assignments as the caQTL results, except for the gene_id column is the Ensembl gene ID

validation_f2-caQTL_hcr-lcr-peak-deseq_overlaps.txt Orthogonal overlap of variant effect on chromatin accessibility/histone modifications, joined by overlapping HCR/LCR and F2 peaks. This table is associated with Figure 6D in the manuscript.

validation_f2-eQTL_hcr-lcr-rnaseq-deseq_overlaps.txt: Orthogonal overlap of variant effect on gene expression, joined by gene_id. This table is associated with Figure 6E in the manuscript.

validation_f2-eQTL_hcr-lcr-Pk2G-correlation_overlaps.txt: Orthogonal overlap of variant effect on gene expression and the Pk2G links identified in the HCR/LCR analysis. This table is associated with Figure 6F in the manuscript.