Additional file 1 of Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns
Creators: name: Zhou, Yang
name: Liu, Shuli
name: Hu, Yan
name: Fang, Lingzhao
name: Gao, Yahui
name: Xia, Han
name: Schroeder, Steven G.
name: Rosen, Benjamin D.
name: Connor, Erin E.
name: Li, Cong-jun
name: Baldwin, Ransom L.
name: Cole, John B.
name: Van Tassell, Curtis P.
name: Yang, Liguo
name: Ma, Li
name: Liu, George E.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Comparison of methylation distribution between two different cattle genome reference assemblies using a sperm sample as an example. Blue line: UMD3.1.1; Green line: ARS-UCD1.2, from top left to down right: chr1-chr29. Figure S2. Comparison of methylation distribution between two different cattle genome reference assemblies using chr28 as an example for all samples. Blue line: UMD3.1.1; Green line: ARS-UCD1.2. Figure S3. Principal component analysis (PCA) for all samples using DNA methylation levels of 500 bp windows: a, PC1 vs. PC2; b, PC1 vs. PC3; and c, PC1 vs. PC4. Figure S4. Correlation analyses for all samples using DNA methylation. Figure S5. Correlation analyses of DNA methylation using different window size. 20 K, 100 K, 500 K and 1 M refer to window sizes of 20 kb, 100 kb, 500 kb and 1 Mb, respectively. Figure S6. Standard division of methylation level across all samples. We defined methylation conserved and variable regions as the bottom and top tails, respectively. Figure S7. Genome features enrichment in hypermethylation conserved regions, including genic region and neCpG island. Figure S8. Gene ontology analyses for the genes located in the methylation level conserved and variable regions. (a) Genes located in the hypermethylation conserved regions; (b) Genes located in the sperm hypomethylation variable regions; (c) Genes located in the sperm hypermethylation variable regions. Figure S9. Genome features enrichment in hypomethylation conserved regions, including promoters, eCpG islands, and tRNA genes. Figure S10. Genome features enrichment in methylation variable regions, including promoter and eCpG island. Note: the enrichment of the cCpG island is mainly caused by eCpG island. Figure S11. GO analysis for the genes overlapped with methylation variable regions. Figure S12. Heatmap analysis using the methylation variable regions. Figure S13. Comparison of gene expressions between genes located in the PMD and non-PMD. Figure S14. Placenta HMDs, as compared to placenta PMDs, were enriched for the gene-related features including genic regions, promoters, eCGI and RefGenes. Figure S15. Comparison of methylation patterns for the gene and the CGI regions between HMD and PMD. Placenta HMDs showed significantly lower methylation patterns around the gene TSS and the CGI, while placenta PMDs were almost indistinguishable from the flanking backgrounds because of their low methylations. Figure S16. Comparison of HMR in terms of location and size among the different clusters. Figure S17. Genome feature enrichment in the HMRs of different clusters. Figure S18. Liver (a) and kidney (b) genes with conserved methylated TSS-HMR between cattle and human were involved in basic biological processes, like RNA processing, protein folding and cell cycle. Figure S19. Comparison of the TSS-HMR core region and the TSS-HMR two flank regions in terms of (a) the CG density; (b) standard deviations of the methylation level; (c) DMC distribution; and (d) methylation level. Figure S20. WGCNA analysis for the RNA sequencing data. (a) cluster dendrogram of the gene expression; (b) heatmap plot for the expression of tissue specific high expression genes. Figure S21. Genome distribution of the eCpG island. (a) Distribution of the eCpG island on the 29 cattle chromosomes. (b) Genomic features enrichment in eCpG island, including promoter (1000 bp around the TSS) and the first exon. Figure S22. The methylation pattern between the eCGI and the neCGI. (a) heatmap of the cCGI methylation level for all samples; the blue bar: eCGI; the green bar: neCGI; (b) comparison of the methylation patterns between the eCGI and the neCGI. Figure S23. Correlation analysis for eCGIs with (a) gene contents and (b) chromosome lengths. Figure S24. Comparison of the distribution on chromosomes between eCGI and the neCGI; red line: eCGI; green line: neCGI. Figure S25. CT heterozygote rate for the two animals in different CGIs; CT heterozygote represent CT and GA heterozygote when consider the two strands of DNA. Figure S26. Methylation level distributions for different genome features and samples. Figure S27. Distributions of 4389 common repeats located in the TSS-HMR.