Enhancer evolution across species and cancer

Datasets used in the article “Emergence of new enhancers at late DNA replicating regions” (doi: https://doi.org/10.1101/2022.12.22.521323) Species evolution All human regions are given in hg19 coordinates, and mouse regions in mm10 coordinates. We gathered human enhancer and promoter regions from PMID: 25635462 and mouse enhancers from PMID: 33602314. Human enhancers were defined as regions enriched in H3K27ac but not H3K4me3, while promoters were regions enriched in H3K4me3. Mouse active enhancers were defined as regions enriched in H3K27ac and H3K4me1 but not H3K4me3. Poised enhancers were those regions enriched in H3K4me1 only. The fourth column of mouse enhancer files indicates the tissue(s) where the enhancers were identified, and the fifth column indicates the enhancer type (active or poised). human_conserved_enhancers_atLeast2otherSp_hg19.bed human_conserved_promoters_atLeast2otherSp_hg19.bed human_recent_enhancers_hg19.bed human_recent_promoters_hg19.bed mouse_conserved_atLeast2otherSp_mm10.bed mouse_recent_mm10.bed Cancer datasets All regions are given in hg19 coordinates. All peaks were distal (> 1Kb) to TSSs. Gained enhancers were defined as those present in cancer cells and not healthy cells. Lost enhancers were those present in healthy cells and not cancer cells Unchanged enhancers were present in both healthy and cancer cells Prostate: PrEC chromatin mark data were used to define healthy candidate enhancers. Enhancers were defined as those regions classified as "Enhancer" in a ChromHMM model (Accession: GSE57498). Candidate cancer enhancers were defined using the union of H3K27ac and H3K4me1 ChIP-seq peaks in LNCaP (GEO Accessions: GSM1902615 and GSM1902616). LNCaP_enh_gains_unique_hg19.bed PReC_enh_losses_unique_hg19.bed PReC_enh_unchanged_unique_hg19.bed Breast: Candidate enhancers were defined as the union of H3K27ac and H3K4me1 peaks in breast cancer cell line MCF-7 and breast epithelium samples (ENCODE Accessions: ENCFF132IWN, ENCFF674BKS, ENCFF569TYE, ENCFF440IVB). breast_cancer_gains_unique_hg19.bed breast_cancer_losses_unique_hg19.bed breast_cancer_unchanged_unique_hg19.bed AML: Candidate enhancers were defined in pre-leukemic and blast cells using matched ATAC-seq data from three individuals (GEO Accession: GSE74912; SU484, SU501, SU654). gains_AML_union_1kb_hg19.bed losses_AML_union_1kb_hg19.bed unchanged_AML_union_1kb_hg19.bed Thyroid: Candidate enhancers were defined in cancer and healthy thyroid using matched ATAC-seq data from three individuals (GEO Accession: GSE162515; C1, C7, C8) gains_thyroid_union_1kb_hg19.bed losses_thyroid_union_1kb_hg19.bed unchanged_thyroid_union_1kb_hg19.bed