Journal: eLife

Article Title: The cis -regulatory effects of modern human-specific variants

doi: 10.7554/eLife.63713

Figure Lengend Snippet: Relative percentage of bases in each chromHMM ( ; ) category throughout the entire genome ( a ), in fixed or nearly fixed modern human-derived variants ( b ), in active sequences ( c ), and in differentially active sequences ( d ), per cell type. See Discussion for cell-type specificity and enhancer enrichment. ( e ) Histogram of the number of tissues and number of sequences with transcription start site- (TSS) or enhancer-related chromHMM marks for all 14,042 sequences. Tissues and cell types investigated include embryonic stem cells (ESCs), osteoblasts, neural progenitor cells (NPCs), mesenchymal stem cells, monocytes, skin fibroblasts, brain hippocampus, skeletal muscle, heart left ventricle, sigmoid colon, ovary, fetal lung, and liver. Inset shows data for ESC, osteoblast, and NPC only.

Article Snippet: Human fetal osteoblasts were purchased from Cell Applications Inc (406 K-05f, tested negative for mycoplasma) and were maintained in Osteoblast Growth Medium (Cell Applications Inc).

Techniques: Derivative Assay

Journal: eLife

Article Title: The cis -regulatory effects of modern human-specific variants

doi: 10.7554/eLife.63713

Figure Lengend Snippet: ( a ) Overlap between cell types of active sequences. Super Exact test p-value is shown for the overlap of the three groups. ( b-d ) Enrichment levels of active and repressive histone modification marks within active sequences. Enrichment is computed compared to inactive sequences. The enrichment of H3K27me3 in embryonic stem cells (ESCs) possibly reflects the presence of this mark in bivalent genes, which become active in later stages of development . For confidence intervals, see . ( e ) Enrichment of differentially active sequences in various chromatin-based genomic annotations. Missing circles reflect no differentially active sequences in that category. Stars mark significant enrichments (false discovery rate [FDR] <0.05). ( f ) Violin plots of DNA methylation levels for active (green) vs. inactive (red) sequences in osteoblasts. Methylation levels per sequence were computed as the mean methylation across all modern and archaic human bone methylation samples. The circle marks mean methylation across all sequences in each group. t -test p-value is shown.

Article Snippet: Human fetal osteoblasts were purchased from Cell Applications Inc (406 K-05f, tested negative for mycoplasma) and were maintained in Osteoblast Growth Medium (Cell Applications Inc).

Techniques: Modification, DNA Methylation Assay, Methylation, Sequencing

Journal: eLife

Article Title: The cis -regulatory effects of modern human-specific variants

doi: 10.7554/eLife.63713

Figure Lengend Snippet: ( a–c ) Violin plots of DNA methylation levels in modern and archaic human bone methylation samples, for differentially active ( a ), promoter differentially active ( b ), and CpG-poor promoter differentially active ( c ) sequences in osteoblasts. Promoter sequences are sequences between 5 kb upstream and 1 kb downstream of a transcription start site (TSS). CpG-poor promoter sequences were defined as the bottom 50% promoter sequences. ( d ) Violin plots of absolute predicted TF binding score difference between modern and archaic sequences. Points show mean.

Article Snippet: Human fetal osteoblasts were purchased from Cell Applications Inc (406 K-05f, tested negative for mycoplasma) and were maintained in Osteoblast Growth Medium (Cell Applications Inc).

Techniques: DNA Methylation Assay, Methylation, Binding Assay

Journal: eLife

Article Title: The cis -regulatory effects of modern human-specific variants

doi: 10.7554/eLife.63713

Figure Lengend Snippet: (a–c) Expression fold-change vs. predicted TF binding fold-change for each sequence. Positive scores represent increased binding in the modern sequence. Parentheses show number of points in each quadrant with a score difference >0. ( d ) Pearson’s correlation between differential expression and predicted differential binding affinity. Only significant TFs (false discovery rate [FDR] ≤0.05, ) are shown for osteoblasts (yellow) and neural progenitor cells (NPCs) (red). ( e ) Expression fold-change vs. predicted TF binding fold-change for ZNF281 in NPCs. Pearson’s r and p-value are shown. ( f ) Enriched Gene Ontology terms for embryonic stem cells (ESCs) (blue), osteoblasts (yellow), and NPCs (red). ( g ) Expression fold-change of differentially active sequences compared to the cis -regulatory expression fold-change between human and chimpanzee of genes associated with these sequences. cis -regulatory expression changes were taken from hybrid human-chimpanzee induced pluripotent stem cells (iPSCs) . ( h ) RT-qPCR validation of NPCs at passage 1 (pink) and passage 10 (red). Expression levels are normalized to HPRT expression.

Article Snippet: Human fetal osteoblasts were purchased from Cell Applications Inc (406 K-05f, tested negative for mycoplasma) and were maintained in Osteoblast Growth Medium (Cell Applications Inc).

Techniques: Expressing, Binding Assay, Sequencing, Quantitative Proteomics, Quantitative RT-PCR, Biomarker Discovery