Daniel Winston Bellott

Supplementary Information for:

Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution

Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page

bioRxiv (2017)

Figures:

Supplemental Figures S1-15: (PDF)

Includes:

• Supplemental Figure S1: Effect of deletion status on autosomal PCT scores
• Supplemental Figure S2: PCT scores of X-Y pairs across 8 mammals
• Supplemental Figure S3: Resampled mean PCT scores of X-linked genes
• Supplemental Figure S4: PCT score comparisons with consistent and variable escape genes separated
• Supplemental Figure S5: Variation in within-UTR conservation does not account for observed differences in PCT score among classes of X-linked genes
• Supplemental Figure S6: Ancestral miRNA targeting of X-Y pairs across 8 mammals
• Supplemental Figure S7: PCT scores of Z-W pairs across 4 and 14 birds
• Supplemental Figure S8: Resampled mean PCT scores of Z-linked genes
• Supplemental Figure S9: Variation in within-UTR conservation cannot account for observed differences in PCT score among classes of Z-linked genes
• Supplemental Figure S10: Ancestral miRNA targeting of Z-W pairs across 4 birds
• Supplemental Figure S11: Ancestral miRNA targeting of predicted Z-W pairs across 14 birds
• Supplemental Figure S12: Gene expression changes following small RNA transfections in human HeLa cells
• Supplemental Figure S13: Gene expression changes following transfection or knockdown of additional miRNAs in human HCT116 or HEK293 cells
• Supplemental Figure S14: Changes in mRNA stability and translational efficiency and gene expression following miR-155 knockout in mouse immune cells
• Supplemental Figure S15: Argonaute binding measured by high-throughput crosslinking-immunopreciptiation (CLIP) following miRNA transfection in HEK293 cells

Tables:

Supplemental Table S1: (XLS)

Information on statistical tests, alternative hypotheses, test statistics, and p-values used

Supplemental Table S2: (XLS)

Genes and ExAC copy number status

Supplemental Table S3: (XLS)

Ancestral X genes, chicken orthologs, Y homologs, and dosage sensitivity statistics

Supplemental Table S4: (XLS)

Ancestral Z genes, human and anolis orthologs, W homologs, and dosage sensitivity statistics

Supplemental Table S5: (TXT)

Gene-miRNA pairs, Pct scores, and UTR conservation bias

Supplemental Table S6: (XLS)

Genes expressed in HEK293, with presence of a AGO-PAR-CLIP cluster after miR-124 or miR-7 transfection indicated