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

Genome Research 28, 474-483 (2018)

Figures:

Supplemental Figure S1: (PDF)

Effect of deletion status on autosomal PCT scores

Supplemental Figure S2: (PDF)

PCT scores of X-Y pairs across 8 mammals

Supplemental Figure S3: (PDF)

Resampled mean PCT scores of X-linked genes

Supplemental Figure S4: (PDF)

PCT score comparisons with consistent and variable escape genes separated

Supplemental Figure S5: (PDF)

PCT score comparisons with discordant genes included as X-inactivated or escape

Supplemental Figure S6: (PDF)

Variation in within-UTR conservation does not account for observed differences in PCT score among classes of X-linked genes

Supplemental Figure S7: (PDF)

Background human-chicken 3' UTR conservation among classes of X-linked genes

Supplemental Figure S8: (PDF)

Ancestral miRNA targeting of X-Y pairs across 8 mammals

Supplemental Figure S9: (PDF)

PCT scores of Z-W pairs across 4 and 14 birds

Supplemental Figure S10: (PDF)

Resampled mean PCT scores of Z-linked genes

Supplemental Figure S11: (PDF)

Variation in within-UTR conservation cannot account for observed differences in PCT score among classes of Z-linked genes

Supplemental Figure S12: (PDF)

Correlation of Z-linked gene-specific dosage compensation with gene-level PCT score

Supplemental Figure S13: (PDF)

Ancestral miRNA targeting of Z-W pairs across 4 birds

Supplemental Figure S14: (PDF)

Ancestral miRNA targeting of predicted Z-W pairs across 14 birds

Supplemental Figure S15: (PDF)

Correlation of Z-linked gene-specific dosage compensation with human-chicken-conserved site excess

Supplemental Figure S16: (PDF)

Gene expression changes following small RNA transfections in human HeLa cells

Supplemental Figure S17: (PDF)

Gene expression changes following transfection or knockdown of additional miRNAs in human HCT116 or HEK293 cells

Supplemental Figure S18: (PDF)

Changes in mRNA stability and translational efficiency and gene expression following miR-155 knockout in mouse immune cells

Supplemental Figure S19: (PDF)

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)

Copy number status in control individuals for autosomal genes from the Exome Aggregation Consortium

Supplemental Table S3: (XLS)

Properties of ancestral X-linked genes assessed in this study

Supplemental Table S4: (XLS)

Properties of ancestral Z-linked genes assessed in this study

Supplemental Table S5: (TXT)

Pct scores, both with and without normalization for within-UTR conservation, for all gene-miRNA interactions

Supplemental Table S6: (XLS)

Gene expression fold changes from transfection of 4 miRNAs into HCT116 or HEK293 cells

Files:

Supplemental Code: (ZIP)

Supplemental Code