Daniel Winston Bellott

Research Scientist

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Supplementary Information for:

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

Daniel W Bellott, Jennifer F Hughes, Helen Skaletsky, Laura G Brown, Tatyana Pyntikova, Ting-Jan Cho, Natalia Koutseva, Sara Zaghlul, Tina Graves, Susie Rock, Colin Kremitzki, Robert S Fulton, Shannon Dugan, Yan Ding, Donna Morton, Ziad Khan, Lora Lewis, Christian Buhay, Qiaoyan Wang, Jennifer Watt, Michael Holder, Sandy Lee, Lynne Nazareth, Jessica Alföldi, Steve Rozen, Donna M Muzny, Wesley C Warren, Richard A Gibbs, Richard K Wilson, David C Page

Nature 508, 494-499 (2014)

Notes:

Supplementary Notes: (PDF)

Includes:

Supplementary Note 1: SHIMS strategy and error estimates
Supplementary Note 2: PANTHER Statistical Overrepresentation Test
Supplementary Note 3: Identification and recalibration of evolutionary strata
Supplementary Note 4: Modeling kinetics of Y-chromosome decay
Supplementary Note 5: Haplolethality of broadly expressed, dosage-sensitive X-Y pair genes

Figures:

Extended Data Figure 1: (JPG) (Figure legend)

Annotated sequence contigs from the MSY of five species

Extended Data Figure 2: (JPG) (Figure legend)

Expression of Y-linked genes across tissues and species

Extended Data Figure 3: (JPG) (Figure legend)

Dot plot of human X orthologues in opossum and chicken

Extended Data Figure 4: (JPG) (Figure legend)

Phylogenetic analysis of stratum one and stratum two genes

Extended Data Figure 5: (JPG) (Figure legend)

Phylogenetic tree showing X-Y gene conversion in AMELX/AMELY and ZFX/ZFY

Extended Data Figure 6: (JPG) (Figure legend)

Y-Y gene conversion within multi-copy gene families

Extended Data Figure 7: (JPG) (Figure legend)

Viable structually variant sex chromosomes in humans

Tables:

Extended Data Table 1: (JPG)

PANTHER statistical overrepresentation results

Extended Data Table 2: (JPG)

Accession numbers of mouse pseudoautosomal region genes

Extended Data Table 3: (JPG)

Patients with structurally variant X and Y Chromosomes

Source Data Figure 1: (XLS)

Status of ancestral genes in each lineage

Source Data Figure 4: (XLS)

Constraints on dynamics of Y-chromosome gene content

Source Data Figure 5: (XLS)

Includes:

(5a) Branch lengths for multi-copy and single-copy X-Y pair genes
(5b) Human haploinsufficiency scores for ancestral genes
(5c) Calculated expression breadth for ancestral genes
(5d) Ensembl human-mouse dN/dS for ancestral genes

Supplementary Tables: (XLS)

Includes:

Supplementary Table 1: BAC clone accession numbers and nucleotide positions in MSY sequence assemblies
Supplementary Table 2: Ancestral genes
Supplementary Table 3: Accession numbers of genes in this study
Supplementary Table 4: PANTHER statistical overrepresentation results
Supplementary Table 5: Values of dN, dS, and dN/dS for all X-Y pairs

Daniel Winston Bellott

Supplementary Information for:

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

Notes:

Supplementary Notes: (PDF)

Figures:

Extended Data Figure 1: (JPG) (Figure legend)

Extended Data Figure 2: (JPG) (Figure legend)

Extended Data Figure 3: (JPG) (Figure legend)

Extended Data Figure 4: (JPG) (Figure legend)

Extended Data Figure 5: (JPG) (Figure legend)

Extended Data Figure 6: (JPG) (Figure legend)

Extended Data Figure 7: (JPG) (Figure legend)

Tables:

Extended Data Table 1: (JPG)

Extended Data Table 2: (JPG)

Extended Data Table 3: (JPG)

Source Data Figure 1: (XLS)

Source Data Figure 4: (XLS)

Source Data Figure 5: (XLS)

Supplementary Tables: (XLS)

Sequences:

Gene Alignments: (TXT)

Gene Sequences: (FASTA)