Daniel Winston Bellott

Supplementary Information for:

The human Y and inactive X chromosomes similarly modulate autosomal gene expression

Adrianna K San Roman, Helen Skaletsky, Alexander K Godfrey, Neha V Bokil, Levi Teitz, Isani Singh, Laura V Blanton, Daniel W Bellott, Tatyana Pyntikova, Julian Lange, Natalia Koutseva, Jennifer F Hughes, Laura Brown, Sidaly Phou, Ashley Buscetta, Paul Kruszka, Nicole Banks, Amalia Dutra, Evgenia Pak, Patricia C Lasutschinkow, Colleen Keen, Shanlee M Davis, Angela E Lin, Nicole R Tartaglia, Carole Samango-Sprouse, Maximilian Muenke, David C Page

bioRxiv (2023)

Tables:

Table S1: (XLS)

Metadata for RNA-seq of LCLs or fibroblasts from individuals with naturally-occurring variations in chromosome copy number or structure related to Figures 1, 3, 4, and 5

Table S2: (XLS)

Expression change per copy of Chr X or Chr Y for expressed autosomal genes in LCLs and fibroblasts, related to Figure 1

Table S3: (XLS)

Reanalysis of publicly available data to identify AR and ER direct target genes, related to Figure 1

Table S4: (XLS)

Genes expressed from the active X chromosome only (silenced on Xi) that significantly change in expression in response to Chr X and Chr Y copy number, related to Figure 2

Table S5: (XLS)

Expression change per copy of Chr 21 for expressed autosomal genes in LCLs, related to Figure 3

Table S6: (XLS)

Differential gene expression analysis as a function of DYZ1 depth of coverage, related to Figure 4

Table S7: (XLS)

Sex chromosome structural variant breakpoints and gene content, related to Figures 4 and 5

Table S8: (XLS)

Sequence motifs in promoters of Chr X- and Y-responsive genes in LCLs and fibroblasts, related to Figure 6

Table S9: (XLS)

Genome-wide binding analysis of ZFX across ENCODE cell lines, related to Figure 6

Table S10: (XLS)

Expression analysis of ZFX and ZFY CRISPRi knockdowns, related to Figure 6

Table S11: (XLS)

Sequence motifs in promoters of genes affected by ZFX and ZFY knockdowns, related to Figure 6

Table S12: (XLS)

Quantification of genome-wide response to Chr X and Y copy number in LCLs and fibroblasts, related to Figures 1 and 2

Files:

Supplemental Information: (PDF)

Includes:

• Figures S1-S19