Genome wide variable replication-timing and expression.

a) Single cell derived ACP clones (color coded) are isolated. The maternal and paternal haplotypes were used to analyze allele-specific replication timing and expression. b) The top panel illustrates the expected replication timing profile in multiple clones across an autosomal region. The regions that display VERT are highlighted by shading. The bottom panel illustrates the expected expression variability in different clones from the same individual. c) We define AEI as an allelic bias that is ≥80% allelic imbalance (AEI ≥ 0.80 or ≤ 0.20). d) Illustration of an Inactivation/Stability Center showing the clonal and allele-restricted variability in replication timing and expression of both protein coding and noncoding genes. e) The standard deviation (Std. Dev.) in 250 kb windows (circles) across human chromosome 1. Outlier windows from all four sets of clones (ACP6, ACP7, EB3-2, and GM12878) are highlighted in different colors as shown. The top panel illustrates the G-banding (blue shading) pattern for human chromosome 1, with 23 VERT regions highlighted in red. The arrow marks the VERT region shown in panels f-h below. f-h) I/SC located between 239 and 242 mb of chromosome 1 (see panel e). f) VERT (shaded region) and AEI of genes (rectangles) detected in the ACP6 clones, each clone was color coded as shown. For replication, the solid lines represent the maternal (Mat.) allele and the dotted line represents the paternal (Pat.) allele. g) VERT (shaded region) and AEI of genes (rectangles) detected in the ACP7 clones, each clone was color coded as shown. h) UCSC Genome Browser view of the genomic region in panels f and g. The shaded area highlights the VERT region. i) Hierarchical clustering of the VERT regions that are shared between 2 or more clone sets showing both ACP and LCL clones. j) Gene Ontology (GO) enrichment analysis of the genes located within the VERT regions, the most significant hits for each set of clones, organized by cell type, are shown. GO analysis of the mouse genes located within the pre-B cell clone VERT regions are also shown.

Examples of I/SCs.

a, d and g) VERT regions on human chromosomes 18, 6 and 9, respectively. The top panels illustrate the G-banding (blue shading) pattern for each human chromosome, with VERT regions highlighted in red. The standard deviation (Std. Dev.) in 250 kb windows (circles) across each human chromosome is shown. Outlier windows from all four sets of clones (ACP6, ACP7, EB3-2, and GM12878) are highlighted in different colors as shown. The arrows and red boxes mark the VERT regions shown in panels b, e, and h. b, e and h) I/SCs highlighted in panels a, d, and g. For replication, the solid lines represent the maternal (Mat.) allele and the dotted line represents the paternal (Pat.) allele. The regions with VERT are shaded and the AEI is shown for each clone in a different color. c, f and i) UCSC Genome Browser views of the genomic regions in panels b, e and h. The shaded areas highlight the VERT regions. Genes with AEI are marked with +, *, or #. b and c) The + marks MOCOS, which shows AEI in ACP cells (Supplemental Table 2) and ++ marks FHOD3, which shows AEI in LCLs 1. e and f) The * marks from DNAH8, ** marks transcripts from KCNK5, and *** marks non-coding transcripts from ENSG00000293066 (also named: TL:6-39.9_1 1). All three of these genes show AEI in LCL clones 1. h and i) The # marks transcripts from DAPK1, ## marks transcripts from SPIN1. Both genes show AEI in LCL clones 1.

Human gene clusters with AEI map to VERT regions.

a and c) VERT regions on human chromosome 9 and 6. The top panels illustrate the G-banding (blue shading) pattern for each human chromosome, with VERT regions highlighted in red. The standard deviation (Std. Dev.) in 250 kb windows (circles) across each human chromosome is shown. Outlier windows from all four sets of clones (ACP6, ACP7, EB3-2, and GM12878) are highlighted in different colors as shown. The arrows and red boxes mark the VERT regions shown in panels b, e, and h. The red box and arrow identify the I/SC in panel b. b) UCSC genome browser view illustrating the genomic location highlighted in panel a. The shaded area highlights the VERT region. The red lines mark 11 olfactory receptor genes, and the green lines mark 6 cytochrome P450 family (CYP4F) genes. d) UCSC Genome Browser view illustrating the genomic location highlighted in panel c. The shaded area highlights the VERT region. The red lines mark 16 HLA genes, and the green lines mark 6 Lymphocyte antigen 6 family (LY6G) genes.

Mouse gene clusters with AEI map to VERT regions.

a and d) VERT regions on mouse chromosome 2 and 18. The standard deviation (Std. Dev.) in 50 kb windows (circles) across each mouse chromosome are shown. Outlier windows from pre-B cell clones are highlighted in orange. The red boxes and arrows identify the VERT regions in panels b (i) and c (ii). b and c) UCSC genome browser views illustrating the genomic locations represented by i and ii in panel a. b) Genome Browser view of the VERT region showing the location of 29 olfactory receptor genes (Or genes). The shaded area represents the VERT region. c) Genome Browser view of the VERT region in ii above, showing the location of 242 olfactory receptor genes (Or genes). The shaded area represents the VERT region. e) Genome Browser view of the VERT region in d above, showing the location of clustered Protocaderhin genes (15 Pcdha, 23 Pcdhb, and 22 Pcdhg genes). The shaded area represents the VERT region.

Human and Mouse syntenic regions display VERT.

a and b) The short arm of human chromosome 5, with 11 VERT regions (panel a) and the centromeric region of mouse chromosome 15, with 4 VERT regions (panel b) are shown. a) Two human VERT regions are highlighted, hi and hii, and are syntenic with locations on mouse chromosome 15, mi and mii, that also show VERT (panel b). Note that the gene order in both syntenic regions are inverted with respect to the telomeres when comparing the human and mouse loci. c) Illustration of the I/SC on human chromosome 5 between 7.75 and 10.5 mb (hi). The shaded area marks the VERT region, and AEI of the coding gene SEMA5A in different clones is highlighted. For replication, the maternal (Mat.) and paternal (Pat.) alleles are indicated. d) UCSC Genome Browser view of the human VERT region (shaded) in hi, showing the location of SEMA5A and a taste receptor gene (TAS2R1). e) UCSC Genome Browser view of the mouse VERT region (shaded) in mi, showing the location of Sema5a and a taste receptor gene (Tas2r119). f) UCSC Genome Browser view of the human VERT region (shaded) in hii above, highlighting the location of the AEI gene RETREG1 45. g) UCSC Genome Browser view of the mouse VERT region (shaded) in mii, showing the synteny between human and mouse for the protein coding genes in panel f, including Retreg1. h) VERT regions on human chromosome 16. The standard deviation (Std. Dev.) in 250 kb windows (circles) across human chromosome 16 is shown. Outlier windows are highlighted in different colors as shown. The red box and arrow mark the genomic location in panel i. i) UCSC Genome Browser view illustrating the genomic location represented in panel h, showing the location of GRIN2A (red box). j) VERT regions on mouse chromosome 16. The standard deviation in 50 kb windows (circles) is shown. Outlier windows from pre-B cell clones are highlighted in orange. k) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) represented in panel j above, with the location of Grin2a highlighted with a red box.

Epilepsy genes map to I/SCs.

a, d, and g) VERT regions on human chromosomes 2, 5, and 21. The top panels illustrate the G-banding (blue shading) pattern for each human chromosome, with VERT regions highlighted in red. The standard deviation (Std. Dev.) in 250 kb windows (circles) across each human chromosome is shown. Outlier windows from all four sets of clones (ACP6, ACP7, EB3-2, and GM12878) are highlighted in different colors as shown. The arrows and red boxes mark the VERT regions shown in panels b, c, e, f, h, i, j and k. b, e, h, j) Illustrations of I/SCs on chromosomes 2, 5, and 8. The shaded areas mark the VERT regions. Each clone was color coded to illustrate the VERT and AEI in different clones. The maternal (Mat.) and paternal (Pat.) alleles are indicated for replication and expression. c) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) represented in panels a and b, with the location of 5 sodium channel genes (SCN3A, SCN2A, SCN1A, SCN9A, and SCN7A) highlighted with a red line. e) Illustration of an I/SC on chromosome 5. The shaded area marks the VERT region. AEI of GABRA1 is shown. f) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) represented in panels d and e above, with the location of 4 GABA receptor genes (GABRB2, GABRBA6, GABRA1, and GABRG2) highlighted with a red line. h) Illustration of a I/SCs (A) on chromosome 8. Each ACP6 clone was color coded to illustrate the VERT and AEI in different clones. The maternal (Mat.) and paternal (Pat.) alleles are indicated for replication and expression. The shaded area marks the VERT region. The location and expression of OXR1 is indicated. i) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) represented in panels g (A) and h above, with the location of the OXR1 gene highlighted with a red line. We note that ANGPT1 (marked with *), located within this I/SC displays AEI (see Supplementary Table 2). j) Illustration of an I/SC (B) on chromosome 8. AEI of SAMD12 is indicated. k) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) represented in panels g (B) and j above, with the location of the SAMD12 highlighted with a red line.

Parkinson disease genes map to I/SCs.

a, c, e, and g) VERT regions on human chromosomes 4, 12, 19, and 20, respectively. The top panels illustrate the G-banding (blue shading) pattern for each human chromosome, with VERT regions highlighted in red. The standard deviation (Std. Dev.) in 250 kb windows (circles) across each human chromosome is shown. Outlier windows from all four sets of clones (ACP6, ACP7, EB3-2, and GM12878) are highlighted in different colors as shown. The arrows and red boxes mark the VERT regions shown in panels b, d, f, and h, respectively. b) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) represented in panel a, with the location of the SNCA gene highlighted with a red line. d) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) highlighted in panel c, with the location of the LRRK2 gene highlighted with a red line. f) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) represented in panel e, with the location of the DNAJC6 gene highlighted with a red line; also highlighted with a green line is the JAK1 gene. h) UCSC Genome Browser view illustrating the genomic location of the VERT region (shaded area) represented in panel g, with the location of the PRKN gene highlighted with a red line.