Table 1. Underrepli cated domains and suppression of underreplication in (UR) SUMM4 subunit mutant alleles.
Domains of UR in euchromatic arms of polytene chromosomes were called in w1118 as described in ‘Materials and methods.’ Their genomic coordinates, approximate cytological location (‘Cyto band’), and average DNA copy numbers (‘<CN>’) in homozygous w1118, SuURES, and mod(mdg4)m9 L3 larvae are shown. <CN> numbers were normalized to the average DNA copy numbers across euchromatic genome. UR percent recovery levels were calculated as (<CN> mut –<CN>w1118) / (1 – <CN >w1118); negative numbers indicate increased UR. UR p-values were calculated using the DESeq2 package by averaging the Wald test p-values of each 5 kbp bin significantly different than the w1118 signal. UR was called as suppressible by a mutant if p<0.01; p-values for regions that exhibit a statistically significant recovery of UR are shown in bold blue. Averages of <CN> across all called underreplicated domains and averages of percent Recovery across all suppressible underreplicated domains (‘<Recovery>’, bottom row) were adjusted for each underreplicated domain length; calculation errors = standard deviations.
| N | Chromosome coordinates | Length | UR, w1118 | UR, SuURES | UR, mod(mdg4)m9 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Arm | Left | Right | Cyto band | <CN> | <CN> | Recovery (%) | p-Value | <CN> | Recovery (%) | p-Value | ||
| 1 | X | 2,950,001 | 3,140,000 | 3C3-C7 | 190,000 | 0.51 | 0.93 | 86 | 7.3E-05 | 0.58 | 14 | 1.1E-02 |
| 2 | X | 4,710,001 | 4,900,000 | 4C15-D5 | 190,000 | 0.56 | 0.96 | 92 | 3.9E-04 | 0.81 | 57 | 6.9E-05 |
| 3 | X | 4,965,001 | 5,070,000 | 4E1-E2 | 105,000 | 0.72 | 0.86 | 50 | 5.6E-04 | 0.80 | 28 | 1.4E-02 |
| 4 | X | 6,415,001 | 6,525,000 | 6A1-B1 | 110,000 | 0.71 | 0.90 | 65 | 1.4E-03 | 0.80 | 29 | 7.3E-03 |
| 5 | X | 7,335,001 | 7,560,000 | 7B1-B4 | 225,000 | 0.65 | 0.98 | 95 | 1.2E-03 | 0.79 | 40 | 2.8E-03 |
| 6 | X | 7,750,001 | 7,865,000 | 7B7-C1 | 115,000 | 0.64 | 0.94 | 84 | 3.0E-09 | 0.84 | 55 | 5.2E-07 |
| 7 | X | 8,880,001 | 9,005,000 | 8B5-C2 | 125,000 | 0.73 | 0.86 | 50 | 5.5E-03 | 0.76 | 9 | 4.6E-03 |
| 8 | X | 9,405,001 | 9,555,000 | 8D12-E7 | 150,000 | 0.72 | 0.91 | 67 | 3.6E-04 | 0.85 | 47 | 3.6E-03 |
| 9 | X | 11,170,001 | 11,325,000 | 10A10-B3 | 155,000 | 0.67 | 0.84 | 53 | 3.2E-03 | 0.78 | 35 | 2.6E-03 |
| 10 | X | 12,040,001 | 12,430,000 | 11A2-A10 | 390,000 | 0.38 | 0.97 | 94 | 1.4E-08 | 0.42 | 6 | 6.8E-03 |
| 11 | X | 13,950,001 | 14,100,000 | 12D1-E1 | 150,000 | 0.69 | 0.72 | 10 | 1.0E-02 | 0.73 | 14 | 1.4E-02 |
| 12 | X | 14,290,001 | 14,565,000 | 12E7-F1 | 275,000 | 0.51 | 0.94 | 87 | 4.1E-04 | 0.69 | 36 | 8.1E-04 |
| 13 | X | 17,925,001 | 18,030,000 | 16F3-F5 | 105,000 | 0.67 | 0.99 | 98 | 1.7E-15 | 0.90 | 68 | 3.4E-05 |
| 14 | X | 20,000,001 | 20,105,000 | 19A4-B1 | 105,000 | 0.79 | 1.12 | 157 | 1.4E-13 | 0.82 | 12 | 6.1E-03 |
| 15 | X | 20,525,001 | 21,020,000 | 19D2-E7 | 495,000 | 0.50 | 0.97 | 93 | 1.3E-07 | 0.51 | 2 | 4.9E-03 |
| 16 | X | 21,630,001 | 22,450,000 | 20A5-C1 | 820,000 | 0.04 | 0.32 | 29 | 1.8E-03 | 0.06 | 2 | 6.4E-03 |
| 17 | X | 22,550,001 | 22,995,000 | 20C2-F3 | 445,000 | 0.48 | 0.81 | 64 | 7.8E-05 | 0.74 | 51 | 3.5E-04 |
| 18 | 2L | 3,920,001 | 4,025,000 | 24D1-D4 | 105,000 | 0.63 | 0.93 | 81 | 7.9E-07 | 0.80 | 46 | 5.9E-05 |
| 19 | 2L | 4,585,001 | 4,790,000 | 25A2-A5 | 205,000 | 0.66 | 0.99 | 98 | 1.9E-08 | 0.78 | 36 | 1.3E-03 |
| 20 | 2L | 5,400,001 | 5,510,000 | 25E1-E4 | 110,000 | 0.82 | 0.99 | 95 | 4.0E-08 | 0.90 | 45 | 8.3E-03 |
| 21 | 2L | 6,155,001 | 6,320,000 | 26B9-C2 | 165,000 | 0.74 | 1.08 | 130 | 7.3E-14 | 0.88 | 54 | 4.7E-04 |
| 22 | 2L | 9,030,001 | 9,150,000 | 29F8-30A2 | 120,000 | 0.76 | 0.98 | 93 | 1.5E-04 | 0.95 | 79 | 3.3E-03 |
| 23 | 2L | 11,535,001 | 11,795,000 | 32F2-33A1 | 260,000 | 0.44 | 0.90 | 83 | 2.9E-04 | 0.57 | 24 | 1.5E-03 |
| 24 | 2L | 12,215,001 | 12,340,000 | 33D3-E1 | 125,000 | 0.58 | 0.86 | 66 | 3.6E-11 | 0.75 | 40 | 1.1E-04 |
| 25 | 2L | 12,765,001 | 12,970,000 | 33F5-34A3 | 205,000 | 0.55 | 0.91 | 79 | 8.8E-04 | 0.73 | 40 | 7.0E-05 |
| 26 | 2L | 14,685,001 | 15,010,000 | 35B4-B8 | 325,000 | 0.41 | 0.88 | 80 | 5.7E-04 | 0.54 | 23 | 7.2E-04 |
| 27 | 2L | 15,295,001 | 15,735,000 | 35D1-D4 | 440,000 | 0.49 | 0.76 | 53 | 2.3E-05 | 0.54 | 9 | 4.0E-03 |
| 28 | 2L | 15,770,001 | 15,900,000 | 35D4-D6 | 130,000 | 0.54 | 0.87 | 71 | 4.5E-08 | 0.68 | 31 | 6.7E-04 |
| 29 | 2L | 15,925,001 | 16,240,000 | 35D6-F1 | 315,000 | 0.29 | 0.90 | 87 | 6.7E-07 | 0.38 | 12 | 1.4E-05 |
| 30 | 2L | 16,925,001 | 17,375,000 | 36B4-C7 | 450,000 | 0.23 | 0.89 | 85 | 1.4E-04 | 0.26 | 4 | 4.3E-03 |
| 31 | 2L | 17,515,001 | 18,100,000 | 36C10-E4 | 585,000 | 0.34 | 0.87 | 80 | 5.0E-06 | 0.36 | 2 | 3.7E-03 |
| 32 | 2L | 18,160,001 | 18,300,000 | 36E6-F2 | 140,000 | 0.67 | 0.99 | 97 | 3.3E-06 | 0.90 | 69 | 3.1E-06 |
| 33 | 2L | 20,110,001 | 20,290,000 | 38C1-C4 | 180,000 | 0.48 | 0.69 | 41 | 8.9E-04 | 0.46 | –5 | 1.8E-03 |
| 34 | 2L | 20,485,001 | 20,620,000 | 38C8-D1 | 135,000 | 0.77 | 0.98 | 93 | 1.0E-06 | 0.99 | 97 | 2.1E-05 |
| 35 | 2L | 21,400,001 | 21,550,000 | 39D3-E2 | 150,000 | 0.10 | 0.15 | 5 | 3.2E-03 | 0.14 | 3 | 4.4E-03 |
| 36 | 2L | 21,805,001 | 22,125,000 | 40A4-E4 | 320,000 | 0.53 | 0.94 | 87 | 6.9E-05 | 0.54 | 1 | 9.5E-03 |
| 37 | 2R | 4,875,001 | 5,050,000 | 41C4-D1 | 175,000 | 0.35 | 0.86 | 78 | 2.3E-10 | 0.34 | –1 | 4.0E-03 |
| 38 | 2R | 5,410,001 | 5,535,000 | 41F1-F3 | 125,000 | 0.58 | 0.79 | 50 | 1.1E-03 | 0.52 | –13 | 2.2E-03 |
| 39 | 2R | 6,290,001 | 6,505,000 | 42A14-B1 | 215,000 | 0.13 | 0.50 | 42 | 9.3E-04 | 0.14 | 1 | 2.7E-03 |
| 40 | 2R | 13,620,001 | 13,760,000 | 50B6-C3 | 140,000 | 0.63 | 0.95 | 88 | 4.1E-18 | 0.78 | 41 | 1.3E-05 |
| 41 | 2R | 20,355,001 | 20,540,000 | 56F17-57A5 | 185,000 | 0.56 | 0.92 | 83 | 2.0E-06 | 0.71 | 35 | 8.2E-04 |
| 42 | 2R | 21,830,001 | 21,945,000 | 58A2-A4 | 115,000 | 0.72 | 0.95 | 83 | 1.1E-05 | 0.71 | –3 | 2.2E-02 |
| 43 | 2R | 23,145,001 | 23,320,000 | 59D1-D6 | 175,000 | 0.62 | 1.04 | 110 | 1.3E-22 | 0.67 | 13 | 7.7E-03 |
| 44 | 3L | 4,840,001 | 5,100,000 | 64C1-C5 | 260,000 | 0.38 | 0.92 | 87 | 3.5E-08 | 0.40 | 3 | 6.6E-03 |
| 45 | 3L | 5,385,001 | 5,510,000 | 64C15-D3 | 125,000 | 0.51 | 0.88 | 76 | 1.9E-22 | 0.73 | 45 | 6.0E-09 |
| 46 | 3L | 6,290,001 | 6,485,000 | 65A11-B3 | 195,000 | 0.52 | 0.89 | 77 | 4.9E-05 | 0.71 | 38 | 1.2E-04 |
| 47 | 3L | 9,180,001 | 9,300,000 | 67A1-A7 | 120,000 | 0.67 | 0.97 | 90 | 6.5E-09 | 0.73 | 20 | 1.0E-02 |
| 48 | 3L | 10,000,001 | 10,195,000 | 67D3-D10 | 195,000 | 0.62 | 0.97 | 93 | 4.4E-13 | 0.79 | 44 | 5.7E-06 |
| 49 | 3L | 13,085,001 | 13,220,000 | 70A1-A2 | 135,000 | 0.66 | 1.01 | 104 | 3.6E-09 | 0.89 | 66 | 2.9E-06 |
| 50 | 3L | 13,550,001 | 13,855,000 | 70B6-C4 | 305,000 | 0.26 | 0.95 | 94 | 1.8E-06 | 0.39 | 18 | 7.3E-04 |
| 51 | 3L | 15,175,001 | 15,500,000 | 71B7-D3 | 325,000 | 0.39 | 0.94 | 89 | 5.6E-04 | 0.46 | 10 | 3.7E-03 |
| 52 | 3L | 17,115,001 | 17,240,000 | 73F1-74A1 | 125,000 | 0.71 | 1.02 | 106 | 4.3E-05 | 0.84 | 45 | 2.7E-03 |
| 53 | 3L | 18,175,001 | 18,525,000 | 75B11-75D2 | 350,000 | 0.45 | 0.87 | 76 | 6.8E-05 | 0.47 | 4 | 4.6E-03 |
| 54 | 3L | 20,555,001 | 20,695,000 | 77D1-77E3 | 140,000 | 0.60 | 1.02 | 106 | 2.2E-22 | 0.84 | 61 | 3.6E-11 |
| 55 | 3R | 6,060,001 | 6,310,000 | 83D2-E4 | 250,000 | 0.70 | 0.92 | 72 | 7.6E-04 | 0.63 | –22 | 1.0E-02 |
| 56 | 3R | 6,495,001 | 6,635,000 | 83F1-84A1 | 140,000 | 0.53 | 0.96 | 91 | 7.8E-08 | 0.71 | 39 | 2.2E-04 |
| 57 | 3R | 6,915,001 | 7,055,000 | 84B1-B2 | 140,000 | 0.64 | 0.93 | 80 | 3.9E-04 | 0.82 | 49 | 1.9E-05 |
| 58 | 3R | 7,550,001 | 7,785,000 | 84D9-84E2 | 235,000 | 0.44 | 0.80 | 65 | 8.0E-06 | 0.51 | 12 | 4.2E-03 |
| 59 | 3R | 10,450,001 | 10,660,000 | 86B6-C4 | 210,000 | 0.55 | 0.98 | 97 | 8.1E-11 | 0.66 | 25 | 7.6E-04 |
| 60 | 3R | 10,910,001 | 11,140,000 | 88C15-86D4 | 230,000 | 0.45 | 0.94 | 89 | 2.3E-10 | 0.46 | 2 | 2.3E-03 |
| 61 | 3R | 12,050,001 | 12,165,000 | 87A5-B1 | 115,000 | 0.63 | 0.96 | 88 | 9.9E-24 | 0.81 | 49 | 5.9E-09 |
| 62 | 3R | 12,745,001 | 12,935,000 | 87C8-D4 | 190,000 | 0.67 | 0.89 | 68 | 7.5E-05 | 0.60 | –21 | 1.1E-02 |
| 63 | 3R | 14,935,001 | 15,055,000 | 88D8-D10 | 120,000 | 0.70 | 0.88 | 61 | 7.6E-06 | 0.84 | 47 | 1.0E-04 |
| 64 | 3R | 16,670,001 | 16,970,000 | 89D6-E5 | 300,000 | 0.40 | 0.92 | 87 | 2.7E-09 | 0.47 | 10 | 3.2E-03 |
| 65 | 3R | 17,160,001 | 17,355,000 | 89F1-90A2 | 195,000 | 0.62 | 0.94 | 84 | 1.0E-03 | 0.86 | 64 | 2.8E-04 |
| 66 | 3R | 20,085,001 | 20,290,000 | 92C4-E1 | 205,000 | 0.61 | 0.81 | 53 | 1.5E-03 | 0.71 | 26 | 3.6E-03 |
| 67 | 3R | 20,340,001 | 20,525,000 | 92E4-E12 | 185,000 | 0.58 | 0.96 | 91 | 5.0E-05 | 0.79 | 50 | 7.2E-04 |
| 68 | 3R | 22,110,001 | 22,295,000 | 94A2-A4 | 185,000 | 0.61 | 0.93 | 83 | 3.4E-11 | 0.76 | 39 | 3.0E-04 |
| 69 | 3R | 28,005,001 | 28,295,000 | 98B7-C3 | 290,000 | 0.40 | 0.91 | 85 | 2.5E-05 | 0.60 | 32 | 6.9E-04 |
| 70 | 3R | 28,370,001 | 28,480,000 | 98C5-D2 | 110,000 | 0.73 | 0.98 | 94 | 1.2E-09 | 0.91 | 66 | 4.3E-07 |
| UR domains: 70 <Length> : 216 ± 64 kbp Average <CN> across all UR domains: 0.49 ± 0.08 |
Suppressed UR domains: 69 <Length> : 217 ± 64 kbp <Recovery> : 78 ± 11% |
Suppressed UR domains: 60 <Length> : 225 ± 67 kbp <Recovery> : 26 ± 9% |
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