Table 1.
Kinetic classifications and boundary analysis of ORFs during productive infection
| ORF |
De novo fibroblasts |
TPA-stimulated reactivation A20-HE2 B cells |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| % peak expression at the following times (h) postinfectiona: |
Kinetic classification |
Predicted transcript structured |
% peak expression at the following times (h) postinductiona: |
Kinetic arraye | ||||||||||||
| 2 | 4 | 6 | 8 | 10 | 12 | 18 | Arrayb | Previousc | Strand | 5′ boundary | 3′ boundary | 6 | 12 | 24 | ||
| M1-M1, secreted superantigen-like | 3.5 | 4.8 | 11.5 | 29.3 | 39.8 | 46.1 | 100.0 | IV | E-L | + | 1,960–1,980 | 3,340–3,360 | 10.2 | 71.5 | 100.0 | II |
| M2-M2, adaptor protein | 1.2 | 5.6 | 13.9 | 19.7 | 34.6 | 48.5 | 100.0 | II | E-L | − | 5,931–5,911 | 3,391–3,371 | 22.3 | 43.4 | 100.0 | III |
| M3-M3, chemokine-binding protein | 1.0 | 9.0 | 36.0 | 64.3 | 76.8 | 91.0 | 100.0 | II | E-L | − | 7,311–7,291 | 6,031–6,011 | 7.6 | 61.0 | 100.0 | II |
| M4-M4, secreted protein | 1.2 | 11.4 | 54.2 | 84.6 | 78.0 | 76.0 | 100.0 | II | IE | + | 8,520–8,540 | 9,840–9,860 | 21.2 | 73.4 | 100.0 | II |
| ORF4, complement control protein | 1.5 | 2.0 | 7.4 | 32.9 | 67.2 | 70.0 | 100.0 | III | E-L | + | 9,880–9,900 | NDf | 56.0 | 65.9 | 100.0 | IV |
| ORF6, single-stranded DNA-binding protein | 1.9 | 12.1 | 38.7 | 53.6 | 71.5 | 75.3 | 100.0 | II | E-L | + | 11,180–11,200 | 14,900–14,920 | 35.2 | 72.8 | 100.0 | III |
| ORF7, DNA-packaging terminase subunit 2 | 9.3 | 12.8 | 23.5 | 36.1 | 45.3 | 49.8 | 100.0 | IV | E-L | + | ND | ND | 81.5 | 84.1 | 100.0 | ND |
| ORF8, envelope glycoprotein B | 1.9 | 2.3 | 13.4 | 49.2 | 78.0 | 83.0 | 100.0 | III | L | + | 16,460–16,480 | 19,120–19,140 | 11.9 | 37.1 | 100.0 | III |
| ORF9, DNA polymerase catalytic subunit | 5.4 | 13.7 | 54.3 | 61.3 | 59.2 | 59.0 | 100.0 | II | E, E-L | + | 19,220–19,240 | ND | 53.2 | 100.0 | 88.0 | I |
| ORF10, protein G10 | 2.3 | 8.5 | 42.1 | 61.5 | 62.9 | 65.5 | 100.0 | II | E-L | + | ND | ND | 24.2 | 100.0 | 62.7 | I |
| ORF11, virion protein G11 | 4.0 | 7.3 | 28.6 | 54.9 | 66.5 | 67.4 | 100.0 | II | L | + | 23,420–23,440 | 24,680–24,700 | 25.1 | 68.4 | 100.0 | II |
| ORF12, mK3, E3 ubiquitin ligase MIR1 | 2.4 | 10.4 | 39.8 | 62.2 | 56.5 | 58.4 | 100.0 | II | IE, L | − | 25,831–25,811 | 24,711–24,691 | 6.4 | 95.3 | 100.0 | II |
| ORF17, capsid maturation protease | 1.8 | 2.1 | 10.6 | 44.7 | 75.1 | 76.2 | 100.0 | III | L | − | 29,991–29,971 | 28,271–28,251 | 11.8 | 40.5 | 100.0 | III |
| ORF17.5, capsid scaffold protein | 2.2 | 2.4 | 17.8 | 71.9 | 91.8 | 99.8 | 100.0 | III | ND | − | ND | 28,271–28,251 | 8.9 | 33.4 | 100.0 | III |
| ORF18, protein UL79 | 1.0 | 1.9 | 23.3 | 43.4 | 49.3 | 52.1 | 100.0 | II | L | + | ND | 30,760–30,780 | 2.3 | 24.2 | 100.0 | III |
| ORF19, DNA-packaging tegument protein UL25 | 3.2 | 3.4 | 16.3 | 69.8 | 99.8 | 95.7 | 100.0 | III | L | − | ND | 30,711–30,691 | 13.4 | 47.1 | 100.0 | III |
| ORF20, nuclear protein UL24 | 2.4 | 2.9 | 14.3 | 62.9 | 93.2 | 93.9 | 100.0 | III | E-L | − | 32,971–32,951 | ND | 41.1 | 96.3 | 100.0 | II |
| ORF21, thymidine kinase | 1.8 | 5.6 | 45.8 | 81.2 | 92.3 | 86.1 | 100.0 | II | E-L | + | 32,860–32,880 | ND | 7.2 | 100.0 | 81.7 | II |
| ORF22, envelope glycoprotein H | 0.9 | 3.6 | 25.3 | 70.6 | 88.1 | 94.2 | 100.0 | II | L | + | ND | 37,000–37,020 | 5.8 | 52.2 | 100.0 | II |
| ORF23, protein UL88 | 0.9 | 1.3 | 10.7 | 35.7 | 58.2 | 68.2 | 100.0 | III | L | − | ND | 37,011–36,991 | 9.3 | 35.5 | 100.0 | III |
| ORF24, virion protein UL87 | 2.7 | 4.1 | 37.5 | 54.5 | 49.3 | 53.7 | 100.0 | II | E | − | ND | ND | 33.1 | 100.0 | 99.1 | II |
| ORF25, major capsid protein | 1.1 | 1.4 | 16.3 | 61.6 | 91.3 | 76.7 | 100.0 | III | E-L | + | 40,240–40,260 | ND | 19.9 | 36.2 | 100.0 | IV |
| ORF26, capsid triplex subunit 2 | 0.9 | 1.2 | 15.9 | 65.4 | 89.8 | 89.7 | 100.0 | III | L | + | ND | ND | 5.5 | 23.6 | 100.0 | III |
| ORF27, envelope glycoprotein 48 | 0.9 | 1.2 | 20.3 | 73.5 | 94.2 | 97.7 | 100.0 | III | L | + | ND | ND | 7.2 | 31.5 | 100.0 | III |
| ORF28, envelope glycoprotein 150 | 0.2 | 0.4 | 20.9 | 81.0 | 97.4 | 100.0 | 99.8 | III | L | + | ND | 46,380–46,400 | 4.6 | 17.9 | 100.0 | III |
| ORF29, DNA-packaging terminase subunit 1 | 1.0 | 1.7 | 8.7 | 28.3 | 38.0 | 51.7 | 100.0 | III | L | − | ND (exon 1)/ 47,531–47,511 (exon 2) | 50,571–50,551 (exon 1)/-46,411–46,391 (exon 2) | 39.5 | 55.3 | 100.0 | IV |
| ORF30, protein UL91 | 1.4 | 3.5 | 22.1 | 52.8 | 75.9 | 80.6 | 100.0 | II | E-L | + | ND | ND | 19.2 | 100.0 | 61.8 | II |
| ORF31, protein UL92 | 1.0 | 3.5 | 28.1 | 66.4 | 80.8 | 89.0 | 100.0 | II | E-L | + | ND | 48,300–48,320 | 15.8 | 100.0 | 54.0 | I |
| ORF32, DNA-packaging tegument protein UL17 | 1.8 | 5.0 | 27.2 | 43.8 | 56.2 | 59.5 | 100.0 | II | E-L | + | 48,300–48,320 | ND | 26.9 | 64.3 | 100.0 | III |
| ORF33, tegument protein UL16 | 1.4 | 2.2 | 17.7 | 53.2 | 74.8 | 75.3 | 100.0 | III | L | + | ND | 50,880–50,900 | 8.6 | 22.8 | 100.0 | IV |
| ORF34, protein UL95 | 3.3 | 10.4 | 59.0 | 64.1 | 58.2 | 61.3 | 100.0 | II | E-L | + | 51,460–51,480 | ND | 58.1 | 95.8 | 100.0 | II |
| ORF35, tegument protein UL14 | 1.2 | 6.2 | 44.8 | 64.8 | 66.8 | 66.7 | 100.0 | II | E-L | + | ND | ND | 57.8 | 77.6 | 100.0 | III |
| ORF36, tegument serine/threonine protein kinase | 1.1 | 40.1 | 75.5 | 78.0 | 77.9 | 81.8 | 100.0 | I | E | + | 52,820–52,840 | ND | 27.4 | 66.8 | 100.0 | III |
| ORF37, SOX, shutoff, and exonuclease | 0.6 | 44.8 | 73.1 | 76.8 | 72.0 | 82.3 | 100.0 | I | E-L | + | ND | ND | 6.4 | 77.1 | 100.0 | II |
| ORF38, myristylated tegument protein | 0.6 | 37.5 | 58.8 | 79.2 | 82.3 | 95.3 | 100.0 | I | IE | + | ND | 55,780–55,800 | 5.6 | 35.5 | 100.0 | II |
| ORF39, envelope glycoprotein M | 1.1 | 1.5 | 10.0 | 55.6 | 79.3 | 91.2 | 100.0 | III | L | − | 57,051–57,031 | 55,791–55,771 | 3.6 | 15.5 | 100.0 | III |
| ORF40, helicase/primase subunit | 0.7 | 9.9 | 24.8 | 32.2 | 38.2 | 50.6 | 100.0 | II | E-L | + | 56,960–56,980 | 58,840–58,860 | 12.0 | 71.7 | 100.0 | II |
| ORF42, tegument protein UL7 | 0.9 | 3.9 | 18.8 | 51.0 | 68.0 | 74.7 | 100.0 | II | L | − | ND | 58,871–58,851 | 8.5 | 61.8 | 100.0 | II |
| ORF43, capsid portal protein | 0.4 | 0.7 | 6.4 | 29.2 | 49.4 | 58.0 | 100.0 | III | E-L | − | ND | ND | 13.4 | 35.0 | 100.0 | III |
| ORF44, helicase/primase helicase subunit | 1.5 | 28.3 | 66.4 | 65.7 | 55.2 | 66.6 | 100.0 | I | E-L | + | 61,260–61,280 | 63,620–63,640 | 21.0 | 96.4 | 100.0 | II |
| ORF45, tegument protein G45 | 0.9 | 2.7 | 13.6 | 50.8 | 71.2 | 86.3 | 100.0 | II | L | − | ND | 63,651–63,631 | 4.3 | 22.6 | 100.0 | III |
| ORF46, uracil-DNA glycosylase | 0.4 | 2.1 | 10.7 | 26.9 | 53.3 | 65.6 | 100.0 | II | L | − | ND | ND | 7.8 | 39.0 | 100.0 | III |
| ORF47, envelope glycoprotein L | 0.5 | 2.0 | 9.0 | 18.3 | 35.2 | 48.8 | 100.0 | II | E-L | − | ND | ND | 13.5 | 30.3 | 100.0 | IV |
| ORF48, tegument protein G48 | 1.0 | 14.1 | 67.5 | 84.8 | 74.7 | 78.4 | 100.0 | II | L | − | 66,591–66,571 | ND | 9.3 | 100.0 | 98.6 | II |
| ORF49, protein G49 | 0.4 | 5.1 | 10.7 | 28.2 | 40.8 | 54.6 | 100.0 | II | E-L | − | 67,731–67,711 | ND | 21.2 | 58.3 | 100.0 | III |
| ORF50, RTA, viral transactivator | 3.4 | 70.6 | 72.2 | 68.7 | 60.8 | 79.8 | 100.0 | I | IE | + | 66,720–66,740 (exon 1)/67,640–67,660 (exon 2) | 66,800–66,820 (exon 1)/69,440–69,460 (exon 2) | 28.0 | 75.8 | 100.0 | II |
| ORF51, M7, envelope glycoprotein gp150 | 9.3 | 10.8 | 12.2 | 32.0 | 48.0 | 55.0 | 100.0 | IV | L | + | ND | 70,920–70,940 | 36.8 | 50.8 | 100.0 | IV |
| ORF52, virion protein G52 | 1.0 | 3.2 | 10.9 | 52.1 | 79.8 | 94.5 | 100.0 | II | L | − | ND | 70,951–70,931 | 2.4 | 10.1 | 100.0 | III |
| ORF53, envelope glycoprotein N | 0.6 | 0.7 | 6.5 | 50.3 | 81.4 | 91.5 | 100.0 | III | L | − | ND | ND | 0.9 | 9.6 | 100.0 | III |
| ORF54, deoxyuridine triphosphatase | 1.1 | 51.0 | 100.0 | 80.4 | 43.7 | 47.4 | 35.4 | I | E | + | 71,780–71,800 | 72,740–72,760 | 14.8 | 100.0 | 60.3 | I |
| ORF55, tegument protein UL51 | 1.1 | 1.4 | 8.5 | 39.9 | 60.3 | 64.7 | 100.0 | III | E-L | − | 73,351–73,331 | ND | 6.5 | 26.4 | 100.0 | III |
| ORF56, helicase/primase primase subunit | 3.4 | 29.8 | 64.1 | 41.5 | 35.2 | 47.2 | 100.0 | I | E-L | + | 73,220–73,240 | ND | 61.6 | 82.9 | 100.0 | III |
| ORF57, multifunctional expression regulator and vMAP | 1.4 | 45.5 | 75.0 | 66.2 | 46.7 | 69.9 | 100.0 | I | IE | + | 75, 980–76,000 (exon 2) | 75,880–75,900 (exon 1)/77,160–77, 180 (exon 2) | 6.3 | 100.0 | 87.7 | II |
| ORF58, envelope protein UL43 | 0.8 | 10.7 | 48.2 | 78.4 | 79.7 | 90.6 | 100.0 | II | L | − | ND | 77,191–77,171 | 5.5 | 52.8 | 100.0 | II |
| ORF59, DNA polymerase processivity subunit | 1.8 | 16.7 | 81.8 | 96.1 | 82.5 | 88.6 | 100.0 | II | L | − | ND | ND | 6.1 | 85.5 | 100.0 | II |
| ORF60, ribonucleotide reductase subunit 2 | 0.7 | 6.4 | 69.1 | 91.8 | 73.6 | 68.9 | 100.0 | II | E-L | − | 80,471–80,451 | ND | 19.9 | 80.6 | 100.0 | II |
| ORF61, ribonucleotide reductase subunit 1 | 1.4 | 44.2 | 65.9 | 73.1 | 71.1 | 91.5 | 100.0 | I | L | − | 82,911–82,891 | 80,491–80,471 | 18.5 | 100.0 | 81.7 | I |
| ORF62, capsid triplex subunit 1 | 1.0 | 1.5 | 5.7 | 38.3 | 67.5 | 80.9 | 100.0 | III | L | − | 83,971–83,951 | ND | 48.7 | 69.4 | 100.0 | III |
| ORF63, tegument protein UL37 | 15.9 | 17.8 | 30.0 | 65.2 | 83.8 | 83.6 | 100.0 | III | E | + | 83,760–83,780 | 86,540–86,560 | 42.1 | 58.0 | 100.0 | IV |
| ORF64, large tegument protein | 14.3 | 16.5 | 22.5 | 46.2 | 63.5 | 69.6 | 100.0 | IV | E | + | 86,580–86,600 | 93,840–93,860 | 36.8 | 54.9 | 100.0 | IV |
| ORF65, M9, small capsid protein | 1.2 | 1.7 | 7.9 | 46.6 | 72.6 | 90.8 | 100.0 | III | L | − | ND | 93,851–93,831 | 2.1 | 9.0 | 100.0 | IV |
| ORF66, protein UL49 | 1.2 | 1.6 | 7.7 | 42.0 | 68.4 | 85.9 | 100.0 | III | L | − | ND | ND | 3.2 | 11.7 | 100.0 | III |
| ORF67, nuclear egress type 2 membrane protein | 1.0 | 1.2 | 5.2 | 35.2 | 62.9 | 79.7 | 100.0 | III | L | − | ND | ND | 3.6 | 18.3 | 100.0 | III |
| ORF67A, DNA-packaging protein UL33 | 0.3 | 0.4 | 3.4 | 33.3 | 63.3 | 79.5 | 100.0 | III | ND | − | ND | ND | 1.9 | 6.2 | 100.0 | IV |
| ORF68, DNA-packaging protein UL32 | 6.8 | 8.6 | 24.3 | 90.7 | 96.3 | 100.0 | 64.7 | III | E | + | ND | ND | 8.2 | 19.3 | 100.0 | IV |
| ORF69, nuclear egress lamina protein | 1.0 | 1.7 | 13.4 | 54.1 | 79.6 | 80.2 | 100.0 | III | L | + | ND | 98,940–98,960 | 3.8 | 30.1 | 100.0 | III |
| ORF72, v-cyclin | 0.6 | 7.2 | 16.3 | 20.4 | 25.4 | 41.4 | 100.0 | II | E-L | − | 103,271–103,251 (ORF exon) | 102,431–102,411 | 13.4 | 100.0 | 50.6 | I |
| M11, v-bcl-2 | 7.6 | 13.7 | 65.9 | 100.0 | 88.7 | 93.2 | 85.4 | II | E-L | + | ND | ND | 11.1 | 100.0 | 68.7 | I |
| ORF73, mLANA | 2.5 | 34.1 | 44.5 | 33.4 | 39.9 | 51.8 | 100.0 | I | IE | − | 104,891–104,871 (ORF exon), 105,011–104,911 | 103,771–103,751 | 29.8 | 51.8 | 100.0 | III |
| ORF74, v-GPCR | 1.2 | 3.9 | 29.5 | 49.8 | 53.5 | 59.9 | 100.0 | II | E-L | + | 104,720–104,740 | 105,800–105,820, 106,620–106,640 | 9.9 | 69.6 | 100.0 | II |
| ORF75C, tegument protein G75C | 1.5 | 2.5 | 6.3 | 38.8 | 74.9 | 69.5 | 100.0 | III | L | − | 110,031–110,011 | 105,831–105,811 | 4.9 | 15.2 | 100.0 | IV |
| ORF75B, protein G75B | 3.2 | 9.7 | 17.4 | 40.3 | 64.5 | 58.4 | 100.0 | II | E | − | ND | ND | 8.3 | 13.0 | 100.0 | IV |
| ORF75A protein G75A | 35.3 | 58.1 | 66.1 | 61.1 | 59.0 | 67.5 | 100.0 | ND | IE, E-L | − | ND | ND | 18.5 | 23.3 | 100.0 | IV |
a
Values represent the percentage of peak expression based on the median normalized, background-subtracted log2 probe value of each ORF.
b
Classifications based on heat map clusters determined in Fig. 2.
c
Classification based on previous studies that are used for color codes of ORF names in Fig. 2 and 3 (2, 18, 40, 59).
d
Consistent with transcripts previously reported: M2 (16); M3 (2, 84); ORF6, ORF8, ORF11, ORF12, ORF51, ORF54, and ORF57 (35); ORF50 (29, 53); ORF57 (56); ORF72 (3, 4); ORF73 (4, 12); ORF74 (86); and ORF52 and ORF67 (56).
e
Classifications based on heat map clusters determined in Fig. 3.
f
ND, not determined.