Table 1. Identified RNA splice junctions (SJ) with ≥10 splice reads from the KSHV WT or 57KO genome in BCBL-1 cells.
The positions of 5′ and 3′ splice sites (SS) are based on the KSHV reference genome GenBank Acc. No. HQ404500. The reads-number represents a total number of splice reads in the WT or 57KO group during lytic replication (see S2 Table for the details). The SJ fold change (FC) represents splice junction-reads change in BCBL-1 cells with the KSHV 57KO versus WT genome during viral lytic replication. The asterisk marks significant (p ≤ 0.05) change by Student t-test. The transcript FC for the annotated genes was determined by Limma Voom differential gene expression analysis (see S1 Table for the details), with the color gradient red for decrease and green for increase. The genes with significant expression changes (p ≤0.01) are marked with an asterisk. N/D—not determined.
| Splice junction | 5′ SS (nt position) | 3′ SS (nt position) | Intron size (nt) | Strand | Reads | Transcript | SJ FC 57KO/WT | FC 57KO/WT | |
|---|---|---|---|---|---|---|---|---|---|
| WT | 57KO | ||||||||
| SJ-1 | 981 | 2625 | 1643 | + | 28 | 42 | K1/ORF4 | 1.50 | 1.23 (K1), -1.05 (ORF4) |
| SJ-2 | 61179 | 61307 | 127 | + | 28 | 27 | ORF40/41 | -1.04 | -2.14*(ORF40), 1.14 (ORF41) |
| SJ-3 | 69364 | 72094 | 2729 | + | 46 | 72 | ORF50 | 1.57 | 1.30 (ORF50) |
| SJ-4 | 71135 | 72094 | 958 | + | 467 | 649 | ORF50 | 1.39 | 1.30 (ORF50) |
| SJ-5 | 74845 | 74993 | 147 | + | 4414 | 4860 | ORF50/K8 | 1.10 | 1.30 (ORF50), 1.09 (K8) |
| SJ-6 | 75085 | 75167 | 81 | + | 3034 | 3796 | ORF50/K8 | 1.25 | 1.30 (ORF50), 1.09 (K8) |
| SJ-7 | 75360 | 75955 | 594 | + | 3800 | 5416 | ORF50/K8 | 1.43 | 1.30 (ORF50), 1.09 (K8) |
| SJ-8 | 75860 | 75955 | 94 | + | 49 | 42 | ORF50/K8/K8.1 | -1.16 | 1.30 (ORF50), 1.09 (K8), 1.03 (K8.1) |
| SJ-9 | 81640 | 81749 | 108 | + | 1885 | 172 | ORF56/ORF57 | -11.11* | -1.65 (ORF56), -9.02* (ORF57) |
| SJ-10 | 82497 | 83069 | 571 | + | 17 | 15 | ORF56/ORF57 | -1.14 | -1.65 (ORF56), -9.02* (ORF57) |
| SJ-11 | 119871 | 127583 | 7711 | + | 29 | 25 | ALT RNA | -1.16 | N/D |
| SJ-12 | 119871 | 128429 | 8557 | + | 23 | 99 | ALT RNA | 4.30* | N/D |
| SJ-13 | 128279 | 128429 | 149 | + | 359 | 223 | K14/ORF74 | -1.61 | -1.54 (K14), -1.28 (ORF74) |
| SJ-14 | 18217 | 18094 | 122 | - | 21 | 4 | ORF2 | -5.26* | -2.60*(ORF2) |
| SJ-15 | 19696 | 19575 | 120 | - | 23 | 57 | ORF70/K3 | 2.48 | -2.67*(ORF70), -1.76* (K3) |
| SJ-16 | 19718 | 19575 | 142 | - | 31 | 36 | ORF70/K3 | 1.16 | -2.67*(ORF70), -1.76* (K3) |
| SJ-17 | 20050 | 19575 | 474 | - | 3393 | 2048 | ORF70/K3 | -1.67 | -2.67*(ORF70), -1.76* (K3) |
| SJ-18 | 20379 | 19575 | 803 | - | 45 | 7 | ORF70/K3 | -6.25* | -2.67*(ORF70), -1.76* (K3) |
| SJ-19 | 20804 | 19575 | 1228 | - | 26 | 38 | ORF70/K3 | 1.46 | -2.67*(ORF70), -1.76* (K3) |
| SJ-20 | 20379 | 20263 | 115 | - | 13 | 13 | ORF70/K3 | 1.00 | -2.67*(ORF70), -1.76* (K3) |
| SJ-21 | 20804 | 20263 | 540 | - | 691 | 1839 | ORF70/K3 | 2.66* | -2.67*(ORF70), -1.76* (K3) |
| SJ-22 | 22790 | 22043 | 746 | - | 12 | 2 | K4.2/K4 | -5.88 | -1.80* (K4.2) -1.03 (K4) |
| SJ-23 | 26260 | 26091 | 168 | - | 625 | 511 | K5 | -1.22 | -1.14 (K5) |
| SJ-24 | 26298 | 26091 | 206 | - | 1622 | 1232 | K5 | -1.32 | -1.14 (K5) |
| SJ-25 | 26447 | 26091 | 355 | - | 11 | 4 | K6/K5 | -2.78 | -1.97* (K6), -1.14 (K5) |
| SJ-26 | 27110 | 26091 | 1018 | - | 64 | 65 | K6/K5 | 1.02 | -1.97* (K6), -1.14 (K5) |
| SJ-27 | 27126 | 26091 | 1034 | - | 96 | 145 | K6/K5 | 1.51 | -1.97* (K6), -1.14 (K5) |
| SJ-28 | 27191 | 26091 | 1099 | - | 139 | 175 | K6/K5 | 1.26 | -1.97* (K6), -1.14 (K5) |
| SJ-29 | 27233 | 26091 | 1141 | - | 146 | 215 | K6/K5 | 1.47 | -1.97* (K6), -1.14 (K5) |
| SJ-30 | 27709 | 26091 | 1617 | - | 15 | 19 | K6/K5 | 1.27 | -1.97* (K6), -1.14 (K5) |
| SJ-31 | 27126 | 27036 | 89 | - | 74 | 15 | K6 | -5.00* | -1.97* (K6) |
| SJ-32 | 27191 | 27036 | 154 | - | 16 | 3 | K6 | -5.26 | -1.97* (K6) |
| SJ-33 | 27233 | 27036 | 196 | - | 14 | 3 | K6 | -4.76* | -1.97* (K6) |
| SJ-34 | 69684 | 42544 | 27139 | - | 17 | 34 | ORF48/ORF25 | 2.00 | 1.51* (ORF48), -1.13 (ORF25) |
| SJ-35 | 69684 | 50027 | 19656 | - | 64 | 107 | ORF48/ORF29 | 1.67 | 1.51* (ORF48), 1.67* (ORF29b) |
| SJ-36 | 69270 | 67968 | 1301 | - | 10 | 36 | ORF47/ORF45 | 3.60 | -1.57 (ORF47), -1.33 (ORF45) |
| SJ-37 | 68506 | 68119 | 386 | - | 64 | 12 | ORF46/ORF45 | -5.26 | -1.77* (ORF46), -1.33 (ORF45) |
| SJ-38 | 69096 | 68119 | 976 | - | 260 | 500 | ORF47/ORF45 | 1.92 | -1.56 (ORF47), -1.33 (ORF45) |
| SJ-39 | 69136 | 68119 | 1016 | - | 13 | 31 | ORF47/ORF45 | 2.38 | -1.56 (ORF47), -1.33 (ORF45) |
| SJ-40 | 69270 | 68119 | 1150 | - | 231 | 833 | ORF47/ORF45 | 3.61* | -1.56 (ORF47), -1.33 (ORF45) |
| SJ-41 | 69684 | 68119 | 1564 | - | 75 | 333 | ORF48/ORF45 | 4.44* | 1.51* (ORF48), -1.33 (ORF45) |
| SJ-42 | 87967 | 87865 | 101 | - | 54 | 25 | K10 (vIRF4) | -2.17 | -1.18 K10 (vIRF4) |
| SJ-43 | 88558 | 88321 | 236 | - | 24 | 15 | K10 (vIRF4) | -1.59 | -1.18 K10 (vIRF4) |
| SJ-44 | 90463 | 90368 | 94 | - | 67 | 80 | K10.5 (vIRF3) | 1.19 | -1.21 K10.5 (vIRF3) |
| SJ-45 | 93163 | 93041 | 121 | - | 37 | 47 | K11 (vIRF2) | 1.27 | -1.30 K11 (vIRF2) |
| SJ-46 | 117854 | 117790 | 63 | - | 13 | 15 | K12 | 1.15 | 1.61* (K12) |
| SJ-47 | 118145 | 117994 | 150 | - | 36 | 71 | ORF72/ORF71 | 1.97 | -1.31* (ORF72), -1.35* (ORF71) |
| SJ-48 | 122790 | 117994 | 4795 | - | 96 | 59 | ORF72/ORF71 | -1.64 | -1.31* (ORF72), -1.35* (ORF71) |
| SJ-49 | 126873 | 122971 | 3901 | - | 27 | 23 | ORF73/ORF72/ORF71 | -1.18 | -1.31 (ORF73), -1.31* (ORF72), -1.35* (ORF71) |
| SJ-50 | 126873 | 126373 | 499 | - | 31 | 17 | ORF73/ORF72/ORF71 | -1.82 | -1.31 (ORF73), -1.31* (ORF72), -1.35* (ORF71) |
| SJ-51 | 134285 | 134199 | 85 | - | 20 | 13 | K15 | -1.54 | 1.10 (K15) |
| SJ-52 | 134469 | 134386 | 82 | - | 18 | 7 | K15 | -2.56 | 1.10 (K15) |
| SJ-53 | 134659 | 134576 | 82 | - | 14 | 16 | K15 | 1.14 | 1.10 (K15) |
| SJ-54 | 134889 | 134811 | 77 | - | 34 | 51 | K15 | 1.50 | 1.10 (K15) |
| SJ-55 | 135067 | 134978 | 88 | - | 29 | 36 | K15 | 1.24 | 1.10 (K15) |
| SJ-56 | 135393 | 135309 | 83 | - | 19 | 51 | K15 | 2.68 | 1.10 (K15) |
| SJ-57 | 135595 | 135485 | 109 | - | 12 | 28 | K15 | 2.33* | 1.10 (K15) |