Table 3. Differentially expressed ncRNAs upon exposure to lethal dose of H2O2.
| NC RNA | chromosome | Log2Fc | Adjusted p-value | Start-End | Overlapping ORFa | Upstream ORFa | Downstream ORFa | perR mutantb |
|---|---|---|---|---|---|---|---|---|
| Up-regulated | ||||||||
| rh34 | NZ_CP011933.1 | 1.218 | 1.23e-30 | 18632–19081 | LIMLP_19345 | LEPIMA _p0012 | LIMLP_19350 | |
| rh36 | NZ_CP011933.1 | 1.368 | 4.02e-37 | 20723–21129 | NA | LIMLP_19355 | LIMLP_19360 | |
| rh47 | NZ_CP011931.1 | 1.150 | 2.80e-57 | 37221–37455 | NA | LIMLP_00160 | LIMLP_00165 | |
| rh49 | NZ_CP011932.1 | 1.013 | 2.50e-47 | 39710–39825 | LEPIMA_CII0041 | LIMLP_18000 | LIMLP_18005 | |
| rh57§ | NZ_CP011933.1 | 1.629 | 1.95e-69 | 23941–24050 | LEPIMA _p0025 | LIMLP_19380 | LIMLP_19385 | |
| rh82 | NZ_CP011933.1 | 1.362 | 3.50e-37 | 32192–32351 | NA | LIMLP_19435 | LEPIMA _p0038 | |
| rh97 | NZ_CP011932.1 | 1.170 | 3.03e-57 | 66008–66133 | LIMLP_18130 | LIMLP_18125 | LEPIMA_CII0073 | |
| rh178 | NZ_CP011933.1 | 1.195 | 2.92e-22 | 57959–58185 | NA | LEPIMA _p0081 | LIMLP_19600 | |
| rh179 | NZ_CP011933.1 | 1.082 | 7.04e-14 | 58957–59117 | LEPIMA _p0083 | LIMLP_19600 | LIMLP_19605* | |
| rh183 | NZ_CP011931.1 | 1.557 | 7.61e-80 | 128941–129006 | NA | LIMLP_00580 | LIMLP_00585 | |
| rh184 | NZ_CP011931.1 | 1.228 | 2.09e-66 | 129119–129450 | LIMLP_00585 | LIMLP_00580 | LIMLP_00595 | |
| rh199 | NZ_CP011933.1 | 1.009 | 7.80e-24 | 63659–64935 | LEPIMA_p0089, LIMLP_19625, LIMLP_19630 | LIMLP_19620 | LIMLP_19635 | |
| rh210 | NZ_CP011931.1 | 1.231 | 1.22e-61 | 158886–159090 | NA | LIMLP_00700* | LIMLP_00705 | |
| rh219 | NZ_CP011932.1 | 1.337 | 2.22e-97 | 147192–147336 | LIMLP_18455** | LIMLP_18450 | LIMLP_18460** | |
| rh288 | NZ_CP011931.1 | 3.812 | 0.00 | 197282–197352 | LIMLP_00895* | LIMLP_00890 | LEPIMA_CI0185 | Up-regulated |
| rh349 | NZ_CP011932.1 | 1.638 | 1.98e-120 | 256577–256639 | NA | LEPIMA_CII0243 | LIMLP_18855 | |
| rh402 | NZ_CP011932.1 | 1.517 | 1.31e-92 | 291497–291605 | LIMLP_18995 | LIMLP_18990** | LIMLP_19000* | |
| rh449 | NZ_CP011931.1 | 2.512 | 0.00 | 351592–351649 | NA | LIMLP_01545* | LIMLP_01550* | |
| rh488 | NZ_CP011932.1 | 1.184 | 1.11e-48 | 352594–352673 | LIMLP_19275 | LIMLP_19270 | LIMLP_19280 | |
| rh490 | NZ_CP011932.1 | 1.277 | 2.18e-49 | 353695–353790 | LIMLP_19280 | LIMLP_19275 | LIMLP_19285 | |
| rh593 | NZ_CP011931.1 | 1.362 | 1.44e-43 | 471763–471828 | LIMLP_02010** | LIMLP_02005 | LEPIMA_CI0422 | |
| rh608 | NZ_CP011931.1 | 2.476 | 0.00 | 479394–479448 | LIMLP_02045* | LIMLP_02040* | LIMLP_02050 | |
| rh625 | NZ_CP011931.1 | 1.077 | 9.15e-49 | 499440–499814 | LIMLP_02100 | LIMLP_02095 | LIMLP_02105* | |
| rh637# | NZ_CP011931.1 | 1.663 | 2.16e-137 | 501388–501477 | NA | LIMLP_02105* | LIMLP_02110 | |
| rh786 | NZ_CP011931.1 | 1.135 | 6.17e-50 | 632024–632186 | LIMLP_02580 | LIMLP_02575 | LIMLP_02585 | |
| rh859# | NZ_CP011931.1 | 4.248 | 0.00 | 683752–684074 | NA | LIMLP_02795* | LEPIMA_CI0612 | Up-regulated |
| rh1048 | NZ_CP011931.1 | 1.059 | 3.63e-43 | 846807–846960 | LIMLP_03520 | LIMLP_03515 | LIMLP_03525 | |
| rh1167 | NZ_CP011931.1 | 1.070 | 2.97e-37 | 943926–943989 | LIMLP_03935 | LIMLP_03930 | LIMLP_03940 | |
| rh1192 | NZ_CP011931.1 | 2.197 | 5.78e-214 | 975150–975213 | LIMLP_04030 | LIMLP_04025 | LIMLP_04035 | |
| rh1210 (RF00059) | NZ_CP011931.1 | 1.236 | 3.67e-37 | 995004–995065 | NA | LIMLP_04090 | LIMLP_04095** | |
| rh1269 | NZ_CP011931.1 | 2.164 | 2.97e-202 | 1038822–1038876 | LIMLP_04290 | LIMLP_04285 | LIMLP_04295* | |
| rh1270 | NZ_CP011931.1 | 1.491 | 2.13e-108 | 1039034–1039628 | LIMLP_04295*, LEPIMA_CI0938 | LIMLP_04290 | LIMLP_04300 | |
| rh1429 | NZ_CP011931.1 | 1.720 | 3.15e-90 | 1181397–1181456 | LIMLP_04840 | LIMLP_04830 | LIMLP_04845 | |
| rh1498 | NZ_CP011931.1 | 1.288 | 1.08e-46 | 1260173–1260234 | NA | LEPIMA_CI1128 | LIMLP_05125* | |
| rh1641 | NZ_CP011931.1 | 2.013 | 2.50e-145 | 1386755–1386830 | LIMLP_05625 | LIMLP_05620* | LIMLP_05630 | |
| rh1807 | NZ_CP011931.1 | 2.928 | 0.00 | 1531048–1531289 | LIMLP_06235 | LIMLP_06230 | LIMLP_06240 | |
| rh2088 | NZ_CP011931.1 | 2.000 | 1.66e-149 | 1780300–1780403 | LIMLP_07195 | LEPIMA_CI1612 | LIMLP_07200 | |
| rh2227 | NZ_CP011931.1 | 3.130 | 0.00 | 1892070–1892135 | NA | LIMLP_07695 | LIMLP_07700 | |
| rh2395 | NZ_CP011931.1 | 1.877 | 2.09e-123 | 2013277–2013341 | LIMLP_08295 | LIMLP_08290 | LIMLP_08300 | |
| rh2487 | NZ_CP011931.1 | 1.230 | 5.68e-66 | 2083779–2083898 | LIMLP_08585 | LEPIMA_CI1903 | LIMLP_08590* | Down-regulated |
| rh2961 | NZ_CP011931.1 | 1.974 | 8.15e-150 | 2474618–2474668 | LIMLP_10350 | LIMLP_10345 | LIMLP_10355 | |
| rh3130# | NZ_CP011931.1 | 7.189 | 0.00 | 2612368–2612495 | LEPIMA_CI2416 | LIMLP_10975* | LEPIMA_CI2417 | |
| rh3147 | NZ_CP011931.1 | 1.230 | 8.22e-39 | 2625684–2625735 | LIMLP_11030 | LIMLP_11025 | LEPIMA_CI2429 | |
| rh3352# | NZ_CP011931.1 | 7.653 | 0.00 | 2787780–2787953 | LIMLP_11710* | LIMLP_11705 | LIMLP_11715* | |
| rh3535 | NZ_CP011931.1 | 1.016 | 1.77e-49 | 2958335–2958610 | NA | LIMLP_12420 | LIMLP_12425* | |
| rh3538 | NZ_CP011931.1 | 1.000 | 2.78e-21 | 2958938–2959002 | LIMLP_12425* | LIMLP_12420 | LIMLP_12430* | |
| rh3726 | NZ_CP011931.1 | 1.010 | 5.62e-46 | 3123653–3123980 | LIMLP_13150 | LIMLP_13145* | LIMLP_13155 | |
| rh3831 | NZ_CP011931.1 | 1.060 | 1.74e-26 | 3214862–3214919 | LIMLP_13525 | LIMLP_13520 | LIMLP_13530 | |
| rh3871 | NZ_CP011931.1 | 2.133 | 2.34e-261 | 3253035–3253139 | LIMLP_13675 | LIMLP_13670* | LIMLP_13680 | |
| rh3894 | NZ_CP011931.1 | 3.784 | 0.00 | 3271638–3271704 | NA | LIMLP_13765* | LIMLP_13770 | |
| rh4111 | NZ_CP011931.1 | 1.340 | 2.82e-76 | 3446561–3446742 | LIMLP_14535 | LIMLP_14530 | LEPIMA_CI3186 | |
| rh4124 | NZ_CP011931.1 | 1.233 | 3.41e-66 | 3459090–3459232 | NA | LIMLP_14580 | LIMLP_14585* | |
| rh4168 | NZ_CP011931.1 | 1.244 | 4.53e-58 | 3487314–3487435 | NA | LIMLP_14710 | LIMLP_14715* | |
| rh4281 | NZ_CP011931.1 | 1.627 | 1.38e-71 | 3584015–3584072 | LIMLP_15080** | LIMLP_15075** | LIMLP_15085 | |
| rh4345 | NZ_CP011931.1 | 1.765 | 8.56e-126 | 3664279–3664343 | LIMLP_15310 | LIMLP_15305 | LIMLP_15315** | |
| rh4413# | NZ_CP011931.1 | 3.507 | 0.00 | 3721204–3721564 | NA | LIMLP_15540* | LIMLP_15545 | |
| rh4459# | NZ_CP011931.1 | 1.059 | 6.95e-29 | 3755947–3756010 | NA | LIMLP_15710 | LEPIMA_CI3455 | |
| rh4542 | NZ_CP011931.1 | 2.748 | 0.00 | 3822746–3823025 | LIMLP_16010 | LIMLP_16005 | LIMLP_16015* | |
| rh4545 | NZ_CP011931.1 | 1.979 | 1.54e-233 | 3825144–3825319 | NA | LIMLP_16015* | LIMLP_16025* | |
| rh4746 | NZ_CP011931.1 | 1.222 | 1.77e-36 | 3987147–3987296 | LEPIMA_CI3684 | LIMLP_16760 | LIMLP_16765* | |
| rh4747 | NZ_CP011931.1 | 1.178 | 9.32e-60 | 3987366–3987576 | LEPIMA_CI3684 | LIMLP_16760 | LIMLP_16765* | |
| rh4854 (RF00174) | NZ_CP011931.1 | 1.023 | 9.20e-41 | 4078407–4078514 | NA | LIMLP_17135 | LIMLP_17140 | |
| rh5034 | NZ_CP011931.1 | 1.628 | 2.24e-72 | 4229144–4229208 | NA | LIMLP_17780 | LIMLP_17785 | |
| Down-regulated | ||||||||
| rh38 | NZ_CP011932.1 | -1.078 | 2.65e-08 | 32083–32148 | LIMLP_17965 | LIMLP_17960 | LIMLP_17970 | |
| rh81 | NZ_CP011931.1 | -1.246 | 3.21e-11 | 67349–67433 | NA | LIMLP_00285 | LIMLP_00290 | |
| rh278 | NZ_CP011932.1 | -1.188 | 8.73e-13 | 202039–202120 | NA | LIMLP_18675 | LEPIMA_CII0202 | |
| rh331 | NZ_CP011931.1 | -1.137 | 9.15e-08 | 245678–245742 | NA | LIMLP_01140 | LEPIMA_CI0236 | |
| rh411 | NZ_CP011931.1 | -1.854 | 1.53e-65 | 310470–310529 | NA | LIMLP_01410** | LIMLP_01415** | |
| rh418 | NZ_CP011931.1 | -1.395 | 9.73e-15 | 317250–317316 | NA | LIMLP_01445 | LIMLP_01450 | |
| rh429 | NZ_CP011932.1 | -1.375 | 2.93e-11 | 311436–311731 | NA | LIMLP_19090 | LIMLP_19095 | |
| rh589 | NZ_CP011931.1 | -1.000 | 3.55e-07 | 469227–469400 | NA | LIMLP_01995 | LIMLP_02000 | |
| rh685 | NZ_CP011931.1 | -1.613 | 1.73e-40 | 541558–541624 | NA | LEPIMA_CI0489 | LIMLP_02275 | |
| rh697 | NZ_CP011931.1 | -1.276 | 3.61e-11 | 549563–549676 | NA | LIMLP_02295 | LIMLP_02300 | |
| rh698 | NZ_CP011931.1 | -1.170 | 8.45e-09 | 549730–549828 | NA | LIMLP_02295 | LIMLP_02300 | |
| rh711 | NZ_CP011931.1 | -1.080 | 1.30e-07 | 562570–562701 | NA | LIMLP_02335 | LIMLP_02340 | |
| rh736 | NZ_CP011931.1 | -1.474 | 3.95e-17 | 582458–582528 | NA | LIMLP_02395** | LIMLP_02400** | |
| rh753 | NZ_CP011931.1 | -1.226 | 1.94e-13 | 602773–602842 | NA | LIMLP_02460 | LIMLP_02465 | |
| rh784 | NZ_CP011931.1 | -1.103 | 1.10e-10 | 630185–630381 | LIMLP_02570 | LIMLP_02565 | LIMLP_02575 | |
| rh967 | NZ_CP011931.1 | -2.662 | 8.54e-202 | 786700–786893 | NA | LIMLP_03220** | LIMLP_03225 | |
| rh1008 | NZ_CP011931.1 | -1.145 | 5.44e-10 | 819424–819662 | NA | LIMLP_03375 | LIMLP_03380 | |
| rh1101 | NZ_CP011931.1 | -2.684 | 4.82e-295 | 888430–888480 | NA | LIMLP_03700 | LIMLP_03705** | |
| rh1102 | NZ_CP011931.1 | -2.149 | 2.11e-80 | 888546–888608 | NA | LIMLP_03700 | LIMLP_03705** | |
| rh1140 | NZ_CP011931.1 | -1.188 | 5.61e-08 | 920214–921272 | NA | LIMLP_03840 | LIMLP_03845 | |
| rh1142 | NZ_CP011931.1 | -1.157 | 6.58e-10 | 920631–920965 | NA | LIMLP_03840 | LIMLP_03845 | |
| rh1253 | NZ_CP011931.1 | -1.608 | 1.10e-30 | 1025093–1025156 | LEPIMA_CI0924 | LEPIMA_CI0923 | LEPIMA_CI0925 | |
| rh1282 | NZ_CP011931.1 | -1.367 | 4.09e-15 | 1046519–1046574 | LEPIMA_CI0946 | LIMLP_04325** | LIMLP_04330 | |
| rh1299 | NZ_CP011931.1 | -1.054 | 9.24e-08 | 1057522–1057700 | LEPIMA_CI0958 | LIMLP_04385 | LIMLP_04390 | |
| rh1382 | NZ_CP011931.1 | -1.036 | 1.69e-05 | 1129722–1129784 | NA | LEPIMA_CI1022 | LEPIMA_CI1023 | |
| rh1651 | NZ_CP011931.1 | -1.354 | 4.48e-12 | 1392744–1392884 | LIMLP_05660 | LIMLP_05655 | LIMLP_05665 | |
| rh1880 | NZ_CP011931.1 | -1.896 | 6.86e-62 | 1592557–1592621 | LEPIMA_CI1441 | LIMLP_06480** | LEPIMA_CI1442 | |
| rh2038 | NZ_CP011931.1 | -1.252 | 1.81e-14 | 1734004–1734144 | NA | LIMLP_07030 | LIMLP_07035 | |
| rh2114 | NZ_CP011931.1 | -1.206 | 2.39e-12 | 1799567–1799634 | NA | LIMLP_07290 | LIMLP_07295 | |
| rh2170 | NZ_CP011931.1 | -1.047 | 1.58e-06 | 1854827–1854890 | LEPIMA_CI1676 | LIMLP_07495 | LIMLP_07500 | |
| rh2222 | NZ_CP011931.1 | -1.199 | 1.09e-12 | 1896532–1896782 | NA | LIMLP_07715 | LIMLP_07725 | |
| rh2311 | NZ_CP011931.1 | -1.115 | 1.01e-06 | 1954525–1954640 | LIMLP_07975 | LIMLP_07970** | LIMLP_07980 | |
| rh2578 | NZ_CP011931.1 | -1.730 | 2.54e-44 | 2165614–2165832 | LIMLP_08925 | LIMLP_08920 | LIMLP_08930** | |
| rh2850 | NZ_CP011931.1 | -1.378 | 1.21e-14 | 2378010–2378075 | LEPIMA_CI2192 | LIMLP_09945 | LIMLP_09950 | |
| rh2882 | NZ_CP011931.1 | -1.299 | 2.18e-12 | 2398625–2398696 | NA | LIMLP_10050** | LEPIMA_CI2213 | |
| rh3186 | NZ_CP011931.1 | -1.963 | 5.74e-64 | 2658407–2658646 | NA | LIMLP_11175** | LIMLP_11180** | |
| rh3190 | NZ_CP011931.1 | -1.874 | 6.42e-47 | 2656130–2656312 | NA | LIMLP_11170** | LIMLP_11175** | |
| rh3335 | NZ_CP011931.1 | -1.382 | 4.99e-21 | 2764692–2764792 | NA | LIMLP_11630 | LIMLP_11635 | |
| rh3711 | NZ_CP011931.1 | -2.030 | 5.35e-87 | 3116206–3116269 | NA | LIMLP_13120 | LEPIMA_CI2881 | |
| rh3945 | NZ_CP011931.1 | -1.465 | 7.13e-22 | 3308829–3309056 | LEPIMA_CI3062 | LIMLP_13935 | LIMLP_13940 | |
| rh3946 | NZ_CP011931.1 | -1.126 | 3.52e-10 | 3309111–3309181 | NA | LEPIMA_CI3062 | LIMLP_13940 | |
| rh4140 | NZ_CP011931.1 | -1.438 | 7.92e-17 | 3467363–3467432 | NA | LIMLP_14615** | LIMLP_14620** | |
| rh4178 | NZ_CP011931.1 | -1.509 | 2.89e-18 | 3496010–3496183 | LEPIMA_CI3239 | LIMLP_14745** | LIMLP_14750 | |
| rh4218 | NZ_CP011931.1 | -1.174 | 6.15e-08 | 3532306–3532358 | NA | LEPIMA_CI3268 | LIMLP_14880 | |
| rh4253 | NZ_CP011931.1 | -1.332 | 9.51e-14 | 3554072–3554567 | NA | LIMLP_14970** | LIMLP_14975 | |
| rh4254 | NZ_CP011931.1 | -1.246 | 1.77e-09 | 3554619–3554683 | NA | LIMLP_14970** | LIMLP_14975 | |
| rh4493 | NZ_CP011931.1 | -1.115 | 2.32e-09 | 3783194–3783362 | NA | LIMLP_15840 | LIMLP_15845 | |
| rh4549 | NZ_CP011931.1 | -1.821 | 7.63e-51 | 3827129–3827377 | LEPIMA_CI3525 | LIMLP_16030 | LIMLP_16035** | |
| rh4607 | NZ_CP011931.1 | -1.280 | 4.56e-14 | 3879350–3879511 | LIMLP_16285 | LIMLP_16280 | LIMLP_16290 | |
| rh4763 | NZ_CP011931.1 | -1.116 | 3.50e-03 | 3984140–3984338 | LIMLP_16745** | LIMLP_16740 | LIMLP_16750 | |
| rh4894 | NZ_CP011931.1 | -1.137 | 3.70e-11 | 4116602–4116674 | LIMLP_17290 | LIMLP_17285 | LIMLP_17295 | |
| rh4918 | NZ_CP011931.1 | -1.256 | 5.77e-17 | 4133590–4133654 | NA | LIMLP_17350 | LIMLP_17355 | |
| rh4938 | NZ_CP011931.1 | -1.064 | 3.10e-08 | 4155394–4155481 | LIMLP_17425** | LIMLP_17420** | LIMLP_17430** |
Significantly differentially-expressed ncRNAs upon 1h exposure to 1 mM H2O2 with Log2FC cutoff of ± 1.0 and a p-value cutoff of 0.05.
a Gene numeration is according to to Satou et al. [17].
b Differential expression of ncRNA upon inactivation of perR (M776 mutant) (see S5 Table).
# ncRNAs significantly up-regulated upon a 30 min exposure to 10 μM H2O2 (Log2FC cutoff of 1, p-value cutoff of 0.05, see S5 Table).
§ ncRNA significantly down-regulated upon a 30 min exposure to 10 μM H2O2 (Log2FC cutoff of -1, p-value cutoff of 0.05, see S5 Table).
* ORFs significantly up-regulated by RNASeq analysis (Log2FC cutoff of 1, adjusted p-value cutoff of 0.05).
** ORFs significantly down-regulated by RNASeq analysis (Log2FC cutoff of -1, adjusted p-value cutoff of 0.05).
NA, non-applicable
The Rfam classification of ncRNAs is indicated into parenthesis.