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. 2014 Apr 4;11(4):373–390. doi: 10.4161/rna.28725

Table 1. List of genes targeted by Dicer-like 1-dependent, Argonaute 1-enriched small RNAs identified on the long non-coding RNAs of Arabidopsis.

Small RNA ID Target transcript Binding site on target transcript Cleavage site supported by
degradome sequencing data		 Target gene Target gene annotation
DCL1_sRNA13855 AT1G12300.1 1550–1570 1561 AT1G12300 Tetratricopeptide repeat (TPR)-like superfamily protein
DCL1_sRNA13839 AT1G12300.1 1551–1571 1562
DCL1_sRNA13855 AT1G12620.1 1706–1726 1717 AT1G12620 Pentatricopeptide repeat (PPR) superfamily protein
DCL1_sRNA13839 AT1G12620.1 1707–1727 1718
DCL1_sRNA13855 AT1G12700.1 1503–1523 1512 AT1G12700 RNA PROCESSING FACTOR 1 (RPF1)
DCL1_sRNA13855 AT1G12775.1 1502–1522 1514 AT1G12775 Pentatricopeptide repeat (PPR) superfamily protein
DCL1_sRNA13839 AT1G12775.1 1503–1523
DCL1_sRNA5687 AT1G16890.1 618–638 627 AT1G16890 UBC36/UBC13B encodes a protein that may play a role in DNA damage responses and error-free post-replicative DNA repair
DCL1_sRNA5409 AT1G16890.1 617–638
DCL1_sRNA5987 AT1G16890.1 615–636
DCL1_sRNA5300 AT1G16890.1 616–637
DCL1_sRNA5729 AT1G16890.1 617–637
DCL1_sRNA5687 AT1G16890.2 637–657 646
DCL1_sRNA5409 AT1G16890.2 636–657
DCL1_sRNA5987 AT1G16890.2 634–655
DCL1_sRNA5300 AT1G16890.2 635–656
DCL1_sRNA5729 AT1G16890.2 636–656
DCL1_sRNA5687 AT1G16890.3 664–684 673
DCL1_sRNA5409 AT1G16890.3 663–684
DCL1_sRNA5987 AT1G16890.3 661–682
DCL1_sRNA5300 AT1G16890.3 662–683
DCL1_sRNA5729 AT1G16890.3 663–683
DCL1_sRNA36672 AT1G27250.1 347–368 360 AT1G27250 Paired amphipathic helix (PAH2) superfamily protein
DCL1_sRNA64198 AT1G31020.1 654–674 665 AT1G31020 Thioredoxin O2 (TO2)
DCL1_sRNA5018 AT1G45688.1 26–47 36 AT1G45688 Unknown protein
DCL1_sRNA5018 AT1G45688.2 12–33 22
DCL1_sRNA25197 AT1G56110.1 1534–1554 1545 AT1G56110 NOP56-like protein
DCL1_sRNA14038 AT1G58400.1 2646–2667 2658 AT1G58400 Disease resistance protein (CC-NBS-LRR class) family
DCL1_sRNA14056 AT1G58400.1 2645–2666
DCL1_sRNA6150 AT1G59830.1 1230–1250 1239 AT1G59830 Encodes one of the isoforms of the catalytic subunit of protein phosphatase 2A
DCL1_sRNA6150 AT1G59830.2 1319–1339 1328
DCL1_sRNA13855 AT1G62860.1 1492–1512 1503 AT1G62860 Pseudogene of pentatricopeptide (PPR) repeat-containing protein
DCL1_sRNA13839 AT1G62860.1 1493–1513 1504
DCL1_sRNA13841 AT1G62910.1 535–555 547 AT1G62910 Pentatricopeptide repeat (PPR) superfamily protein
DCL1_sRNA13811 AT1G62910.1 535–556
DCL1_sRNA13841 AT1G62914.1 517–537 529 AT1G62914 Pentatricopeptide (PPR) repeat-containing protein
DCL1_sRNA13811 AT1G62914.1 517–538
DCL1_sRNA13922 AT1G62930.1 1458–1478 1469 AT1G62930 RPF3 encodes a pentatricopeptide repeat (PPR) protein involved in 5′ processing of different mitochondrial mRNAs
DCL1_sRNA13817 AT1G62930.1 1457–1477
DCL1_sRNA13816 AT1G62930.1
DCL1_sRNA13922 AT1G63080.1 1501–1521 1512 AT1G63080 Transacting siRNA generating locus
DCL1_sRNA13816 AT1G63080.1 1500–1520
DCL1_sRNA13841 AT1G63130.1 650–670 662 AT1G63130 Transacting siRNA generating locus
DCL1_sRNA13811 AT1G63130.1 650–671
DCL1_sRNA13841 AT1G63150.1 535–555 547 AT1G63150 Transacting siRNA generating locus
DCL1_sRNA13811 AT1G63150.1 535–556
DCL1_sRNA13829 AT1G63230.1 1230–1251 1242 AT1G63230 Tetratricopeptide repeat (TPR)-like superfamily protein
DCL1_sRNA13800 AT1G63230.1 1230–1250
DCL1_sRNA13829 AT1G63630.1 542–563 554 AT1G63630 Tetratricopeptide repeat (TPR)-like superfamily protein
DCL1_sRNA13800 AT1G63630.1 542–562
DCL1_sRNA13829 AT1G63630.2 591–612 603
DCL1_sRNA13800 AT1G63630.2 591–611
DCL1_sRNA5518 AT1G64720.1 1139–1161 1151 AT1G64720 Membrane related protein CP5
DCL1_sRNA6493 AT1G64720.1 1138–1159 1150
DCL1_sRNA5389 AT1G64720.1 1140–1161 1151
DCL1_sRNA4887 AT1G64720.1 1141–1161 1151
DCL1_sRNA5993 AT1G72050.1 1293–1314 1304 AT1G72050 Encodes a transcriptional factor TFIIIA required for transcription of 5S rRNA gene
DCL1_sRNA5733 AT1G72050.1 1293–1313
DCL1_sRNA5031 AT1G72050.1 1292–1313
DCL1_sRNA5993 AT1G72050.2 1060–1081 1071
DCL1_sRNA5733 AT1G72050.2 1060–1080
DCL1_sRNA5031 AT1G72050.2 1059–1080
DCL1_sRNA46232 AT1G73500.1 127–149 140 AT1G73500 Member of MAP Kinase Kinase family
DCL1_sRNA5231 AT1G75220.1 1802–1823 1815 AT1G75220 Encodes a vacuolar glucose exporter
DCL1_sRNA64537 AT2G01010.1 1649–1669 1661 AT2G01010 18SrRNA
DCL1_sRNA3154 AT2G12440.1 4625–4648 4640 AT2G12440 Transposable element gene
DCL1_sRNA1263 AT2G12440.1 4629–4648
DCL1_sRNA1141 AT2G17442.1 672–695 687 AT2G17442 Unknown protein
DCL1_sRNA1141 AT2G17442.2 696–719 711
DCL1_sRNA1141 AT2G17442.3 693–716 708
DCL1_sRNA1141 AT2G17442.4 645–668 660
DCL1_sRNA1141 AT2G17442.5 644–667 659
DCL1_sRNA31206 AT2G27740.1 20–43 32 AT2G27740 Family of unknown function (DUF662)
DCL1_sRNA5477 AT2G28350.1 2179–2200 2192 AT2G28350 AUXIN RESPONSE FACTOR 10 (ARF10), involved in root cap cell differentiation
DCL1_sRNA26509 AT2G28550.1 1558–1577 1568 AT2G28550 Related to AP2.7 (RAP2.7)
DCL1_sRNA26510 AT2G28550.1 1556–1577
DCL1_sRNA26509 AT2G28550.2 1630–1649 1640
DCL1_sRNA26510 AT2G28550.2 1628–1649
DCL1_sRNA26509 AT2G28550.3 1603–1622 1613
DCL1_sRNA26510 AT2G28550.3 1601–1622
DCL1_sRNA62245 AT2G33860.1 1673–1693/1793–1813 1685/1804 AT2G33860 ETTIN (ETT)
DCL1_sRNA62203 AT2G33860.1 1673–1694/1793–1814 1686/1805
DCL1_sRNA62205 AT2G33860.1 1674–1694/1794–1814 1686/1805
DCL1_sRNA62234 AT2G33860.1 1674–1694/1794–1814 1686/1805
DCL1_sRNA62237 AT2G33860.1 1675–1694/1795–1814 1686/1805
DCL1_sRNA62218 AT2G33860.1 1675–1695/1795–1815 1686/1805
DCL1_sRNA62198 AT2G33860.1 1675–1695/1795–1815 1686/1805
DCL1_sRNA24900 AT2G33860.1 1676–1696/1796–1816 1686/1805
DCL1_sRNA57442 AT2G35430.1 844–865 854 AT2G35430 Zinc finger C-x8-C-x5-C-x3-H type family protein
DCL1_sRNA7007 AT2G36380.1 4448–4469 4461 AT2G36380 Pleiotropic drug resistance 6 (PDR6)
DCL1_sRNA6129 AT2G37370.1 1365–1386 1378 AT2G37370 Unknown protein
DCL1_sRNA3463 AT2G37370.1 1419–1438 1427
DCL1_sRNA31206 AT2G37890.1 1447–1470 1461 AT2G37890 Mitochondrial substrate carrier family protein
DCL1_sRNA13846 AT2G39681.1 724–744 735 AT2G39681 Trans-acting siRNA primary transcript
DCL1_sRNA10442 AT2G39681.1 724–744
DCL1_sRNA13822 AT2G39681.1 585–606 597
DCL1_sRNA13851 AT2G39681.1 585–605
DCL1_sRNA13822 AT2G41950.1 422–443 434 AT2G41950 Unknown protein
DCL1_sRNA13851 AT2G41950.1 422–442 434
DCL1_sRNA6760 AT2G47160.1 2252–2273 2262 AT2G47160 Boron transporter
DCL1_sRNA6760 AT2G47160.2 2331–2352 2341
DCL1_sRNA4906 AT3G03040.1 1099–1120 1109 AT3G03040 F-box/RNI-like superfamily protein
DCL1_sRNA4946 AT3G03040.1 1098–1118
DCL1_sRNA9465 AT3G04730.1 752–773 762 AT3G04730 INDOLEACETIC ACID-INDUCED PROTEIN 16 (IAA16)
DCL1_sRNA62220 AT3G05340.1 2296–2318 2310 AT3G05340 Tetratricopeptide repeat (TPR)-like superfamily protein
DCL1_sRNA62220 AT3G05345.1 19–41 33 AT3G05345 Chaperone DnaJ-domain superfamily protein
DCL1_sRNA5844 AT3G05590.1 740–761 753 AT3G05590 RIBOSOMAL PROTEIN L18 (RPL18)
DCL1_sRNA13818 AT3G15605.1 1791–1811 1803 AT3G15605 Nucleic acid binding
DCL1_sRNA13818 AT3G15605.2 1785–1805 1797
DCL1_sRNA13818 AT3G15605.3 1608–1628 1620
DCL1_sRNA13818 AT3G15605.4 1540–1560 1552
DCL1_sRNA4896 AT3G22010.1 715–735 726 AT3G22010 Receptor-like protein kinase-related family protein
DCL1_sRNA5080 AT3G22990.1 877–900 890 AT3G22990 LEAF AND FLOWER RELATED (LFR)
DCL1_sRNA5467 AT3G23000.1 1138–1159 1148 AT3G23000 CBL-INTERACTING PROTEIN KINASE 7 (CIPK7)
DCL1_sRNA30437 AT3G25470.1 1095–1118 1110 AT3G25470 Bacterial hemolysin-related
DCL1_sRNA64537 AT3G41768.1 1649–1669 1661 AT3G41768 18SrRNA
DCL1_sRNA4900 AT3G44310.1 757–777 768 AT3G44310 NITRILASE 1 (NIT1)
DCL1_sRNA4900 AT3G44310.2 639–659 650
DCL1_sRNA4900 AT3G44310.3 757–777 768
DCL1_sRNA26509 AT3G54990.1 965–985 976 AT3G54990 Encodes a AP2 domain transcription factor that can repress flowering
DCL1_sRNA22374 AT3G54990.1
DCL1_sRNA26510 AT3G54990.1 964–985
DCL1_sRNA6738 AT3G56730.1 605–625 616 AT3G56730 Putative endonuclease or glycosyl hydrolase
DCL1_sRNA6738 AT3G56730.2 660–680 671
DCL1_sRNA31732 AT4G06708.1 15–38 28 AT4G06708 Transposable element gene
DCL1_sRNA6150 AT4G12730.1 1364–1384 1376 AT4G12730 FASCICLIN-LIKE ARABINOGALACTAN 2 (FLA2)
DCL1_sRNA7163 AT4G15830.1 855–876 868 AT4G15830 ARM repeat superfamily protein
DCL1_sRNA47338 AT4G16830.1 119–139 130 AT4G16830 Hyaluronan/mRNA binding family
DCL1_sRNA47338 AT4G16830.2 95–115 106
DCL1_sRNA47338 AT4G16830.3 119–139 130
DCL1_sRNA15973 AT4G18120.1 2301–2322 2314 AT4G18120 MEI2-LIKE 3 (ML3)
DCL1_sRNA15973 AT4G18120.2 2152–2173 2165
DCL1_sRNA7119 AT4G23450.2 180–201 192 AT4G23450 ABA INSENSITIVE RING PROTEIN 1 (AIRP1)
DCL1_sRNA17116 AT4G29770.1 728–748 739 AT4G29770 Target of trans acting-siR480/255
DCL1_sRNA61901 AT4G29770.1 726–747
DCL1_sRNA61963 AT4G29770.1 728–748
DCL1_sRNA17095 AT4G29770.1 728–748
DCL1_sRNA17297 AT4G29770.1 729–748
DCL1_sRNA17118 AT4G29770.1 728–748
DCL1_sRNA61866 AT4G29770.1 727–748
DCL1_sRNA17098 AT4G29770.1 729–748
DCL1_sRNA61962 AT4G29770.1 728–748
DCL1_sRNA61865 AT4G29770.1 728–748
DCL1_sRNA17097 AT4G29770.1 731–748
DCL1_sRNA61867 AT4G29770.1 729–748
DCL1_sRNA17116 AT4G29770.2 770–790 781
DCL1_sRNA61901 AT4G29770.2 768–789
DCL1_sRNA61963 AT4G29770.2 770–790
DCL1_sRNA17095 AT4G29770.2 770–790
DCL1_sRNA17297 AT4G29770.2 771–790
DCL1_sRNA17118 AT4G29770.2 770–790
DCL1_sRNA61866 AT4G29770.2 769–790
DCL1_sRNA17098 AT4G29770.2 771–790
DCL1_sRNA61962 AT4G29770.2 770–790
DCL1_sRNA61865 AT4G29770.2 770–790
DCL1_sRNA17097 AT4G29770.2 773–790
DCL1_sRNA61867 AT4G29770.2 771–790
DCL1_sRNA7075 AT4G33280.1 808–829 818 AT4G33280 AP2/B3-like transcriptional factor family protein
DCL1_sRNA26509 AT4G36920.1 1329–1349 1340 AT4G36920 APETALA 2 (AP2)
DCL1_sRNA22374 AT4G36920.1
DCL1_sRNA26510 AT4G36920.1 1328–1349
DCL1_sRNA26509 AT4G36920.2 1293–1313 1304
DCL1_sRNA22374 AT4G36920.2
DCL1_sRNA26510 AT4G36920.2 1292–1313
DCL1_sRNA22374 AT5G04275.1 1–21 12 AT5G04275 MICRORNA172B (MIR172B), a microRNA that targets several genes containing AP2 domains
DCL1_sRNA12080 AT5G08590.1 34–56 48 AT5G08590 SNF1-RELATED PROTEIN KINASE 2.1 (SNRK2.1)
DCL1_sRNA10500 AT5G11660.1 803–824 815 AT5G11660 Protein of Unknown Function (DUF239)
DCL1_sRNA7229 AT5G13800.1 1654–1675 1667 AT5G13800 PHEOPHYTINASE (PPH)
DCL1_sRNA5234 AT5G14565.1 1896–1916 1907 AT5G14565 MICRORNA398C (MIR398C)
DCL1_sRNA13841 AT5G16640.1 581–601 593 AT5G16640 Pentatricopeptide repeat (PPR) superfamily protein
DCL1_sRNA13811 AT5G16640.1 581–602 593
DCL1_sRNA6198 AT5G16800.1 1222–1242 1233 AT5G16800 Acyl-CoA N-acyltransferases (NAT) superfamily protein
DCL1_sRNA6198 AT5G16800.2 1139–1159 1150
DCL1_sRNA6198 AT5G16800.3 1148–1168 1159
DCL1_sRNA17116 AT5G18040.1 675–695 686 AT5G18040 Unknown protein
DCL1_sRNA61901 AT5G18040.1 672–694
DCL1_sRNA17095 AT5G18040.1 675–695
DCL1_sRNA17297 AT5G18040.1 676–695
DCL1_sRNA17118 AT5G18040.1 675–695
DCL1_sRNA61866 AT5G18040.1 674–695
DCL1_sRNA17098 AT5G18040.1 676–695
DCL1_sRNA61865 AT5G18040.1 675–695
DCL1_sRNA17097 AT5G18040.1 678–695
DCL1_sRNA61867 AT5G18040.1 676–695
DCL1_sRNA17116 AT5G18065.1 726–746 737 AT5G18065 Unknown protein
DCL1_sRNA61901 AT5G18065.1 723–745
DCL1_sRNA17095 AT5G18065.1 726–746
DCL1_sRNA17297 AT5G18065.1 727–746
DCL1_sRNA17118 AT5G18065.1 726–746
DCL1_sRNA61866 AT5G18065.1 725–746
DCL1_sRNA17098 AT5G18065.1 727–746
DCL1_sRNA61865 AT5G18065.1 726–746
DCL1_sRNA17097 AT5G18065.1 729–746
DCL1_sRNA61867 AT5G18065.1 727–746
DCL1_sRNA6188 AT5G33406.1 1505–1525 1517 AT5G33406 hAT dimerization domain-containing protein/transposase-related
DCL1_sRNA59503 AT5G40810.1 1015–1038 1027 AT5G40810 Cytochrome C1 family
DCL1_sRNA59503 AT5G40810.2 1344–1367 1356
DCL1_sRNA7136 AT5G51300.1 2469–2488 2477 AT5G51300 Splicing factor-related
DCL1_sRNA6885 AT5G51300.1 2468–2488
DCL1_sRNA5824 AT5G59732.1 1537–1558 1548 AT5G59732 Potential natural antisense gene, locus overlaps with AT5G59730
DCL1_sRNA26509 AT5G60120.1 1647–1667 1658 AT5G60120 TARGET OF EARLY ACTIVATION TAGGED 2 (TOE2)
DCL1_sRNA22374 AT5G60120.1
DCL1_sRNA26510 AT5G60120.1 1646–1667
DCL1_sRNA26509 AT5G60120.2 1810–1830 1821
DCL1_sRNA22374 AT5G60120.2
DCL1_sRNA26510 AT5G60120.2 1809–1830
DCL1_sRNA62203 AT5G60450.1 1873–1894/2083–2104 1885/2095 AT5G60450 AUXIN RESPONSE FACTOR 4 (ARF4)
DCL1_sRNA62218 AT5G60450.1 1875–1895/2085–2105
DCL1_sRNA24900 AT5G60450.1 1876–1896/2086–2106
DCL1_sRNA62205 AT5G60450.1 1874–1894/2084–2104
DCL1_sRNA62237 AT5G60450.1 1875–1894/2085–2104
DCL1_sRNA62234 AT5G60450.1 1874–1894/2084–2104
DCL1_sRNA62245 AT5G60450.1 1873–1893/2083–2103
DCL1_sRNA62198 AT5G60450.1 1875–1895/2085–2105
DCL1_sRNA62203 AT5G62000.1 1836–1857 1848 AT5G62000 AUXIN RESPONSE FACTOR 2 (ARF2)
DCL1_sRNA62218 AT5G62000.1 1838–1858
DCL1_sRNA24900 AT5G62000.1 1839–1859
DCL1_sRNA62205 AT5G62000.1 1837–1857
DCL1_sRNA62237 AT5G62000.1 1838–1857
DCL1_sRNA62234 AT5G62000.1 1837–1857
DCL1_sRNA62245 AT5G62000.1 1836–1856
DCL1_sRNA62198 AT5G62000.1 1838–1858
DCL1_sRNA62203 AT5G62000.2 1734–1755 1746
DCL1_sRNA62218 AT5G62000.2 1736–1756
DCL1_sRNA24900 AT5G62000.2 1737–1757
DCL1_sRNA62205 AT5G62000.2 1735–1755
DCL1_sRNA62237 AT5G62000.2 1736–1755
DCL1_sRNA62234 AT5G62000.2 1735–1755
DCL1_sRNA62245 AT5G62000.2 1734–1754
DCL1_sRNA62198 AT5G62000.2 1736–1756
DCL1_sRNA62203 AT5G62000.3 1734–1755 1746
DCL1_sRNA62218 AT5G62000.3 1736–1756
DCL1_sRNA24900 AT5G62000.3 1737–1757
DCL1_sRNA62205 AT5G62000.3 1735–1755
DCL1_sRNA62237 AT5G62000.3 1736–1755
DCL1_sRNA62234 AT5G62000.3 1735–1755
DCL1_sRNA62245 AT5G62000.3 1734–1754
DCL1_sRNA62198 AT5G62000.3 1736–1756
DCL1_sRNA62203 AT5G62000.4 1734–1755 1746
DCL1_sRNA62218 AT5G62000.4 1736–1756
DCL1_sRNA24900 AT5G62000.4 1737–1757
DCL1_sRNA62205 AT5G62000.4 1735–1755
DCL1_sRNA62237 AT5G62000.4 1736–1755
DCL1_sRNA62234 AT5G62000.4 1735–1755
DCL1_sRNA62245 AT5G62000.4 1734–1754
DCL1_sRNA62198 AT5G62000.4 1736–1756
DCL1_sRNA26509 AT5G67180.1 1297–1318 1309 AT5G67180 TARGET OF EARLY ACTIVATION TAGGED 3 (TOE3)
DCL1_sRNA26510 AT5G67180.1 1296–1318

Please refer to Figure S2 for degradome sequencing data-based cleavage evidences.