Identification of host miRNAs that may limit human rhinovirus replication

Table 1 Sequence details of miR-18a, -19b, -106b, -128, -155

miR name in text	miRBase accession number	mature miR sequence
miR-18a	MIMAT0000072	UAAGGUGCAUCUAGUGCAGAUAG
miR-19b	MIMAT0000074	UGUGCAAAUCCAUGCAAAACUGA
miR-106b	MIMAT0000680	UAAAGUGCUGACAGUGCAGAU
miR-128	MIMAT0000424	UCACAGUGAACCGGUCUCUUU
miR-155	MIMAT0000646	UUAAUGCUAAUCGUGAUAGGGGU

Table 2 MicroRNAs expressed in healthy primary bronchial epithelial cells

Let-7a	miR-149	miR-218	miR-345	miR-501-5p	miR-93
Let-7b	miR-152	miR-221	miR-34a	miR-502-3p	miR-9
let-7c	miR-155	miR-222	miR-34c-5p	miR-502-5p	miR-95
let-7d	miR-15a	miR-223	miR-361-5p	miR-503	miR-96
let-7e	miR-15b	miR-22	miR-362-3p	miR-505	miR-98
let-7f	miR-16	miR-224	miR-362-5p	miR-519a	miR-99a
let-7g	miR-17	miR-23a	miR-365	miR-523	miR-99b
miR-100	miR-181a	miR-23b	miR-374a	miR-532-3p
miR-101	miR-181c	miR-24	miR-374b	miR-532-5p
miR-103	miR-182	miR-25	miR-375	miR-542-3p
miR-106a	miR-183	miR-26a	miR-376a	miR-545
miR-106b	miR-184	miR-26b	miR-376c	miR-548d-5p
miR-107	miR-185	miR-27a	miR-379	miR-574-3p
miR-10a	miR-186	miR-27b	miR-410	miR-576-3p
miR-125a-3p	miR-18a	miR-28-3p	miR-411	miR-579
miR-125a-5p	miR-18b	miR-28-5p	miR-422a	miR-582-3p
miR-125b	miR-191	miR-296-5p	miR-423-5p	miR-582-5p
miR-126	miR-192	miR-29a	miR-424	miR-589
miR-127-3p	miR-193a-3p	miR-29b	miR-425	miR-590-5p
miR-128	miR-193a-5p	miR-29c	miR-429	miR-597
miR-129-3p	miR-193b	miR-301a	miR-449a	miR-598
miR-130a	miR-194	miR-301b	miR-449b	miR-618
miR-130b	miR-195	miR-30b	miR-450a	miR-625
miR-132	miR-197	miR-30c	miR-450b-5p	miR-627
miR-134	miR-198	miR-31	miR-452	miR-628-5p
miR-135a	miR-19a	miR-320	miR-454	miR-629
miR-135b	miR-19b	miR-323-3p	miR-455-3p	miR-636
miR-136	miR-200a	miR-32	miR-455-5p	miR-642
miR-138	miR-200b	miR-324-3p	miR-483-5p	miR-652
miR-139-5p	miR-200c	miR-324-5p	miR-484	miR-655
miR-140-3p	miR-202	miR-328	miR-485-3p	miR-660
miR-140-5p	miR-203	miR-330-3p	miR-486-3p	miR-671-3p
miR-141	miR-204	miR-331-3p	miR-486-5p	miR-708
miR-142-3p	miR-205	miR-331-5p	miR-487a	miR-744
miR-145	miR-20a	miR-335	miR-489	miR-758
miR-146a	miR-20b	miR-339-3p	miR-491-5p	miR-885-5p
miR-146b-5p	miR-210	miR-339-5p	miR-494	miR-886-3p
miR-148a	miR-212	miR-340	miR-495	miR-886-5p
miR-148b	miR-21	miR-342-3p	miR-500	miR-92a

Here are reported only the miRs with Ct values lower than 40, in at least 2 (out of 4) samples of primary bronchial epithelial cells (PBECs) from healthy donors.

Table 3 Targetscan predictions on human rhinovirus -1B, -16, -14, -27

Virus	MiR	Site type	Site start	Site end	Context+ score		Alignment
HRV-1B	18a	7mer-1a	7053	7059	0.163	site:	GUGCACUGUAUAUCCCACCUUAU
							| | | | | | | | | | | |
						miR:	GAUAGACGUGAUCUAC----- -GUGGAAU
HRV-1B	128	7mer-m8	1822	1828	-0.017	site:	AAACAUUAGUAUGUACACUGUGC
							| | | | | | |
						miR:	UUUCUCUGGCCAAGUGACACU
HRV-1B	155	7mer-m8	3716	3722	-0.014	site:	AUAAAUCCAAUCAAU- ---AGCAUUAG
							| | | | | | | | | | |
						miR:	UGGGGAUAGUGCUAAUCGUAAUU
HRV-1B	155	7mer-m8	5998	6004	-0.013	site:	UGAUUCUAAACCAAUAGCAUUAG
							| | | | | | |
						miR:	UGGGGAUAGUGCUAAUCGUAAUU
HRV-1B	19b	8mer-1a	5088	5095	0.021	Site:	UAAUUUACAAAUUGUUUUGCACA
							| | | | | | |
						miR:	AGUCAAAACGUACCUAAACGUGU
HRV-1B	106b	7mer-m8	5471	5477	0.025	Site:	CCAGAAUGUAAUUUAGCACUUUC
							| | | | | | |
						miR:	UAGACGUGACAGUCGUGAAAU
HRV-16	128	7mer-m8	3593	3599	-0.04	Site:	GAUCUUAGACACUUUCACUGUGC
							| | | | | | | | | | |
						miR:	UUUCUCUGGCCAAGUGACACU
HRV-16	155	7mer-m8	6133	6139	-0.036	Site:	UUCCAAACUUAAGCUAGCAUUAG
							| | | | | | |
						miR:	UGGGGAUAGUGCUAAUCGUAAUU
HRV-16	106b	7mer-1a	3802	3808	0.107	Site:	GCAAACAAUAAUUGCCACUUUAA
							| | | | | |
						miR:	UAGACGUGACAGUCGUGAAAU
HRV-14	128	7mer-1a	620	626	-0.059	Site:	CAUAUAUAUACAUAUACUGUGAU
							| | | | | |
						miR:	UUUCUCUGGCCAAGUGACACU
HRV-14	155	7mer-m8	6082	6088	-0.056	Site:	ACUUACACUAAAAGAAGCAUUAU
							| | | | | | |
						miR:	UGGGGAUAGUGCUAAUCGUAAUU
HRV-14	19b	7mer-m8	5255	5261	-0.001	Site:	GGACCAAACACAGAAUUUGCACU
							| | | | | | |
						miR:	AGUCAAAACGUACCUAAACGUGU
HRV-14	106b	8mer-1a	2503	2510	0.047	Site:	CAGAACUACCUACAUGCACUUUA
							| | | | | | |
						miR:	UAGACGUGACAGUCGUGAAAU
HRV-14	106b	7mer-m8	4414	4420	0.057	Site:	UCCACCAGAUCCCAAGCACUUUG
							| | | | | | |
						miR:	UAGACGUGACAGUCGUGAAAU
HRV-27	18a	7mer-1a	7121	7127	-0.134	Site:	AGGUUCUUGUGAUACCACCUUAC
							| | | | | |
						miR:	GAUAGACGUGAUCUACGUGGAAU
HRV-27	19b	7mer-m8	66	72	-0.11	Site:	CUGGUAUUUUGUACC---UUUGCACG
							| | | | | | | | | | | |
						miR:	AGUCAAAACGUACCUAAACGUGU
HRV-27	128	7mer-1a	619	625	-0.053	Site:	AUAUAUAGCAUAUAUACUGUGAU
							||||||
						miR:	UUUCUCUGGCCAAGUGACACU
HRV-27	155	7mer-1a	6152	6158	0.018	Site:	CUUAUGUUAGUUUGGGCAUUAAG
							| | | | | |
						miR:	UGGGGAUAGUGCUAAUCGUAAUU
HRV-27	106b	8mer-1a	1193	1200	0.025	Site:	CAAAAUUUCACAGUG--GCACUUUA
							| | | | | | | | | |
						miR:	UAGACGUGACAGUCGUGAAAU
HRV-27	128	7mer-1a	1552	1558	0.049	Site:	CCCAGUAUACCUGUU--ACUGUGAC
							| | | | | | | | |
						miR:	UUUCUCUGGCCAAGUGACACU
HRV-27	19b	7mer-m8	4192	4198	0.058	Site:	CAAAUGUCUCAGAAGUUUGCACC
							| | | | | | |
						miR:	AGUCAAAACGUACCUAAACGUGU
HRV-27	155	7mer-m8	4632	4638	0.097	Site:	UGUGUUGAACCCUGAAGCAUUAG
							| | | | | | |
						miR:	UGGGGAUAGUGCUAAUCGUAAUU

HRV: Human rhinovirus.

Table 4 MiRanda predictions on human rhinovirus-1B

Virus	miR	Site start	Site end	Score	Energy (kcal/mol)		Alignment
HRV-1B	106b	2257	2276	141	-18.24	miR:	uaGACGUGACAGUCGUGAAAu
							||||| | | | || |||||
						site:	uuCUGCA-UGUAAGGACUUUu
HRV-1B	155	3704	3723	156	-17.59	miR:	ugGGGAUAGUGCUAAUCGUAAUu
							:|| |||| | ||||||||
						site:	aaUCCAAUCA-- --A-UAGCAUUAg
HRV-1B	106b	5459	5478	160	-14.6	miR:	uagACGUGACAGUCGUGAAAu
							||: | | | : | |||||||
						site:	gaaUGUAAU--UUAGCACUUUc
HRV-1B	155	2878	2901	144	-14.2	miR:	ugGGGAUAGU--GCUAAUCGUAAUu
							| : : | | || : | | | | | | | | :
						site:	cuCUUUACCAUUUCUUAGCAUUGc
HRV-1B	155	5984	6005	159	-13.65	miR:	ugGGGAUAGUGCUAAUCGUAAUu
							: : ||| | | | | | | | | | | |
						Site:	gaUUCUA--AACCAAUAGCAUUAg
HRV-1B	128	1809	1829	147	-13.12	miR:	uuucucuggcCAAGUGACACu
							| | |||||||
						Site:	acauuaguauGUACACUGUGc
HRV-1B	19b	5071	5095	153	-10.35	miR:	agucaAAACG---UACCUAAACGUGu
							| | | | | | | |||||||
						Site:	uguaaUUUACAAAUUGUUUUGCACa

HRV: Human rhinovirus.

Table 5 PITA predictions on human rhinovirus-1B

Virus	miR	Site start	Site end	dG duplex	ddG		Alignment
HRV-1B	155	2901	2893	-15.12	-11.87	Site:	UCUUUACCAUUUCUUAGCAUUGCG
							|| || | | | || | | |:
						miR:	UGGGGAUAGU-GCUAAUCGUAAUU
HRV-1B	128	1562	1554	-16.4	-11.11	Site:	CUAACAUAAGACCAAUCACUGUAUCA
							| | | | | | |
						miR:	UUUCUCUGGCCAAGUGACACU
HRV-1B	106b	2276	2268	-17.2	-10.9	Site:	GUUUCUGCAUGUAAGGACUUUUG
							| | | || | | | | |
						miR:	UAGACGUGACAGUCGUGAAAU

The cut off was set at -10 (ddG). HRV: Human rhinovirus.

Table 6 Full target site list predicted by PITA on human rhinovirus-1B

Virus	microRNA	Start	End	dGduplex	dGopen	ddG
HRV-1B	miR-155	2901	2893	-15.12	-3.24	-11.87
HRV-1B	miR-128	1562	1554	-16.4	-5.28	-11.11
HRV-1B	miR-106b	2276	2268	-17.2	-6.29	-10.9
HRV-1B	miR-18a	2124	2116	-14.81	-4.9	-9.9
HRV-1B	miR-106b	4777	4769	-17.81	-7.96	-9.84
HRV-1B	miR-19b	6668	6660	-14.1	-5.07	-9.02
HRV-1B	miR-18a	7047	7039	-23.1	-15.01	-8.08
HRV-1B	miR-155	3186	3178	-14.3	-7.56	-6.73
HRV-1B1	miR-155	3723	3715	-14.9	-8.5	-6.39
HRV-1B	miR-19b	2016	2008	-12.11	-5.91	-6.19
HRV-1B	miR-18a	2570	2562	-16.8	-11.26	-5.53
HRV-1B	miR-18a	3108	3100	-13.5	-8.1	-5.39
HRV-1B	miR-128	3609	3601	-11.5	-6.32	-5.17
HRV-1B1	miR-19b	5095	5088	-12.53	-7.64	-4.88
HRV-1B1	miR-106b	5478	5470	-15.3	-10.46	-4.83
HRV-1B1	miR-155	6005	5997	-11.6	-7.01	-4.58
HRV-1B	miR-18a	4144	4138	-12.06	-7.91	-4.14
HRV-1B	miR-128	3513	3505	-14.3	-10.41	-3.88
HRV-1B	miR-19b	77	70	-10.42	-6.61	-3.8
HRV-1B	miR-106b	5542	5534	-10.6	-6.95	-3.64
HRV-1B	miR-155	5028	5020	-8.1	-4.94	-3.15
HRV-1B	miR-18a	4792	4784	-11.5	-8.37	-3.12
HRV-1B	miR-155	3552	3544	-12.6	-9.54	-3.05
HRV-1B	miR-106b	3585	3577	-12	-9.41	-2.58
HRV-1B	miR-18a	1686	1680	-14.19	-11.87	-2.31
HRV-1B	miR-106b	722	714	-4.36	-2.12	-2.23
HRV-1B	miR-128	2562	2554	-14.3	-12.1	-2.19
HRV-1B	miR-155	3975	3967	-13.8	-11.77	-2.02
HRV-1B	miR-128	442	434	-17.2	-15.21	-1.98
HRV-1B	miR-155	6621	6613	-6.5	-4.56	-1.93
HRV-1B	miR-155	4551	4543	-7.3	-5.68	-1.61
HRV-1B	miR-155	5978	5970	-7.9	-6.41	-1.48
HRV-1B	miR-18a	1431	1423	-6.6	-5.13	-1.46
HRV-1B	miR-19b	3248	3240	-8.71	-7.66	-1.04
HRV-1B	miR-106b	6598	6590	-11.8	-10.94	-0.85
HRV-1B1	miR-128	1829	1822	-12.9	-12.08	-0.81
HRV-1B	miR-155	6962	6954	-6	-5.38	-0.61
HRV-1B	miR-106b	569	563	-10.2	-9.77	-0.42
HRV-1B	miR-155	870	862	-9.57	-9.26	-0.3
HRV-1B	miR-18a	5478	5471	-10.7	-10.46	-0.23
HRV-1B	miR-155	3584	3576	-9.6	-9.41	-0.18
HRV-1B	miR-155	6258	6250	-9.17	-8.98	-0.18
HRV-1B	miR-19b	3550	3542	-10.4	-10.38	-0.019
HRV-1B	miR-106b	5269	5261	-10	-10	0.0096
HRV-1B	miR-106b	6533	6525	-11.4	-11.44	0.047
HRV-1B1	miR-18a	7059	7053	-18.7	-19.34	0.64
HRV-1B	miR-19b	2309	2301	-6.4	-7.08	0.68
HRV-1B	miR-19b	5076	5068	-9.2	-10.03	0.83
HRV-1B	miR-106b	177	169	-14.3	-15.51	1.21
HRV-1B	miR-155	624	616	-9.39	-11.23	1.84
HRV-1B	miR-106b	1105	1098	-9.2	-11.47	2.27
HRV-1B	miR-155	4265	4257	-6.91	-9.29	2.38
HRV-1B	miR-155	6641	6633	-5.8	-8.21	2.41
HRV-1B	miR-18a	4866	4858	-8.3	-11.02	2.72
HRV-1B	miR-18a	569	561	-7	-9.77	2.77
HRV-1B	miR-106b	6286	6278	-3.51	-6.53	3.02
HRV-1B	miR-128	6964	6956	-5.69	-8.77	3.08
HRV-1B	miR-155	2384	2376	-4.1	-7.44	3.34
HRV-1B	miR-155	234	226	-6.15	-9.76	3.61
HRV-1B	miR-19b	622	614	-7.4	-11.06	3.66
HRV-1B	miR-106b	441	435	-10.5	-15.27	4.77
HRV-1B	miR-155	6240	6232	-6	-12.02	6.02
HRV-1B	miR-106b	6184	6176	-7.9	-14.56	6.66
HRV-1B	miR-106b	549	541	-6.3	-15.77	9.47
HRV-1B	miR-106b	7007	6999	-7.61	-18.39	10.78

¹Sites identified also by targetscan. HRV: Human rhinovirus.