ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaUCGGAGGUACUUAAGACUAc 5' | || |||| ||||||| Target 5' tgAACCCCCAT---TTCTGATt 3'	137 - 155	157.00	-12.40
2	miRNA 3' gaUCGGAGGUACUUAAGAC-UAc 5' :||:||||| ||:|| || Target 5' atGGCTTCCAT--CTTTTGCATc 3'	105 - 125	116.00	-13.04
3	miRNA 3' gaUCGGAGGUACUUAAGACUac 5' || || |: |||:||: Target 5' -aAGACT-CGCCCATTTTGGaa 3'	1 - 20	99.00	-6.00

Mutant ID	Mutant Position	Mutant Source
COSN30695702	4	COSMIC
COSN30448327	11	COSMIC
COSN18730962	21	COSMIC
COSN30177974	53	COSMIC
COSN31577469	56	COSMIC
COSN30478655	66	COSMIC
COSN31662475	98	COSMIC
COSN20459273	104	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1485567929	5	dbSNP
rs757036275	7	dbSNP
rs10819	8	dbSNP
rs754085793	9	dbSNP
rs766548140	11	dbSNP
rs1232964112	13	dbSNP
rs1308402549	18	dbSNP
rs756506378	20	dbSNP
rs1220017461	26	dbSNP
rs372496406	27	dbSNP
rs369867107	28	dbSNP
rs762220335	30	dbSNP
rs1163358168	34	dbSNP
rs896114493	38	dbSNP
rs773950892	40	dbSNP
rs72847228	45	dbSNP
rs72847227	49	dbSNP
rs547295168	50	dbSNP
rs1172575154	51	dbSNP
rs1428432778	59	dbSNP
rs1371625215	60	dbSNP
rs11264	63	dbSNP
rs1393518808	65	dbSNP
rs1179107513	75	dbSNP
rs1440410294	84	dbSNP
rs532235248	86	dbSNP
rs1245760882	89	dbSNP
rs1317297468	100	dbSNP
rs1340132888	121	dbSNP
rs1226165150	141	dbSNP
rs1273844574	146	dbSNP
rs1048885	150	dbSNP
rs1246149117	154	dbSNP
rs1219680402	162	dbSNP
rs979474614	165	dbSNP
rs1253762014	173	dbSNP
rs1386630559	173	dbSNP
rs1441538948	173	dbSNP
rs3219189	173	dbSNP
rs1453508487	196	dbSNP
rs967733074	197	dbSNP
rs1056054179	200	dbSNP
rs1291100751	201	dbSNP
rs1301506419	201	dbSNP
rs929673028	203	dbSNP
rs1021164216	208	dbSNP

- mBio, 2013

UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.

- Genome research, 2016

DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.