A Computational Approach for Predicting Role of Human MicroRNAs in MERS-CoV Genome

Box 1

Hybridization between microRNA and viral RNA using RNA hybrid program. The program finds the energetically most favorable hybridization sites of a miRNA in a large hairpin of viral RNA.

(A) MD5 & hsa-miR-628-5p  (MFE: −23.5 kcal/mol)   (B) MD17 & hsa-miR-6804-3p (MFE: −23.3 kcal/mol)

 MD5  5 ′ G    CA   GCAGCUUG   C 3 ′     target 5 ′ A U  A U    A   A    3 ′

      CUCUAGUG  AAUG    GUUGGCA           CU UGG UG GAGG AGGU

      GAGAUCAU  UUAU    CAGUCGU           GA ACC AC CUCC UCCA

 miRNA 3 ′ G        A         A 5 ′                           miRNA      3 ′           C          C       U            G            CGC 5 ′

(C) MD110 & hsa-miR-3934-5p (MFE: −17.1 kcal/mol)  (D) MD110 & hsa-miR-4474-5p (MFE: −26.7 kcal/mol)

 target 5 ′          A            UC                  UG        C       3′                                     target 5′     A                       GU                   C         3′

              CUUA       UCUAC        CU                                                         GUCUGAU     UGAGAC

              GAGU       AGGUG        GA                                                         CAGACUA     ACUCUG

 miRNA   3′ GACG           CAA                 UG      CU 5′                                                               miRNA      3′ ACA                      GU                 AUU  5′

(E) MD157& hsa-miR-4289 (MFE: −21.7 kcal/mol)     (F) MD244 & hsa-miR-208a-3p (MFE: −19.4 kcal/mol)

 target 5 ′ C        U                 A                               G 3′                                     target 5′ G                            GC       GAA             A 3′

                                         G          UAGC     UUGUGCAGUG                                           AUGAGCUUU      GU         UCUUA

                                         C          AUCG     GACGUGUUAC                                           UGUUCGAAA      CG         AGAAU

 miRNA   3′   A        U                 G                               G 5′                                                            miRNA   3^′                               AA       AGC             A 5′

(G) MD186 & hsa-miR-7974 (MFE: −31.1 kcal/mol)     (H) MD186 & hsa-miR-6856-5p (MFE: −29.8 kcal/mol)

 target 5 ′    C                    CA             G          U         C 3 ′                                target 5′      G          A               G                   C       AA        A 3′

                                         GCUUAGG      AGCA    CAC  GCC                                            GC        AGCA    CACUGC    CC      UCU

                                         CGAGUCC      UCGU    GUG  CGG                                             UG        UCGU    GUGACG    GG      AGA

 miRNA   3 ′ CC                      UC            A          U        A 5 ′                                                        miRNA    3′    GG                           G                    A      AG        A 5′

(I) MD366 & hsa-miR-510-3p (MFE: −26.4 kcal/mol)    (J) MR175 & hsa-miR-18a-3p (MFE: −20.9 kcal/mol)

 target 5 ′ G                      G                  A                      3′                                target 5′      G           CAA                     CA                    G 3′

                                       UCCACUC    UAGAGG                                                                    UAGA        GAGCGCU             CAGU

                                       AGGUGAG    AUCUCC                                                                    GUCU        CUCGUGA             GUCA

 miRNA      3′                         A                   AAAGUUA 5′                                                       miRNA      3′      G           UC                       AUCCC                  5′

(K) MR201 & has-miR-329-3p (−22.4 kcal/mol)      (L) MR268 & hsa-miR-548ax (MFE: −28.5 kcal/mol)

 target 5 ′         U                     CA              AA      A 3′                                target 5′ A                   C             G                 G          C 3′

                                               GAGGUUA    CAGGU      GU                                             UGGCAA    GCCG    AAUUA    UUC

                                               CUCCAAU    GUCCA      CA                                             ACCGUU    UGGC    UUAAU    AAG

 miRNA        3′ UUU                     UG              CA      A 5′                                                        miRNA      3′                      U             G                 G          A 5′

(M) MR282 & hsa-miR-342-3p (MFE: −33.5 kcal/mol)

 target 5 ′ G                              GUGCG           A           U 3′

                                       ACGGGUGCGA               CUG    GUGA

                                       UGCCCACGCU               GAC    CACU

 miRNA      3^′                                AAA                  A            CU 5′