Table 1.
Intergenic and intragenic tumor‐suppressive micro RNA (TS‐miRNA) genes (miRNA number in a name < 700): These intergenic TS‐miRNA genes and protein‐coding host genes harboring intragenic TS‐miRNA genes are located within 500 bp downstream of CpG islands
| miRNA genes (ID < 700) | Loci | Distances from 5′ end of miRNA genes to 3′ end of their CpG islands (bp) | Targets | References indicating tumor suppressive functions of miRNA | Host gene | Distances from TSS of host genes to 3′ end of their CpG islands (bp) | Distances from 5′ end of miRNA genes to 3′ end of CpG islands around TSS of host genes (bp) |
|---|---|---|---|---|---|---|---|
| Intergenic miRNA genes | |||||||
| hsa‐mir‐9‐3 | 15q26.1 | 0 | NF‐kappaB1, Androgen receptor (AR) | Guo, 2009; Ostling, 2011 | None | — | — |
| hsa‐mir‐34b | 11q23.1 | 0 | CDK6, c‐MYC, E2F3, MET, CCNE2, CDK4, CAV1, MYB, SFRS2, CREB | Corney, 2007t; Kozaki et al.19; Toyota et al.20 | None | — | — |
| hsa‐mir‐34c | 11q23.1 | 272 | CDK6, c‐MYC, E2F3, MET, CCNE2, CDK4, CAV1, MYB, SFRS2, Androgen receptor (AR) | Corney, 2007; Toyota et al.20; Ostling, 2011 | None | — | — |
| hsa‐mir‐92b | 1q22 | 0 | PRMT5 | Pal, 2007 | None | — | — |
| hsa‐mir‐124‐1 | 8p23.1 | 0 | CDK6, C/EBPα, SMYD3, VIM, IQGAP1, IGFBP7 | Silber, 2008; Furuta, 2010 | None | — | — |
| hsa‐mir‐124‐3 | 20q13.33 | 0 | CDK6, C/EBPα, SMYD3, VIM, IQGAP1, IGFBP7 | Silber, 2008; Furuta, 2010 | None | — | — |
| hsa‐mir‐127 | 14q32.2 | 0 | BCL6 | Saito et al.17 | None | — | — |
| hsa‐mir‐129‐2 | 11p11.2 | 0 | SOX4 | Dyrskjot, 2009; Huang, 2009 | None | — | — |
| hsa‐mir‐137 | 1p21.3 | 0 | CDK6, MITF, Cdc42 | Kozaki et al.19; Bemis, 2008; Liu et al.65 | None | — | — |
| hsa‐mir‐148a | 7p15.2 | 406 | DNMT‐1, TGIF2 | Braconi et al.60 | None | — | — |
| hsa‐mir‐193a | 17q11.2 | 0 | E2F6, c‐kit | Kozaki et al.19; Gao, 2011 | None | — | — |
| hsa‐mir‐196b | 7p15.2 | 0 | c‐myc | Bhatia, 2010 | None | — | — |
| hsa‐mir‐203 | 14q32.33 | 0 | ABCE1, ABL | Kozaki et al.19; Bueno, 2008; Furuta, 2010 | None | — | — |
| hsa‐mir‐210 | 11p15.5 | 0 | FGFRL1 | Camps, 2008; Tsuchiya, 2011 | None | — | — |
| hsa‐mir‐212 | 17p13.3 | 0 | MeCP2, PED | Incoronato, 2010; Wada, 2010 | None | — | — |
| hsa‐mir‐375 | 2q35 | 0 | PDK1, 14‐3‐3zeta, RASD1, YAP | Tsukamoto, 2010; Liu, 2010; de Souza Rocha Simonini, 2010 | None | — | — |
| hsa‐mir‐409 | 14q32.31 | 0 | RDX | Zheng, 2011 | None | — | — |
| hsa‐mir‐424 | Xq26.3 | 0 | PLAG1 | Pallasch, 2009 | None | — | — |
| hsa‐mir‐663 | 20p11.1 | 0 | JunB, JunD, TGFβ1, p21/Waf1/Cip1 | Pan, 2010; Tili, 2010; Tili, 2010 | None | — | — |
| Intragenic miRNA genes | |||||||
| hsa‐mir‐1‐1 | 20q13.33 | 3 | HDAC4, FoxP1, MET | Datta et al.44 | C20orf166 | 0 | 3726 |
| hsa‐mir‐15b | 3q25.33 | 3498 | BCL2 | Cimmino, 2005; Xia, 2008 | SMC4 | 0 | 3498 |
| hsa‐mir‐16‐2 | 3q25.33 | 3655 | BCL2 | Cimmino, 2005; Xia, 2008 | SMC4 | 0 | 3655 |
| hsa‐mir‐23b | 9q22.32 | 554 | GLS, uPA, c‐Met | Gao, 2009; Salvi, 2009 | C9orf3 | 0 | 358 318 |
| hsa‐mir‐26a‐1 | 3p22.2 | 24 730 | EZH2, cyclins D2, cyclin E2 | Lu et al.48; Sander, 2008; Kota et al.47 | CTDSPL | 0 | 106 856 |
| hsa‐mir‐26a‐2 | 12q14.1 | 20 365 | EZH2, cyclins D2, cyclin E2 | Sander, 2008; Kota et al.47 | CTDSP2 | 0 | 20 365 |
| hsa‐mir‐26b | 2q35 | 1813 | SLC7A11 | Ma, 2010 #133; Liu et al.65 | CTDSP1 | 0 | 1813 |
| hsa‐mir‐27b | 9q22.32 | 317 | CYP1B1 | Tsuchiya, 2006 | C9orf3 | 0 | 358 555 |
| hsa‐mir‐30c‐1 | 1p34.1 | 26 046 | BCL2‐like 11 (BIM) | Garofalo, 2011 | NFYC | 0 | 64 981 |
| hsa‐mir‐33a | 22q13.2 | 8601 | Pim‐1 | Thomas, 2011 | SREBF2 | 0 | 66 964 |
| hsa‐mir‐95 | 4p16.1 | 65 175 | SNX1 | Huang, 2011 | ABLIM2 | 0 | 152 620 |
| hsa‐mir‐101‐2 | 9p24.1 | 45 517 | EZH2, COX‐2, Mcl‐1 | Varambally, 2008; Strillacci, 2009; Su, 2009 | RCL1 | 0 | 56 744 |
| hsa‐mir‐107 | 10q23.31 | 51 653 | CDK6, PLAG1, HIF‐1β, PKCɛ | Lee, 2009; Pallasch, 2009; Yamakuchi, 2010; Datta, 2011 | PANK1 | 281 | 51 653 |
| hsa‐mir‐126 | 9q34.3 | 0 | IRS‐1, SLC7A5, SOX2, VEGFA, PIK3R2 | Tavazoie et al.34; Zhang et al.35 | EGFL7 | 0 | 4049 |
| hsa‐mir‐128‐1 | 2q21.3 | 76 097 | E2F3a, Bmi‐1, NTRK3 | Zhang, 2009; Godlewski, 2008; Guidi, 2010 | R3HDM1 | 0 | 133 252 |
| hsa‐mir‐133a‐2 | 20q13.33 | 10 216 | FSCN1 | Chiyomaru et al.55; Kano, 2010 | C20orf166 | 0 | 14 332 |
| hsa‐mir‐139 | 11q13.4 | 24 361 | ROCK2 | Wong, 2011 | PDE2A | 0 | 27 048 |
| hsa‐mir‐149 | 2q37.3 | 0 | Akt1, E2F1 | Lin et al.27 | GPC1 | 0 | 19 098 |
| hsa‐mir‐152 | 17q21.32 | 0 | DNMT1, E2F3, MET, Rictor | Huang et al.61; Das, 2010; Tsuruta et al.24 | COPZ2 | 93 | 0 |
| hsa‐mir‐153‐1 | 2q35 | 516 | Bcl‐2, Mcl‐1 | Xu, 2010 | PTPRN | 12 | 14 948 |
| hsa‐mir‐153‐2 | 7q36.3 | 2006 | Bcl‐2, Mcl‐1 | Xu, 2010 | PTPRN2 | 0 | 1 012 214 |
| hsa‐mir‐185 | 22q11.21 | 11 562 | Six1, RhoA, Cdc42, Androgen receptor (AR) | Imam, 2010; Liu et al.65; Ostling, 2011 | C22orf25 | 0 | 11 562 |
| hsa‐mir‐186 | 1p31.1 | 13 087 | P2X7 | Zhou, 2008 | ZRANB2 | 189 | 13 087 |
| hsa‐mir‐198 | 3q13.33 | 45 984 | c‐MET | Tan, 2011 | FSTL1 | 0 | 54 626 |
| hsa‐mir‐218‐1 | 4p15.31 | 171 810 | ECOP, IKK‐b, LASP1, PXN, Robo1, BIRC5, GJA1, Rictor | Martinez, 2008; Wu et al.56; Alajez et al.49; Uesugi et al.23 | SLIT2 | 0 | 273 030 |
| hsa‐mir‐218‐2 | 5q34 | 188 233 | ECOP, IKK‐b, LASP1, PXN, Robo1, BIRC5, GJA1, Rictor | Martinez, 2008; Wu et al.56; Alajez et al.49; Uesugi et al.23 | SLIT3 | 0 | 532 169 |
| hsa‐mir‐326 | 11q13.4 | 15 994 | Notch, MRP‐1/ABCC1 | Kefas, 2009; Liang, 2010 | ARRB1 | 0 | 15 994 |
| hsa‐mir‐335 | 7q32.2 | 2841 | SOX4 | Tavazoie et al.34 | MEST | 0 | 2841 |
| hsa‐mir‐338 | 17q25.3 | 2999 | SMO | Huang, 2011 | AATK | 0 | 39 752 |
| hsa‐mir‐340 | 5q35.3 | 55 894 | MITF, c‐Met | Goswami, 2010; Wu, 2011 | RNF130 | 0 | 55 894 |
| hsa‐mir‐346 | 14q32.2 | 1172 | Androgen receptor (AR) | Grady et al.43 | GRID1 | 0 | 98 379 |
| hsa‐mir‐449a | 5q11.2 | 2333 | HDAC‐1, E2F1, Androgen receptor (AR) | Noonan, 2009; Yang, 2009; Lize, 2009; Ostling, 2011 | CDC20B | 0 | 2333 |
| hsa‐mir‐449b | 5q11.2 | 2213 | E2F1, Androgen receptor (AR) | Yang, 2009; Lize, 2009; Ostling, 2011 | CDC20B | 0 | 2213 |
| hsa‐mir‐486 | 8p11.21 | 6311 | OLFM4 | Oh, 2011 | ANK1 | 0 | 235 314 |
| hsa‐mir‐488 | 1q25.2 | 134 811 | Androgen receptor (AR) | Sikand, 2010 | ASTN1 | 178 | 134 811 |
| hsa‐mir‐489 | 7q21.3 | 90 754 | PTPN11 | Kikkawa, 2010 | CALCR | 43 | 90 754 |
| hsa‐mir‐548d‐1 | 8q24.13 | 47 722 | ERBB2 | Chen, 2009; Heyn, 2011 | ATAD2 | 0 | 47 722 |
| hsa‐mir‐559 | 2p21 | 7558 | ERBB2 | Chen, 2009 | EPCAM | 343 | 7558 |
| hsa‐mir‐562 | 2q37.1 | 178 223 | EYA1 | Drake, 2009 | DIS3L2 | 0 | 210 527 |
| hsa‐mir‐591 | 7q21.3 | 101 711 | – | Shohet, 2011 | SLC25A13 | 0 | 101 711 |
| hsa‐mir‐593 | 7q32.1 | 22 182 | PLK1 | Ito, 2010 | SND1 | 0 | 429 362 |
| hsa‐mir‐634 | 17q24.2 | 47 907 | Androgen receptor (AR) | Ostling, 2011 | PRKCA | 0 | 483 573 |
TSS, transcription start site. These data were obtained from the miRBase database (Release 18: November 2011) (http://www.mirbase.org/index.shtml), UCSC Genome Browser on Human February 2009 Assembly (hg19) (http://genome.ucsc.edu/cgi-bin/hgGateway) and PubMed (http://www.ncbi.nlm.nih.gov/pubmed). All intragenic miRNA genes, indicated in this table, are transcribed in the same direction as those of their host genes.