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      KCI등재 SCOPUS SCIE

      Identification of Loop Nucleotide Polymorphisms Affecting MicroRNA Processing and Function

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      https://www.riss.kr/link?id=A104830262

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      다국어 초록 (Multilingual Abstract)

      MicroRNAs are short 21-22 nucleotide single strand RNAs that are involved in post-transcriptional regulation of gene expression. Most microRNAs are first transcribed as long primary microRNAs and then undergo a two step-wise sequential processing to yield single-stranded mature microRNAs. It has been suggested that the loop region of primary microRNAs plays an important role in regulating microRNA biogenesis and target recognition. However, despite the fact that several single nucleotide polymorphisms have been identified in mature microRNA sequences and are related to human diseases, it remains unclear whether and how the single nucleotide polymorphisms in the loop regions of primary microRNAs would affect the biogenesis and function of microRNAs. Herein, we provide evidence that primary microRNAs loop nucleo-tides control the accuracy and efficiency of microRNA processing. Accordingly, we identified 32 single nucleotide polymorphisms in the loop regions of human primary microRNAs using bioinformatics, and further validated three loss-of-function and one gain-of-function single nucleotide polymorphisms using dual-luciferase assays. Thus, these results reveal a critical regulatory role encoded in the loop nucleotides of primary microRNAs for microRNA processing and function.
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      MicroRNAs are short 21-22 nucleotide single strand RNAs that are involved in post-transcriptional regulation of gene expression. Most microRNAs are first transcribed as long primary microRNAs and then undergo a two step-wise sequential processing to y...

      MicroRNAs are short 21-22 nucleotide single strand RNAs that are involved in post-transcriptional regulation of gene expression. Most microRNAs are first transcribed as long primary microRNAs and then undergo a two step-wise sequential processing to yield single-stranded mature microRNAs. It has been suggested that the loop region of primary microRNAs plays an important role in regulating microRNA biogenesis and target recognition. However, despite the fact that several single nucleotide polymorphisms have been identified in mature microRNA sequences and are related to human diseases, it remains unclear whether and how the single nucleotide polymorphisms in the loop regions of primary microRNAs would affect the biogenesis and function of microRNAs. Herein, we provide evidence that primary microRNAs loop nucleo-tides control the accuracy and efficiency of microRNA processing. Accordingly, we identified 32 single nucleotide polymorphisms in the loop regions of human primary microRNAs using bioinformatics, and further validated three loss-of-function and one gain-of-function single nucleotide polymorphisms using dual-luciferase assays. Thus, these results reveal a critical regulatory role encoded in the loop nucleotides of primary microRNAs for microRNA processing and function.

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      참고문헌 (Reference)

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      2 Ouyang, Y.B, "miR-181 targets multiple Bcl-2 family members and influences apoptosis and mitochondrial function in astrocytes" 12 : 213-219, 2012

      3 Ouyang, Y.B, "miR-181 regulates GRP78 and influences outcome from cerebral ischemia in vitro and in vivo" 45 : 555-563, 2012

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      10 Trujillo, R.D, "The potential functions of primary microRNAs in target recognition and repression" 29 : 3272-3285, 2010

      1 Wu, H, "miRNA profiling of naive, effector and memory CD8 T cells" 2 : e1020-, 2007

      2 Ouyang, Y.B, "miR-181 targets multiple Bcl-2 family members and influences apoptosis and mitochondrial function in astrocytes" 12 : 213-219, 2012

      3 Ouyang, Y.B, "miR-181 regulates GRP78 and influences outcome from cerebral ischemia in vitro and in vivo" 45 : 555-563, 2012

      4 Cimmino, A, "miR-15 and miR-16 induce apoptosis by targeting BCL2" 102 : 13944-13949, 2005

      5 Cheng, L.C, "miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche" 12 : 399-408, 2009

      6 Li, Q.J, "miR- 181a is an intrinsic modulator of T cell sensitivity and selection" 129 : 147-161, 2007

      7 O’Donnell, K.A, "c-Myc-regulated microRNAs modulate E2F1 expression" 435 : 839-843, 2005

      8 Yuan, M, "Yes-associated protein (YAP) functions as a tumor suppressor in breast" 15 : 1752-1759, 2008

      9 Zhang, X, "The terminal loop region controls microRNA processing by Drosha and Dicer" 38 : 7689-7697, 2010

      10 Trujillo, R.D, "The potential functions of primary microRNAs in target recognition and repression" 29 : 3272-3285, 2010

      11 Lee, Y., "The nuclear RNase III Drosha initiates microRNA processing" NATURE PUBLISHING GROUP 425 : 415-419, 2003

      12 Gu, S, "The loop position of shRNAs and premiRNAs is critical for the accuracy of dicer processing in vivo" 151 : 900-911, 2012

      13 Ambros, V., "The functions of animal microRNAs" 431 : 350-355, 2004

      14 Trabucchi, M, "The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs" 459 : 1010-1014, 2009

      15 Xu, P, "The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism" 13 : 790-795, 2003

      16 Lee, R.C, "The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14" 75 : 843-854, 1993

      17 Heo, I., "TUT4 in Concert with Lin28 Suppresses MicroRNA Biogenesis through Pre-MicroRNA Uridylation" CELL PRESS 138 : 696-708, 2009

      18 Duan, R, "Single nucleotide polymor-phism associated with mature miR-125a alters the processing of pri-miRNA" 16 : 1124-1131, 2007

      19 Viswanathan, S.R, "Selective blockade of microRNA processing by Lin28" 320 : 97-100, 2008

      20 Silva, J.M, "Second-generation shRNA libraries covering the mouse and human genomes" 37 : 1281-1288, 2005

      21 Sun, G, "SNPs in human miRNA genes affect biogenesis and function" 15 : 1640-1651, 2009

      22 Chaulk, S.G, "Role of pri-miRNA tertiary structure in miR- 17~92 miRNA biogenesis" 8 : 1105-1114, 2011

      23 Paddison, P.J, "RNA interference: the new somatic cell genetics" 2 : 17-23, 2002

      24 Zhang, J., "Propofol induces apoptosis of hepatocellular carcinoma cells by upregulation of microRNA-199a expression" 37 : 227-232, 2013

      25 Lewis, B.P, "Prediction of mammalian microRNA targets" 115 : 787-798, 2003

      26 Liu, G., "Pre-miRNA loop nucleotides control the distinct activities of mir-181a-1 and mir- 181c in early T cell development" 3 : e3592-, 2008

      27 Wightman, B, "Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans" 75 : 855-862, 1993

      28 Jazdzewski, K, "Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer" 106 : 1502-1505, 2009

      29 Xia, X.G, "Pol II-expressed shRNA knocks down Sod2 gene expression and causes phenotypes of the gene knockout in mice" 2 : e10-, 2006

      30 Schopman, N.C, "Optimization of shRNA inhibitors by variation of the terminal loop sequence" 86 : 204-211, 2010

      31 Miyagishi, M, "Optimization of an siRNA-expression system with an improved hairpin and its significant suppressive effects in mammalian cells" 6 : 715-723, 2004

      32 Hinton, T.M, "Native microRNA loop sequences can improve short hairpin RNA processing for virus gene silencing in animal cells" 4 : 295-301, 2008

      33 Mencia, A, "Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss" 41 : 609-613, 2009

      34 Han, J., "Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex" CELL PRESS 125 : 887-901, 2006

      35 Nam, Y, "Molecular basis for interaction of let-7 microRNAs with Lin28" 147 : 1080-1091, 2011

      36 Bartel, D.P., "MicroRNAs: target recognition and regulatory functions" 136 : 215-233, 2009

      37 Gangaraju, V.K, "MicroRNAs: key regulators of stem cells" 10 : 116-125, 2009

      38 Bartel, D.P., "MicroRNAs: genomics, biogenesis, mechanism, and function" 116 : 281-297, 2004

      39 Chen, C.Z, "MicroRNAs modulate hematopoietic lineage differentiation" 303 : 83-86, 2004

      40 Arnold, C.P, "MicroRNA programs in normal and aberrant stem and progenitor cells" 21 : 798-810, 2011

      41 Frenquelli, M, "MicroRNA and proliferation control in chronic lymphocytic leukemia: functional relationship between miR-221/222 cluster and p27" 115 : 3949-3959, 2010

      42 Lerner, M., "MiRNA-27a controls FBW7/hCDC4- dependent cyclin E degradation and cell cycle progression" 10 : 2172-2183, 2011

      43 Yue, S.B, "Loop nucleotides control primary and mature miRNA function in target recognition and repression" 8 : 1115-1123, 2011

      44 Heo, I., "Lin28 Mediates the Terminal Uridylation of let-7 Precursor MicroRNA" CELL PRESS 32 : 276-284, 2008

      45 Newman, M.A, "Lin- 28 interaction with the Let-7 precursor loop mediates regulated microRNA processing" 14 : 1539-1549, 2008

      46 Sun, Q, "Hsa-mir-27a genetic variant contributes to gastric cancer susceptibility through affecting miR-27a and target gene expression" 101 : 2241-2247, 2010

      47 Gong, J, "Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis" 33 : 254-263, 2012

      48 Ryan, B.M, "Genetic variation in microRNA networks: the implications for cancer research" 10 : 389-402, 2010

      49 Yi, R, "Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs" 17 : 3011-3016, 2003

      50 Park, J.E, "Dicer recognizes the 5′ end of RNA for efficient and accurate processing" 475 : 201-205, 2011

      51 Li, L, "Defining the optimal parameters for hairpin-based knockdown constructs" 13 : 1765-1774, 2007

      52 Kim, V.N, "Biogenesis of small RNAs in animals" 10 : 126-139, 2009

      53 Auyeung, V.C, "Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing" 152 : 844-858, 2013

      54 Zhou, Y, "Association analysis of genetic variants in microRNA networks and gastric cancer risk in a Chinese Han population" 138 : 939-945, 2012

      55 Michlewski, G, "Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis" 17 : 1011-1018, 2010

      56 Livak, K.J, "Analysis of relative gene expression data using real-time quantitative PCR and the 2(- Delta Delta C(T)) method" 25 : 402-408, 2001

      57 Hammond, S.M, "An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells" 404 : 293-296, 2000

      58 Brummelkamp, T.R, "A system for stable expression of short interfering RNAs in mammalian cells" 296 : 550-553, 2002

      59 Hutvagner, G, "A cellular function for the RNAinterference enzyme Dicer in the maturation of the let-7 small temporal RNA" 293 : 834-838, 2001

      60 Chin, L.J, "A SNP in a let- 7 microRNA complementary site in the KRAS 3′ untranslated region increases non-small cell lung cancer risk" 68 : 8535-8540, 2008

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      2023 평가예정 해외DB학술지평가 신청대상 (해외등재 학술지 평가)
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      기준연도 WOS-KCI 통합IF(2년) KCIF(2년) KCIF(3년)
      2016 2.77 0.19 1.85
      KCIF(4년) KCIF(5년) 중심성지수(3년) 즉시성지수
      1.37 1.11 0.379 0.03
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