메뉴 건너뛰기




Volumn 544, Issue 1, 2014, Pages 1-7

A challenge for miRNA: Multiple isomiRs in miRNAomics

Author keywords

Evolutionary pattern; Expression pattern; IsomiR; MicroRNA (miRNA)

Indexed keywords

BIOLOGICAL MARKER; ISOMICRORNA; MESSENGER RNA; MICRORNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

EID: 84899895387     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.04.039     Document Type: Review
Times cited : (98)

References (76)
  • 1
    • 28044471565 scopus 로고    scopus 로고
    • MicroRNA functions in animal development and human disease
    • Alvarez-Garcia I., Miska E.A. MicroRNA functions in animal development and human disease. Development 2005, 132:4653-4662.
    • (2005) Development , vol.132 , pp. 4653-4662
    • Alvarez-Garcia, I.1    Miska, E.A.2
  • 2
    • 84883651731 scopus 로고    scopus 로고
    • Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes
    • Baran-Gale J., Fannin E.E., Kurtz C.L., Sethupathy P. Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes. PLoS One 2013, 8:e73240.
    • (2013) PLoS One , vol.8
    • Baran-Gale, J.1    Fannin, E.E.2    Kurtz, C.L.3    Sethupathy, P.4
  • 3
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: genomics, biogenesis, mechanism, and function
    • Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 4
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: target recognition and regulatory functions
    • Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 13
    • 65849172363 scopus 로고    scopus 로고
    • Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
    • Ebhardt H.A., Tsang H.H., Dai D.C., Liu Y.F., Bostan B., Fahlman R.P. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Research 2009, 37:2461-2470.
    • (2009) Nucleic Acids Research , vol.37 , pp. 2461-2470
    • Ebhardt, H.A.1    Tsang, H.H.2    Dai, D.C.3    Liu, Y.F.4    Bostan, B.5    Fahlman, R.P.6
  • 18
    • 27744537851 scopus 로고    scopus 로고
    • Human RISC couples microRNA biogenesis and posttranscriptional gene silencing
    • Gregory R.I., Chendrimada T.P., Cooch N., Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 2005, 123:631-640.
    • (2005) Cell , vol.123 , pp. 631-640
    • Gregory, R.I.1    Chendrimada, T.P.2    Cooch, N.3    Shiekhattar, R.4
  • 21
    • 77955328547 scopus 로고    scopus 로고
    • The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule?
    • Guo L., Lu Z. The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule?. PLoS One 2010, 5:e11387.
    • (2010) PLoS One , vol.5
    • Guo, L.1    Lu, Z.2
  • 22
    • 77955422438 scopus 로고    scopus 로고
    • Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data
    • Guo L., Lu Z. Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. Computational Biology and Chemistry 2010, 34:165-171.
    • (2010) Computational Biology and Chemistry , vol.34 , pp. 165-171
    • Guo, L.1    Lu, Z.2
  • 23
    • 79957561785 scopus 로고    scopus 로고
    • Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications
    • Guo L., Liang T., Gu W., Xu Y., Bai Y., Lu Z. Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. PLoS One 2011, 6:e20517.
    • (2011) PLoS One , vol.6
    • Guo, L.1    Liang, T.2    Gu, W.3    Xu, Y.4    Bai, Y.5    Lu, Z.6
  • 24
    • 79953753919 scopus 로고    scopus 로고
    • A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing
    • Guo L., Liang T., Lu Z. A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing. Bio Systems 2011, 104:87-93.
    • (2011) Bio Systems , vol.104 , pp. 87-93
    • Guo, L.1    Liang, T.2    Lu, Z.3
  • 25
    • 79959386594 scopus 로고    scopus 로고
    • A comprehensive survey of miRNA repertoire and 3' addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing
    • Guo L., Yang Q., Lu J., Li H., Ge Q., Gu W., Bai Y., Lu Z. A comprehensive survey of miRNA repertoire and 3' addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing. PLoS One 2011, 6:e21072.
    • (2011) PLoS One , vol.6
    • Guo, L.1    Yang, Q.2    Lu, J.3    Li, H.4    Ge, Q.5    Gu, W.6    Bai, Y.7    Lu, Z.8
  • 26
    • 84864280682 scopus 로고    scopus 로고
    • Consistent isomiR expression patterns and 3' addition events in miRNA gene clusters and families implicate functional and evolutionary relationships
    • Guo L., Li H., Liang T., Lu J., Yang Q., Ge Q., Lu Z. Consistent isomiR expression patterns and 3' addition events in miRNA gene clusters and families implicate functional and evolutionary relationships. Molecular Biology Reports 2012, 39:6699-6706.
    • (2012) Molecular Biology Reports , vol.39 , pp. 6699-6706
    • Guo, L.1    Li, H.2    Liang, T.3    Lu, J.4    Yang, Q.5    Ge, Q.6    Lu, Z.7
  • 27
    • 84860348037 scopus 로고    scopus 로고
    • Tracking miRNA precursor metabolic products and processing sites through completely analyzing high-throughput sequencing data
    • Guo L., Li H., Lu J., Yang Q., Ge Q., Gu W., Bai Y., Lu Z. Tracking miRNA precursor metabolic products and processing sites through completely analyzing high-throughput sequencing data. Molecular Biology Reports 2012, 39:2031-2038.
    • (2012) Molecular Biology Reports , vol.39 , pp. 2031-2038
    • Guo, L.1    Li, H.2    Lu, J.3    Yang, Q.4    Ge, Q.5    Gu, W.6    Bai, Y.7    Lu, Z.8
  • 28
    • 84881551262 scopus 로고    scopus 로고
    • Close association between paralogous multiple isomiRs and paralogous/orthologues miRNA sequences implicates dominant sequence selection across various animal species
    • Guo L., Zhao Y., Zhang H., Yang S., Chen F. Close association between paralogous multiple isomiRs and paralogous/orthologues miRNA sequences implicates dominant sequence selection across various animal species. Gene 2013, 527:624-629.
    • (2013) Gene , vol.527 , pp. 624-629
    • Guo, L.1    Zhao, Y.2    Zhang, H.3    Yang, S.4    Chen, F.5
  • 29
    • 84895382187 scopus 로고    scopus 로고
    • Multiple isomiRs and diversity of miRNA sequences unveil evolutionary roles and functional relationships across animals
    • Guo L., Chen F., Lu Z. Multiple isomiRs and diversity of miRNA sequences unveil evolutionary roles and functional relationships across animals. MicroRNA and Non-Coding RNA: Technology, Developments and Applications 2013, 127-144.
    • (2013) MicroRNA and Non-Coding RNA: Technology, Developments and Applications , pp. 127-144
    • Guo, L.1    Chen, F.2    Lu, Z.3
  • 30
    • 84899952353 scopus 로고    scopus 로고
    • In-depth exploration of miRNA: a new approach to study miRNA at the miRNA/isomiR levels
    • Guo L., Zhang H., Zhao Y., Yang S., Chen F. In-depth exploration of miRNA: a new approach to study miRNA at the miRNA/isomiR levels. Current Bioinformatics 2014, 10.2174/1574893608666131120234836.
    • (2014) Current Bioinformatics
    • Guo, L.1    Zhang, H.2    Zhao, Y.3    Yang, S.4    Chen, F.5
  • 31
    • 84887233887 scopus 로고    scopus 로고
    • Selected isomiR expression profiles via arm switching?
    • Guo L., Zhang H., Zhao Y., Yang S., Chen F. Selected isomiR expression profiles via arm switching?. Gene 2014, 533:149-155.
    • (2014) Gene , vol.533 , pp. 149-155
    • Guo, L.1    Zhang, H.2    Zhao, Y.3    Yang, S.4    Chen, F.5
  • 35
    • 78751477191 scopus 로고    scopus 로고
    • Gene silencing by microRNAs: contributions of translational repression and mRNA decay
    • Huntzinger E., Izaurralde E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nature Reviews Genetics 2011, 12:99-110.
    • (2011) Nature Reviews Genetics , vol.12 , pp. 99-110
    • Huntzinger, E.1    Izaurralde, E.2
  • 36
    • 77349092849 scopus 로고    scopus 로고
    • Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development
    • Jagadeeswaran G., Zheng Y., Sumathipala N., Jiang H.B., Arrese E.L., Soulages J.L., Zhang W.X., Sunkar R. Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 2010, 11:52.
    • (2010) BMC Genomics , vol.11 , pp. 52
    • Jagadeeswaran, G.1    Zheng, Y.2    Sumathipala, N.3    Jiang, H.B.4    Arrese, E.L.5    Soulages, J.L.6    Zhang, W.X.7    Sunkar, R.8
  • 37
    • 61449186404 scopus 로고    scopus 로고
    • Selective stabilization of mammalian microRNAs by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2
    • Katoh T., Sakaguchi Y., Miyauchi K., Suzuki T., Kashiwabara S., Baba T., Suzuki T. Selective stabilization of mammalian microRNAs by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes & Development 2009, 23:433-438.
    • (2009) Genes & Development , vol.23 , pp. 433-438
    • Katoh, T.1    Sakaguchi, Y.2    Miyauchi, K.3    Suzuki, T.4    Kashiwabara, S.5    Baba, T.6    Suzuki, T.7
  • 38
    • 84880819629 scopus 로고    scopus 로고
    • MicroRNA-17~92 regulates effector and memory CD8 T-cell fates by modulating proliferation in response to infections
    • Khan A.A., Penny L.A., Yuzefpolskiy Y., Sarkar S., Kalia V. MicroRNA-17~92 regulates effector and memory CD8 T-cell fates by modulating proliferation in response to infections. Blood 2013, 121:4473-4483.
    • (2013) Blood , vol.121 , pp. 4473-4483
    • Khan, A.A.1    Penny, L.A.2    Yuzefpolskiy, Y.3    Sarkar, S.4    Kalia, V.5
  • 41
    • 84883183693 scopus 로고    scopus 로고
    • Regulation of huntingtin gene expression by miRNA-137, -214, -148a, and their respective isomiRs
    • Kozlowska E., Krzyzosiak W.J., Koscianska E. Regulation of huntingtin gene expression by miRNA-137, -214, -148a, and their respective isomiRs. International Journal of Molecular Sciences 2013, 14:16999-17016.
    • (2013) International Journal of Molecular Sciences , vol.14 , pp. 16999-17016
    • Kozlowska, E.1    Krzyzosiak, W.J.2    Koscianska, E.3
  • 42
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: integrating microRNA annotation and deep-sequencing data
    • Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research 2011, 39:D152-D157.
    • (2011) Nucleic Acids Research , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 43
    • 77955902024 scopus 로고    scopus 로고
    • The widespread regulation of microRNA biogenesis, function and decay
    • Krol J., Loedige I., Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nature Reviews Genetics 2010, 11:597-610.
    • (2010) Nature Reviews Genetics , vol.11 , pp. 597-610
    • Krol, J.1    Loedige, I.2    Filipowicz, W.3
  • 52
    • 84862262444 scopus 로고    scopus 로고
    • MiRNA arm selection and isomiR distribution in gastric cancer
    • Li S.C., Liao Y.L., Ho M.R., Tsai K.W., Lai C.H., Lin W.C. miRNA arm selection and isomiR distribution in gastric cancer. BMC Genomics 2012, 13(Suppl. 1):S13.
    • (2012) BMC Genomics , vol.13 , Issue.Suppl. 1
    • Li, S.C.1    Liao, Y.L.2    Ho, M.R.3    Tsai, K.W.4    Lai, C.H.5    Lin, W.C.6
  • 57
    • 41949102707 scopus 로고    scopus 로고
    • MiRiad roles for the miR-17-92 cluster in development and disease
    • Mendell J.T. miRiad roles for the miR-17-92 cluster in development and disease. Cell 2008, 133:217-222.
    • (2008) Cell , vol.133 , pp. 217-222
    • Mendell, J.T.1
  • 59
    • 84867736206 scopus 로고    scopus 로고
    • IsomiRs - the overlooked repertoire in the dynamic microRNAome
    • Neilsen C.T., Goodall G.J., Bracken C.P. IsomiRs - the overlooked repertoire in the dynamic microRNAome. Trends in Genetics 2012, 28:544-549.
    • (2012) Trends in Genetics , vol.28 , pp. 544-549
    • Neilsen, C.T.1    Goodall, G.J.2    Bracken, C.P.3
  • 62
    • 70449122099 scopus 로고    scopus 로고
    • Distinct mechanisms for microRNA strand selection by Drosophila Argonautes
    • Okamura K., Liu N., Lai E.C. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Molecular Cell 2009, 36:431-444.
    • (2009) Molecular Cell , vol.36 , pp. 431-444
    • Okamura, K.1    Liu, N.2    Lai, E.C.3
  • 66
    • 84881480813 scopus 로고    scopus 로고
    • IsomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets
    • Sablok G., Milev I., Minkov G., Minkov I., Varotto C., Yahubyan G., Baev V. isomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets. FEBS Lett 2013, 587:2629-2634.
    • (2013) FEBS Lett , vol.587 , pp. 2629-2634
    • Sablok, G.1    Milev, I.2    Minkov, G.3    Minkov, I.4    Varotto, C.5    Yahubyan, G.6    Baev, V.7
  • 67
    • 38349081145 scopus 로고    scopus 로고
    • Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA* strands in flies
    • Seitz H., Ghildiyal M., Zamore P.D. Argonaute loading improves the 5' precision of both MicroRNAs and their miRNAe* H., Ghildiya strands in flies. Current Biology 2008, 18:147-151.
    • (2008) Current Biology , vol.18 , pp. 147-151
    • Seitz, H.1    Ghildiyal, M.2    Zamore, P.D.3
  • 69
    • 84881549174 scopus 로고    scopus 로고
    • Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis
    • Shao C., Wu Q., Qiu J., Jin S., Zhang B., Qian J., Chen M., Meng Y. Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis. Gene 2013, 527:477-483.
    • (2013) Gene , vol.527 , pp. 477-483
    • Shao, C.1    Wu, Q.2    Qiu, J.3    Jin, S.4    Zhang, B.5    Qian, J.6    Chen, M.7    Meng, Y.8
  • 70
    • 84860624552 scopus 로고    scopus 로고
    • Two miRNA clusters, Mir-17-92 (Mirc1) and Mir-106b-25 (Mirc3), are involved in the regulation of spermatogonial differentiation in mice
    • Tong M.H., Mitchell D.A., McGowan S.D., Evanoff R., Griswold M.D. Two miRNA clusters, Mir-17-92 (Mirc1) and Mir-106b-25 (Mirc3), are involved in the regulation of spermatogonial differentiation in mice. Biology of Reproduction 2012, 86:72.
    • (2012) Biology of Reproduction , vol.86 , pp. 72
    • Tong, M.H.1    Mitchell, D.A.2    McGowan, S.D.3    Evanoff, R.4    Griswold, M.D.5
  • 74
    • 45749124784 scopus 로고    scopus 로고
    • A computational screen for mouse signaling pathways targeted by microRNA clusters
    • Xu J.Z., Wong C.W. A computational screen for mouse signaling pathways targeted by microRNA clusters. RNA-A Publication of the RNA Society 2008, 14:1276-1283.
    • (2008) RNA-A Publication of the RNA Society , vol.14 , pp. 1276-1283
    • Xu, J.Z.1    Wong, C.W.2
  • 76
    • 84875471108 scopus 로고    scopus 로고
    • A genome-wide survey of microRNA truncation and 3' nucleotide addition events in larch (Larix leptolepis)
    • Zhang J., Zhang S., Li S., Han S., Wu T., Li X., Qi L. A genome-wide survey of microRNA truncation and 3' nucleotide addition events in larch (Larix leptolepis). Planta 2013, 237:1047-1056.
    • (2013) Planta , vol.237 , pp. 1047-1056
    • Zhang, J.1    Zhang, S.2    Li, S.3    Han, S.4    Wu, T.5    Li, X.6    Qi, L.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.