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Volumn 44, Issue 9, 2016, Pages

Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation

Author keywords

[No Author keywords available]

Indexed keywords

ELAV LIKE PROTEIN 1; MESSENGER RNA; MICRORNA; RNA BINDING PROTEIN; SMALL INTERFERING RNA; 3' UNTRANSLATED REGION; PUM1 PROTEIN, HUMAN; PUM2 PROTEIN, HUMAN;

EID: 84970005633     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw048     Document Type: Article
Times cited : (29)

References (46)
  • 1
    • 84886095882 scopus 로고    scopus 로고
    • Quaking, an RNA-binding protein, is a critical regulator of vascular smooth muscle cell phenotype
    • van der Veer, E., de Bruin, R., Kraaijeveld, A., de Vries, M., Bot, I. et al. (2013) Quaking, an RNA-binding protein, is a critical regulator of vascular smooth muscle cell phenotype. Circ. Res., 113, 1065-1075.
    • (2013) Circ. Res. , vol.113 , pp. 1065-1075
    • Vander Veer, E.1    De Bruin, R.2    Kraaijeveld, A.3    De Vries, M.4    Bot, I.5
  • 5
    • 27944508215 scopus 로고    scopus 로고
    • CLIP:A method for identifying protein-RNA interaction sites in living cells
    • Ule, J., Jensen, K., Mele, A., Darnell, R.B. (2005) CLIP:A method for identifying protein-RNA interaction sites in living cells. Methods, 37, 376-386.
    • (2005) Methods , vol.37 , pp. 376-386
    • Ule, J.1    Jensen, K.2    Mele, A.3    Darnell, R.B.4
  • 8
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis, B.P., Burge, C.B., Bartel, D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 10
    • 80052041185 scopus 로고    scopus 로고
    • MicroRNA regulation by RNA-binding proteins and its implications for cancer
    • Kouwenhove, M.V., Kedde, M., Agami, R. (2011) MicroRNA regulation by RNA-binding proteins and its implications for cancer. Nat. Rev. Cancer, 11, 644-656.
    • (2011) Nat. Rev. Cancer , vol.11 , pp. 644-656
    • Kouwenhove, M.V.1    Kedde, M.2    Agami, R.3
  • 11
    • 84890289270 scopus 로고    scopus 로고
    • Competition and collaboration between RNA-binding proteins and microRNAs
    • Ho, J.J., Marsden, P.A. (2014) Competition and collaboration between RNA-binding proteins and microRNAs. Wiley Interdiscip. Rev. RNA, 5, 69-86.
    • (2014) Wiley Interdiscip. Rev. RNA , vol.5 , pp. 69-86
    • Ho, J.J.1    Marsden, P.A.2
  • 12
    • 84924330592 scopus 로고    scopus 로고
    • Competition between target sites of regulators shapes post-transcriptional gene regulation
    • Jens, M., Rajewsky, N. (2015) Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat. Rev. Genet., 16, 113-126.
    • (2015) Nat. Rev. Genet. , vol.16 , pp. 113-126
    • Jens, M.1    Rajewsky, N.2
  • 13
    • 77957564277 scopus 로고    scopus 로고
    • A pumilio-induced RNA structure switch in p27-3-UTR controls MIR-221 and MIR-222 accessibility
    • Kedde, M., Kouwenhove, M.V., Zwart, W., Vrielink, J. A.O., Elkon, R., Agami, R. (2010) A pumilio-induced RNA structure switch in p27-3-UTR controls miR-221 and miR-222 accessibility. Nat. Cell Biol., 12, 1014-1020.
    • (2010) Nat. Cell Biol. , vol.12 , pp. 1014-1020
    • Kedde, M.1    Kouwenhove, M.V.2    Zwart, W.3    Vrielink, J.A.O.4    Elkon, R.5    Agami, R.6
  • 14
    • 79953797091 scopus 로고    scopus 로고
    • Repression of VEGFA by CA-rich element-binding microRNAs is modulated by hnRNP L
    • Jafarifar, J., Yao, P., Eswarappa, S.M., Fox, P.L. (2011) Repression of VEGFA by CA-rich element-binding microRNAs is modulated by hnRNP L. EMBO J., 30, 1324-1334.
    • (2011) EMBO J. , vol.30 , pp. 1324-1334
    • Jafarifar, J.1    Yao, P.2    Eswarappa, S.M.3    Fox, P.L.4
  • 16
    • 84878480000 scopus 로고    scopus 로고
    • Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in transcript decay
    • Jiang, P., Singh, M., Coller, H.A. (2013) Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in transcript decay. PLoS Comput. Biol., 9, e1003075.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003075
    • Jiang, P.1    Singh, M.2    Coller, H.A.3
  • 19
    • 84891687767 scopus 로고    scopus 로고
    • Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs
    • Friedersdorf, M.B., Keene, J.D. (2014) Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. Genome Biol, 15, R2.
    • (2014) Genome Biol , vol.15 , pp. R2
    • Friedersdorf, M.B.1    Keene, J.D.2
  • 21
    • 0031440357 scopus 로고    scopus 로고
    • The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins
    • Zamore, P.D., Williamson, J.R., Lehman, R. (1997) The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. RNA, 3, 1421-1433.
    • (1997) RNA , vol.3 , pp. 1421-1433
    • Zamore, P.D.1    Williamson, J.R.2    Lehman, R.3
  • 22
    • 44949255018 scopus 로고    scopus 로고
    • Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets
    • Morris, A.R., Mukharjee, N., Keene, J.D. (2008) Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. Mol. Cell. Biol., 12, 4093-4103.
    • (2008) Mol. Cell. Biol. , vol.12 , pp. 4093-4103
    • Morris, A.R.1    Mukharjee, N.2    Keene, J.D.3
  • 23
    • 52349122355 scopus 로고    scopus 로고
    • Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system
    • Galgano, A., Forrer, M., Jaskiewicz, L., Kanitz, A., Zavolan, M., Gerber, A.P. (2008) Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One, 3, e3164.
    • (2008) PLoS One , vol.3 , pp. e3164
    • Galgano, A.1    Forrer, M.2    Jaskiewicz, L.3    Kanitz, A.4    Zavolan, M.5    Gerber, A.P.6
  • 26
  • 27
    • 84940502214 scopus 로고    scopus 로고
    • Predicting effective microRNA target sites in mammalian mRNAs
    • Agarwal, V., Bell, G., Nam, J., Bartel, D. (2015) Predicting effective microRNA target sites in mammalian mRNAs. eLife, 4, e05005.
    • (2015) ELife , vol.4 , pp. e05005
    • Agarwal, V.1    Bell, G.2    Nam, J.3    Bartel, D.4
  • 30
    • 84919783215 scopus 로고    scopus 로고
    • Annexin-A1 regulates microRNA-26b∗and microRNA-562 to directly target NF--B and angiogenesis in breast cancer cells
    • Anbalagan, D., Yap, G., Yuan, Y., Pandey, V.K., Lau, W.H., Arora, S., Bist, P., Wong, J.S., Sethi, G., Nissom, P.M. et al. (2014) Annexin-A1 regulates microRNA-26b∗and microRNA-562 to directly target NF--B and angiogenesis in breast cancer cells. PLoS One, 9, e114507.
    • (2014) PLoS One , vol.9 , pp. e114507
    • Anbalagan, D.1    Yap, G.2    Yuan, Y.3    Pandey, V.K.4    Lau, W.H.5    Arora, S.6    Bist, P.7    Wong, J.S.8    Sethi, G.9    Nissom, P.M.10
  • 31
    • 33644853766 scopus 로고    scopus 로고
    • Local RNA base pairing probabilities in large sequences
    • Bernhart, S.H., Hofacker, I.L., Stadler, P.F. (2006) Local RNA base pairing probabilities in large sequences. Bioinformatics, 22, 614-615.
    • (2006) Bioinformatics , vol.22 , pp. 614-615
    • Bernhart, S.H.1    Hofacker, I.L.2    Stadler, P.F.3
  • 33
    • 84871806618 scopus 로고    scopus 로고
    • X-inactivation: Quantitative predictions of protein interactions in the Xist network
    • Agostini, F., Cirillo, D., Bolognesi, B., Tartaglia, G. (2012) X-inactivation: quantitative predictions of protein interactions in the Xist network. Nucleic Acids Res., 41, e31.
    • (2012) Nucleic Acids Res. , vol.41 , pp. e31
    • Agostini, F.1    Cirillo, D.2    Bolognesi, B.3    Tartaglia, G.4
  • 35
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey, J.D., Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U.S.A., 100, 9440-9445.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 36
    • 77950537175 scopus 로고    scopus 로고
    • Regularization paths for generalized linear models via coordinate descent
    • Friedman, J., Tibshirani, R., Hastie, T. (2010) Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw., 33, 1-22.
    • (2010) J. Stat. Softw. , vol.33 , pp. 1-22
    • Friedman, J.1    Tibshirani, R.2    Hastie, T.3
  • 37
    • 84926507971 scopus 로고    scopus 로고
    • Limma powers differential expression analyses for RNA-sequencing and microarray studies
    • Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., Smyth, G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47.
    • (2015) Nucleic Acids Res. , vol.43 , pp. e47
    • Ritchie, M.E.1    Phipson, B.2    Wu, D.3    Hu, Y.4    Law, C.W.5    Shi, W.6    Smyth, G.K.7
  • 38
    • 84859320008 scopus 로고    scopus 로고
    • PrimerBank: A PCR primer database for quantitative gene expression analysis, 2012 update
    • Wang, X., Spandidos, A., Wang, H., Seed, B. (2012) PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. Nucleic Acids Res., 40, D1144-D1149.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D1144-D1149
    • Wang, X.1    Spandidos, A.2    Wang, H.3    Seed, B.4
  • 39
    • 5644245066 scopus 로고    scopus 로고
    • mRNA openers and closers: Modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure
    • Meisner, N.C., Hackermuller, J., Uhl, V., Aszodi, A., Jaritz, M., Auer, M. (2004) mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure. Chembiochem, 5, 1432-1447.
    • (2004) Chembiochem , vol.5 , pp. 1432-1447
    • Meisner, N.C.1    Hackermuller, J.2    Uhl, V.3    Aszodi, A.4    Jaritz, M.5    Auer, M.6
  • 40
    • 0037162703 scopus 로고    scopus 로고
    • Modular recognition of RNA by a human pumilio-homology domain
    • Wang, X., McLachlan, J., Zamore, P.D., Hall, T.M.T. (2002) Modular recognition of RNA by a human pumilio-homology domain. Cell, 110, 501-512.
    • (2002) Cell , vol.110 , pp. 501-512
    • Wang, X.1    McLachlan, J.2    Zamore, P.D.3    Hall, T.M.T.4
  • 41
    • 78049275913 scopus 로고    scopus 로고
    • RNAcontext: A new method for learning the sequence and structure binding preferences of RNA-binding proteins
    • Kazan, H., Ray, D., Chan, E.T., Hughes, T.R., Morris, Q. (2010) RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comp. Biol., 6, e1000832.
    • (2010) PLoS Comp. Biol. , vol.6 , pp. e1000832
    • Kazan, H.1    Ray, D.2    Chan, E.T.3    Hughes, T.R.4    Morris, Q.5
  • 42
    • 84892636681 scopus 로고    scopus 로고
    • GraphProt: Modeling binding preferences of RNA-binding proteins
    • Maticzka, D., Lange, S., Costa, F., Backofen, R. (2014) GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol., 15, R17.
    • (2014) Genome Biol. , vol.15 , pp. R17
    • Maticzka, D.1    Lange, S.2    Costa, F.3    Backofen, R.4
  • 44
    • 84893351549 scopus 로고    scopus 로고
    • Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
    • Rouskin, S., Zubradt, M., Washietl, S., Kellis, M., Weissman, J.S. (2014) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature, 505, 701-705.
    • (2014) Nature , vol.505 , pp. 701-705
    • Rouskin, S.1    Zubradt, M.2    Washietl, S.3    Kellis, M.4    Weissman, J.S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.