-
1
-
-
6944256813
-
Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise
-
Mendell, J.T., Sharifi, N.A., Meyers, J.L., Martinez-Murillo, F., Dietz, H.C. (2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet., 36, 1073-1078.
-
(2004)
Nat. Genet.
, vol.36
, pp. 1073-1078
-
-
Mendell, J.T.1
Sharifi, N.A.2
Meyers, J.L.3
Martinez-Murillo, F.4
Dietz, H.C.5
-
2
-
-
32044454232
-
HUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay
-
Wittmann, J., Hol, E.M., Jack, H.M. (2006) hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Mol. Cell. Biol., 26, 1272-1287.
-
(2006)
Mol. Cell. Biol.
, vol.26
, pp. 1272-1287
-
-
Wittmann, J.1
Hol, E.M.2
Jack, H.M.3
-
3
-
-
81755172088
-
Autoregulation of the nonsense-mediated mRNA decay pathway in human cells
-
Yepiskoposyan, H., Aeschimann, F., Nilsson, D., Okoniewski, M., Muhlemann, O. (2011) Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. RNA, 17, 2108-2118.
-
(2011)
RNA
, vol.17
, pp. 2108-2118
-
-
Yepiskoposyan, H.1
Aeschimann, F.2
Nilsson, D.3
Okoniewski, M.4
Muhlemann, O.5
-
4
-
-
84873828345
-
Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability
-
Tani, H., Imamachi, N., Salam, K.A., Mizutani, R., Ijiri, K., Irie, T., Yada, T., Suzuki, Y., Akimitsu, N. (2012) Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability. RNA Biol., 9, 1370-1379.
-
(2012)
RNA Biol.
, vol.9
, pp. 1370-1379
-
-
Tani, H.1
Imamachi, N.2
Salam, K.A.3
Mizutani, R.4
Ijiri, K.5
Irie, T.6
Yada, T.7
Suzuki, Y.8
Akimitsu, N.9
-
5
-
-
0032837376
-
Nonsense-mediated mRNA decay in health and disease
-
Frischmeyer, P.A., Dietz, H.C. (1999) Nonsense-mediated mRNA decay in health and disease. Hum. Mol. Genet., 8, 1893-1900.
-
(1999)
Hum. Mol. Genet.
, vol.8
, pp. 1893-1900
-
-
Frischmeyer, P.A.1
Dietz, H.C.2
-
6
-
-
77952380547
-
Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay
-
Pastor, F., Kolonias, D., Giangrande, P.H., Gilboa, E. (2010) Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay. Nature, 465, 227-230.
-
(2010)
Nature
, vol.465
, pp. 227-230
-
-
Pastor, F.1
Kolonias, D.2
Giangrande, P.H.3
Gilboa, E.4
-
7
-
-
84891488177
-
Expression of new antigens on tumor cells by inhibiting nonsense-mediated mRNA decay
-
Gilboa, E. (2013) Expression of new antigens on tumor cells by inhibiting nonsense-mediated mRNA decay. Immunol. Res., 57, 44-51.
-
(2013)
Immunol. Res.
, vol.57
, pp. 44-51
-
-
Gilboa, E.1
-
8
-
-
34247588271
-
PTC124 targets genetic disorders caused by nonsense mutations
-
Welch, E.M., Barton, E.R., Zhuo, J., Tomizawa, Y., Friesen, W.J., Trifillis, P., Paushkin, S., Patel, M., Trotta, C.R., Hwang, S. et al. (2007) PTC124 targets genetic disorders caused by nonsense mutations. Nature, 447, 87-91.
-
(2007)
Nature
, vol.447
, pp. 87-91
-
-
Welch, E.M.1
Barton, E.R.2
Zhuo, J.3
Tomizawa, Y.4
Friesen, W.J.5
Trifillis, P.6
Paushkin, S.7
Patel, M.8
Trotta, C.R.9
Hwang, S.10
-
9
-
-
84873020912
-
Ataluren as an agent for therapeutic nonsense suppression
-
Peltz, S.W., Morsy, M., Welch, E.M., Jacobson, A. (2013) Ataluren as an agent for therapeutic nonsense suppression. Annu. Rev. Med., 64, 407-425.
-
(2013)
Annu. Rev. Med.
, vol.64
, pp. 407-425
-
-
Peltz, S.W.1
Morsy, M.2
Welch, E.M.3
Jacobson, A.4
-
10
-
-
84877818178
-
Nonsense-mediated mRNA decay-mechanisms of substrate mRNA recognition and degradation in mammalian cells
-
Schweingruber, C., Rufener, S.C., Zund, D., Yamashita, A., Muhlemann, O. (2013) Nonsense-mediated mRNA decay-mechanisms of substrate mRNA recognition and degradation in mammalian cells. Biochim. Biophys. Acta, 1829, 612-623.
-
(2013)
Biochim. Biophys. Acta
, vol.1829
, pp. 612-623
-
-
Schweingruber, C.1
Rufener, S.C.2
Zund, D.3
Yamashita, A.4
Muhlemann, O.5
-
11
-
-
74549134095
-
How and where are nonsense mRNAs degraded in mammalian cells?
-
Muhlemann, O., Lykke-Andersen, J. (2010) How and where are nonsense mRNAs degraded in mammalian cells? RNA Biol., 7, 28-32.
-
(2010)
RNA Biol.
, vol.7
, pp. 28-32
-
-
Muhlemann, O.1
Lykke-Andersen, J.2
-
12
-
-
84867850145
-
NMD: A multifaceted response to premature translational termination
-
Kervestin, S., Jacobson, A. (2012) NMD: a multifaceted response to premature translational termination. Nat. Rev. Mol. Cell. Biol., 13, 700-712.
-
(2012)
Nat. Rev. Mol. Cell. Biol.
, vol.13
, pp. 700-712
-
-
Kervestin, S.1
Jacobson, A.2
-
13
-
-
84888617099
-
Organizing principles of mammalian nonsense-mediated mRNA decay
-
Popp, M.W., Maquat, L.E. (2013) Organizing principles of mammalian nonsense-mediated mRNA decay. Annu. Rev. Genet., 47, 139-165.
-
(2013)
Annu. Rev. Genet.
, vol.47
, pp. 139-165
-
-
Popp, M.W.1
Maquat, L.E.2
-
14
-
-
34247205419
-
An alternative branch of the nonsense-mediated decay pathway
-
Chan, W., Huang, L., Gudikote, J.P., Chang, Y., Imam, J.S., MacLean, J.A.I., Wilkinson, M.F. (2007) An alternative branch of the nonsense-mediated decay pathway. EMBO J., 26, 1820-1830.
-
(2007)
EMBO J.
, vol.26
, pp. 1820-1830
-
-
Chan, W.1
Huang, L.2
Gudikote, J.P.3
Chang, Y.4
Imam, J.S.5
MacLean, J.A.I.6
Wilkinson, M.F.7
-
15
-
-
34948854852
-
Failsafe nonsense-mediated mRNA decay does not detectably target eIF4E-bound mRNA
-
Matsuda, D., Hosoda, N., Kim, Y.K., Maquat, L.E. (2007) Failsafe nonsense-mediated mRNA decay does not detectably target eIF4E-bound mRNA. Nat. Struct. Mol. Biol., 14, 974-979.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 974-979
-
-
Matsuda, D.1
Hosoda, N.2
Kim, Y.K.3
Maquat, L.E.4
-
16
-
-
84884692094
-
Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways
-
Metze, S., Herzog, V.A., Ruepp, M.D., Muhlemann, O. (2013) Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways. RNA, 19, 1432-1448.
-
(2013)
RNA
, vol.19
, pp. 1432-1448
-
-
Metze, S.1
Herzog, V.A.2
Ruepp, M.D.3
Muhlemann, O.4
-
17
-
-
25844512736
-
Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements
-
Gehring, N.H., Kunz, J.B., Neu-Yilik, G., Breit, S., Viegas, M.H., Hentze, M.W., Kulozik, A.E. (2005) Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell, 20, 65-75.
-
(2005)
Mol. Cell
, vol.20
, pp. 65-75
-
-
Gehring, N.H.1
Kunz, J.B.2
Neu-Yilik, G.3
Breit, S.4
Viegas, M.H.5
Hentze, M.W.6
Kulozik, A.E.7
-
18
-
-
0031840487
-
At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: A possible link between nuclear splicing and cytoplasmic translation
-
Zhang, J., Sun, X., Qian, Y., LaDuca, J.P., Maquat, L.E. (1998) At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation. Mol. Cell. Biol., 18, 5272-5283.
-
(1998)
Mol. Cell. Biol.
, vol.18
, pp. 5272-5283
-
-
Zhang, J.1
Sun, X.2
Qian, Y.3
LaDuca, J.P.4
Maquat, L.E.5
-
19
-
-
0035801373
-
The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay
-
Le Hir, H., Gatfield, D., Izaurralde, E., Moore, M.J. (2001) The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J., 20, 4987-4997.
-
(2001)
EMBO J.
, vol.20
, pp. 4987-4997
-
-
Le Hir, H.1
Gatfield, D.2
Izaurralde, E.3
Moore, M.J.4
-
20
-
-
33744994837
-
EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3-UTR length
-
Bühler, M., Steiner, S., Mohn, F., Paillusson, A., Mühlemann, O. (2006) EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3-UTR length. Nat. Struct. Mol. Biol., 13, 462-464.
-
(2006)
Nat. Struct. Mol. Biol.
, vol.13
, pp. 462-464
-
-
Bühler, M.1
Steiner, S.2
Mohn, F.3
Paillusson, A.4
Mühlemann, O.5
-
21
-
-
43249093760
-
Posttranscriptional gene regulation by spatial rearrangement of the 3-untranslated region
-
Eberle, A.B., Stalder, L., Mathys, H., Orozco, R.Z., Muhlemann, O. (2008) Posttranscriptional gene regulation by spatial rearrangement of the 3-untranslated region. PLoS Biol., 6, e92.
-
(2008)
PLoS Biol.
, vol.6
, pp. e92
-
-
Eberle, A.B.1
Stalder, L.2
Mathys, H.3
Orozco, R.Z.4
Muhlemann, O.5
-
22
-
-
0034751160
-
Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4)
-
Serin, G., Gersappe, A., Black, J.D., Aronoff, R., Maquat, L.E. (2001) Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4). Mol. Cell. Biol., 21, 209-223.
-
(2001)
Mol. Cell. Biol.
, vol.21
, pp. 209-223
-
-
Serin, G.1
Gersappe, A.2
Black, J.D.3
Aronoff, R.4
Maquat, L.E.5
-
23
-
-
37849005006
-
NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity
-
Chamieh, H., Ballut, L., Bonneau, F., Le Hir, H. (2008) NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. Nat. Struct. Mol. Biol., 15, 85-93.
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 85-93
-
-
Chamieh, H.1
Ballut, L.2
Bonneau, F.3
Le Hir, H.4
-
24
-
-
78049447110
-
SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay
-
Kashima, I., Jonas, S., Jayachandran, U., Buchwald, G., Conti, E., Lupas, A.N., Izaurralde, E. (2010) SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay. Genes Dev., 24, 2440-2450.
-
(2010)
Genes Dev.
, vol.24
, pp. 2440-2450
-
-
Kashima, I.1
Jonas, S.2
Jayachandran, U.3
Buchwald, G.4
Conti, E.5
Lupas, A.N.6
Izaurralde, E.7
-
25
-
-
10744232514
-
Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7
-
Ohnishi, T., Yamashita, A., Kashima, I., Schell, T., Anders, K.R., Grimson, A., Hachiya, T., Hentze, M.W., Anderson, P., Ohno, S. (2003) Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Mol. Cell, 12, 1187-1200.
-
(2003)
Mol. Cell
, vol.12
, pp. 1187-1200
-
-
Ohnishi, T.1
Yamashita, A.2
Kashima, I.3
Schell, T.4
Anders, K.R.5
Grimson, A.6
Hachiya, T.7
Hentze, M.W.8
Anderson, P.9
Ohno, S.10
-
26
-
-
58149291462
-
Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex
-
Cho, H., Kim, K.M., Kim, Y.K. (2009) Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex. Mol. Cell, 33, 75-86.
-
(2009)
Mol. Cell
, vol.33
, pp. 75-86
-
-
Cho, H.1
Kim, K.M.2
Kim, Y.K.3
-
27
-
-
84856858152
-
N-and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD
-
Okada-Katsuhata, Y., Yamashita, A., Kutsuzawa, K., Izumi, N., Hirahara, F., Ohno, S. (2012) N-and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD. Nucleic Acids Res., 40, 1251-1266.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 1251-1266
-
-
Okada-Katsuhata, Y.1
Yamashita, A.2
Kutsuzawa, K.3
Izumi, N.4
Hirahara, F.5
Ohno, S.6
-
28
-
-
84890703972
-
The role of disordered protein regions in the assembly of decapping complexes and RNP granules
-
Jonas, S., Izaurralde, E. (2013) The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Gene Dev., 27, 2628-2641.
-
(2013)
Gene Dev.
, vol.27
, pp. 2628-2641
-
-
Jonas, S.1
Izaurralde, E.2
-
29
-
-
58149265041
-
SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells
-
Eberle, A.B., Lykke-Andersen, S., Muhlemann, O., Jensen, T.H. (2009) SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nat. Struct. Mol. Biol., 16, 49-55.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 49-55
-
-
Eberle, A.B.1
Lykke-Andersen, S.2
Muhlemann, O.3
Jensen, T.H.4
-
30
-
-
57049126216
-
SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan
-
Huntzinger, E., Kashima, I., Fauser, M., Sauliere, J., Izaurralde, E. (2008) SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. RNA, 14, 2609-2617.
-
(2008)
RNA
, vol.14
, pp. 2609-2617
-
-
Huntzinger, E.1
Kashima, I.2
Fauser, M.3
Sauliere, J.4
Izaurralde, E.5
-
31
-
-
13944259434
-
SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway
-
Fukuhara, N., Ebert, J., Unterholzner, L., Lindner, D., Izaurralde, E., Conti, E. (2005) SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. Mol. Cell, 17, 537-547.
-
(2005)
Mol. Cell
, vol.17
, pp. 537-547
-
-
Fukuhara, N.1
Ebert, J.2
Unterholzner, L.3
Lindner, D.4
Izaurralde, E.5
Conti, E.6
-
32
-
-
84885356907
-
The SMG5-SMG7 heterodimer directly recruits the CCR4-NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2
-
Loh, B., Jonas, S., Izaurralde, E. (2013) The SMG5-SMG7 heterodimer directly recruits the CCR4-NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2. Genes Dev., 27, 2125-2138.
-
(2013)
Genes Dev.
, vol.27
, pp. 2125-2138
-
-
Loh, B.1
Jonas, S.2
Izaurralde, E.3
-
33
-
-
84906218594
-
Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5-SMG7 and SMG6
-
Chakrabarti, S., Bonneau, F., Schussler, S., Eppinger, E., Conti, E. (2014) Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5-SMG7 and SMG6. Nucleic Acids Res., 42, 9447-9460.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 9447-9460
-
-
Chakrabarti, S.1
Bonneau, F.2
Schussler, S.3
Eppinger, E.4
Conti, E.5
-
34
-
-
33750490399
-
Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex
-
Glavan, F., Behm-Ansmant, I., Izaurralde, E., Conti, E. (2006) Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J., 25, 5117-5125.
-
(2006)
EMBO J.
, vol.25
, pp. 5117-5125
-
-
Glavan, F.1
Behm-Ansmant, I.2
Izaurralde, E.3
Conti, E.4
-
35
-
-
2942595765
-
Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila
-
Gatfield, D., Izaurralde, E. (2004) Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature, 429, 575-578.
-
(2004)
Nature
, vol.429
, pp. 575-578
-
-
Gatfield, D.1
Izaurralde, E.2
-
36
-
-
0036790995
-
Beta-Globin mRNA decay in erythroid cells: UG site-preferred endonucleolytic cleavage that is augmented by a premature termination codon
-
Stevens, A., Wang, Y., Bremer, K., Zhang, J., Hoepfner, R., Antoniou, M., Schoenberg, D.R., Maquat, L.E. (2002) Beta-Globin mRNA decay in erythroid cells: UG site-preferred endonucleolytic cleavage that is augmented by a premature termination codon. Proc. Natl. Acad. Sci. U.S.A., 99, 12741-12746.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 12741-12746
-
-
Stevens, A.1
Wang, Y.2
Bremer, K.3
Zhang, J.4
Hoepfner, R.5
Antoniou, M.6
Schoenberg, D.R.7
Maquat, L.E.8
-
37
-
-
84884575975
-
SMG6 cleavage generates metastable decay intermediates from nonsense-containing beta-globin mRNA
-
Mascarenhas, R., Dougherty, J.A., Schoenberg, D.R. (2013) SMG6 cleavage generates metastable decay intermediates from nonsense-containing beta-globin mRNA. PLoS ONE, 8, e74791.
-
(2013)
PLoS ONE
, vol.8
, pp. e74791
-
-
Mascarenhas, R.1
Dougherty, J.A.2
Schoenberg, D.R.3
-
38
-
-
84919843479
-
3-UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons
-
Boehm, V., Haberman, N., Ottens, F., Ule, J., Gehring, N.H. (2014) 3-UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons. Cell Rep., 9, 555-568.
-
(2014)
Cell Rep.
, vol.9
, pp. 555-568
-
-
Boehm, V.1
Haberman, N.2
Ottens, F.3
Ule, J.4
Gehring, N.H.5
-
39
-
-
49449118943
-
Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
-
German, M.A., Pillay, M., Jeong, D.H., Hetawal, A., Luo, S., Janardhanan, P., Kannan, V., Rymarquis, L.A., Nobuta, K., German, R. et al. (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol., 26, 941-946.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 941-946
-
-
German, M.A.1
Pillay, M.2
Jeong, D.H.3
Hetawal, A.4
Luo, S.5
Janardhanan, P.6
Kannan, V.7
Rymarquis, L.A.8
Nobuta, K.9
German, R.10
-
40
-
-
43449091567
-
Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
-
Addo-Quaye, C., Eshoo, T.W., Bartel, D.P., Axtell, M.J. (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol., 18, 758-762.
-
(2008)
Curr. Biol.
, vol.18
, pp. 758-762
-
-
Addo-Quaye, C.1
Eshoo, T.W.2
Bartel, D.P.3
Axtell, M.J.4
-
41
-
-
44449142226
-
A link between RNA metabolism and silencing affecting Arabidopsis development
-
Gregory, B.D., O'Malley, R.C., Lister, R., Urich, M.A., Tonti-Filippini, J., Chen, H., Millar, A.H., Ecker, J.R. (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Dev. Cell, 14, 854-866.
-
(2008)
Dev. Cell
, vol.14
, pp. 854-866
-
-
Gregory, B.D.1
O'Malley, R.C.2
Lister, R.3
Urich, M.A.4
Tonti-Filippini, J.5
Chen, H.6
Millar, A.H.7
Ecker, J.R.8
-
42
-
-
77955492563
-
Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases
-
Karginov, F.V., Cheloufi, S., Chong, M.M., Stark, A., Smith, A.D., Hannon, G.J. (2010) Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol. Cell, 38, 781-788.
-
(2010)
Mol. Cell
, vol.38
, pp. 781-788
-
-
Karginov, F.V.1
Cheloufi, S.2
Chong, M.M.3
Stark, A.4
Smith, A.D.5
Hannon, G.J.6
-
43
-
-
77955475953
-
Expanding the microRNA targeting code: Functional sites with centered pairing
-
Shin, C., Nam, J.W., Farh, K.K., Chiang, H.R., Shkumatava, A., Bartel, D.P. (2010) Expanding the microRNA targeting code: functional sites with centered pairing. Mol. Cell, 38, 789-802.
-
(2010)
Mol. Cell
, vol.38
, pp. 789-802
-
-
Shin, C.1
Nam, J.W.2
Farh, K.K.3
Chiang, H.R.4
Shkumatava, A.5
Bartel, D.P.6
-
44
-
-
80052191259
-
Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage
-
Bracken, C.P., Szubert, J.M., Mercer, T.R., Dinger, M.E., Thomson, D.W., Mattick, J.S., Michael, M.Z., Goodall, G.J. (2011) Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage. Nucleic Acids Res., 39, 5658-5668.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 5658-5668
-
-
Bracken, C.P.1
Szubert, J.M.2
Mercer, T.R.3
Dinger, M.E.4
Thomson, D.W.5
Mattick, J.S.6
Michael, M.Z.7
Goodall, G.J.8
-
45
-
-
84863895769
-
Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae
-
Harigaya, Y., Parker, R. (2012) Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A., 109, 11764-11769.
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 11764-11769
-
-
Harigaya, Y.1
Parker, R.2
-
46
-
-
82955207556
-
MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs
-
Zhai, J., Jeong, D.H., De Paoli, E., Park, S., Rosen, B.D., Li, Y., González, A.J., Yan, Z., Kitto, S.L., Grusak, M.A. et al. (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev., 25, 2540-2553.
-
(2011)
Genes Dev.
, vol.25
, pp. 2540-2553
-
-
Zhai, J.1
Jeong, D.H.2
De Paoli, E.3
Park, S.4
Rosen, B.D.5
Li, Y.6
González, A.J.7
Yan, Z.8
Kitto, S.L.9
Grusak, M.A.10
-
47
-
-
84879704714
-
Comprehensive investigation of MicroRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage
-
Jeong, D.H., Thatcher, S.R., Brown, R.S.H., Zhai, J.X., Park, S., Rymarquis, L.A., Meyers, B.C., Green, P.J. (2013) Comprehensive investigation of MicroRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage. Plant Physiol., 162, 1225-1245.
-
(2013)
Plant Physiol.
, vol.162
, pp. 1225-1245
-
-
Jeong, D.H.1
Thatcher, S.R.2
Brown, R.S.H.3
Zhai, J.X.4
Park, S.5
Rymarquis, L.A.6
Meyers, B.C.7
Green, P.J.8
-
48
-
-
84890844310
-
Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon
-
Jeong, D.H., Schmidt, S.A., Rymarquis, L.A., Park, S., Ganssmann, M., German, M.A., Accerbi, M., Zhai, J., Fahlgren, N., Fox, S.E. et al. (2013) Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biol., 14, 1-22.
-
(2013)
Genome Biol.
, vol.14
, pp. 1-22
-
-
Jeong, D.H.1
Schmidt, S.A.2
Rymarquis, L.A.3
Park, S.4
Ganssmann, M.5
German, M.A.6
Accerbi, M.7
Zhai, J.8
Fahlgren, N.9
Fox, S.E.10
-
49
-
-
57749084495
-
Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation
-
Jiao, Y., Riechmann, J.L., Meyerowitz, E.M. (2008) Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. Plant Cell, 20, 2571-2585.
-
(2008)
Plant Cell
, vol.20
, pp. 2571-2585
-
-
Jiao, Y.1
Riechmann, J.L.2
Meyerowitz, E.M.3
-
50
-
-
79951527525
-
Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories
-
Rymarquis, L.A., Souret, F.F., Green, P.J. (2011) Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories. RNA, 17, 501-511.
-
(2011)
RNA
, vol.17
, pp. 501-511
-
-
Rymarquis, L.A.1
Souret, F.F.2
Green, P.J.3
-
51
-
-
84883156624
-
A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon
-
Zhang, J., Mao, Z., Chong, K. (2013) A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon. Genome Biol., 14, 1-19.
-
(2013)
Genome Biol.
, vol.14
, pp. 1-19
-
-
Zhang, J.1
Mao, Z.2
Chong, K.3
-
52
-
-
12844285549
-
Nonsense-associated alternative splicing of T-cell receptor beta genes: No evidence for frame dependence
-
Mohn, F., Buhler, M., Muhlemann, O. (2005) Nonsense-associated alternative splicing of T-cell receptor beta genes: no evidence for frame dependence. RNA, 11, 147-156.
-
(2005)
RNA
, vol.11
, pp. 147-156
-
-
Mohn, F.1
Buhler, M.2
Muhlemann, O.3
-
53
-
-
63849207321
-
Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome
-
German, M.A., Luo, S., Schroth, G., Meyers, B.C., Green, P.J. (2009) Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat. Protoc., 4, 356-362.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 356-362
-
-
German, M.A.1
Luo, S.2
Schroth, G.3
Meyers, B.C.4
Green, P.J.5
-
54
-
-
84869998333
-
Methods for validation of miRNA sequence variants and the cleavage of their targets
-
Jeong, D.H., Green, P.J. (2012) Methods for validation of miRNA sequence variants and the cleavage of their targets. Methods, 58, 135-143.
-
(2012)
Methods
, vol.58
, pp. 135-143
-
-
Jeong, D.H.1
Green, P.J.2
-
55
-
-
84888250605
-
Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates
-
Schapire, A.L., Bologna, N.G., Moro, B., Zhai, J., Meyers, B.C., Palatnik, J.F. (2013) Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates. Methods, 64, 283-291.
-
(2013)
Methods
, vol.64
, pp. 283-291
-
-
Schapire, A.L.1
Bologna, N.G.2
Moro, B.3
Zhai, J.4
Meyers, B.C.5
Palatnik, J.F.6
-
56
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, 1-10.
-
(2009)
Genome Biol.
, vol.10
, pp. 1-10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
57
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, 1-13.
-
(2013)
Genome Biol.
, vol.14
, pp. 1-13
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
58
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks, G.E., Hon, G., Chandonia, J.M., Brenner, S.E. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
59
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang da, W., Sherman, B.T., Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
60
-
-
33747784589
-
Upf1, an RNA helicase required for nonsense-mediated mRNA decay, modulates the transcriptional response to oxidative stress in fission yeast
-
Rodriguez-Gabriel, M.A., Watt, S., Bahler, J., Russell, P. (2006) Upf1, an RNA helicase required for nonsense-mediated mRNA decay, modulates the transcriptional response to oxidative stress in fission yeast. Mol. Cell. Biol., 26, 6347-6356.
-
(2006)
Mol. Cell. Biol.
, vol.26
, pp. 6347-6356
-
-
Rodriguez-Gabriel, M.A.1
Watt, S.2
Bahler, J.3
Russell, P.4
-
61
-
-
44349167189
-
Hypoxic inhibition of nonsense-mediated RNA decay regulates gene expression and the integrated stress response
-
Gardner, L.B. (2008) Hypoxic inhibition of nonsense-mediated RNA decay regulates gene expression and the integrated stress response. Mol. Cell. Biol., 28, 3729-3741.
-
(2008)
Mol. Cell. Biol.
, vol.28
, pp. 3729-3741
-
-
Gardner, L.B.1
-
62
-
-
84861434815
-
RNA surveillance is required for endoplasmic reticulum homeostasis
-
Sakaki, K., Yoshina, S., Shen, X., Han, J., DeSantis, M.R., Xiong, M., Mitani, S., Kaufman, R.J. (2012) RNA surveillance is required for endoplasmic reticulum homeostasis. Proc. Natl. Acad. Sci. U.S.A., 109, 8079-8084.
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 8079-8084
-
-
Sakaki, K.1
Yoshina, S.2
Shen, X.3
Han, J.4
DeSantis, M.R.5
Xiong, M.6
Mitani, S.7
Kaufman, R.J.8
-
63
-
-
80052979901
-
RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD
-
Huang, L., Lou, C.H., Chan, W., Shum, E.Y., Shao, A., Stone, E., Karam, R., Song, H.W., Wilkinson, M.F. (2011) RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD. Mol. Cell, 43, 950-961.
-
(2011)
Mol. Cell
, vol.43
, pp. 950-961
-
-
Huang, L.1
Lou, C.H.2
Chan, W.3
Shum, E.Y.4
Shao, A.5
Stone, E.6
Karam, R.7
Song, H.W.8
Wilkinson, M.F.9
-
64
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider, T.D., Stephens, R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
65
-
-
84887562180
-
The UPF3B gene, implicated in intellectual disability, autism, ADHD and childhood onset schizophrenia regulates neural progenitor cell behaviour and neuronal outgrowth
-
Jolly, L.A., Homan, C.C., Jacob, R., Barry, S., Gecz, J. (2013) The UPF3B gene, implicated in intellectual disability, autism, ADHD and childhood onset schizophrenia regulates neural progenitor cell behaviour and neuronal outgrowth. Hum. Mol. Genet., 22, 4673-4687.
-
(2013)
Hum. Mol. Genet.
, vol.22
, pp. 4673-4687
-
-
Jolly, L.A.1
Homan, C.C.2
Jacob, R.3
Barry, S.4
Gecz, J.5
-
66
-
-
77953914253
-
Mutations of the UPF3B gene, which encodes a protein widely expressed in neurons, are associated with nonspecific mental retardation with or without autism
-
Laumonnier, F., Shoubridge, C., Antar, C., Nguyen, L.S., Van Esch, H., Kleefstra, T., Briault, S., Fryns, J.P., Hamel, B., Chelly, J. et al. (2010) Mutations of the UPF3B gene, which encodes a protein widely expressed in neurons, are associated with nonspecific mental retardation with or without autism. Mol. Psych., 15, 767-776.
-
(2010)
Mol. Psych.
, vol.15
, pp. 767-776
-
-
Laumonnier, F.1
Shoubridge, C.2
Antar, C.3
Nguyen, L.S.4
Van Esch, H.5
Kleefstra, T.6
Briault, S.7
Fryns, J.P.8
Hamel, B.9
Chelly, J.10
-
67
-
-
34548353924
-
Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation
-
Tarpey, P.S., Raymond, F.L., Nguyen, L.S., Rodriguez, J., Hackett, A., Vandeleur, L., Smith, R., Shoubridge, C., Edkins, S., Stevens, C. et al. (2007) Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation. Nat. Genet., 39, 1127-1133.
-
(2007)
Nat. Genet.
, vol.39
, pp. 1127-1133
-
-
Tarpey, P.S.1
Raymond, F.L.2
Nguyen, L.S.3
Rodriguez, J.4
Hackett, A.5
Vandeleur, L.6
Smith, R.7
Shoubridge, C.8
Edkins, S.9
Stevens, C.10
-
68
-
-
43249084802
-
A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay
-
Singh, G., Rebbapragada, I., Lykke-Andersen, J. (2008) A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay. PLoS Biol., 6, e111.
-
(2008)
PLoS Biol.
, vol.6
, pp. e111
-
-
Singh, G.1
Rebbapragada, I.2
Lykke-Andersen, J.3
-
69
-
-
84874720941
-
SMG5-PNRC2 is functionally dominant compared with SMG5-SMG7 in mammalian nonsense-mediated mRNA decay
-
Cho, H., Han, S., Choe, J., Park, S.G., Choi, S.S., Kim, Y.K. (2013) SMG5-PNRC2 is functionally dominant compared with SMG5-SMG7 in mammalian nonsense-mediated mRNA decay. Nucleic Acids Res., 41, 1319-1328.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 1319-1328
-
-
Cho, H.1
Han, S.2
Choe, J.3
Park, S.G.4
Choi, S.S.5
Kim, Y.K.6
-
70
-
-
85008740092
-
Up-frameshift protein 1 (UPF1): Multitalented entertainer in RNA decay
-
Imamachi, N., Tani, H., Akimitsu, N. (2012) Up-frameshift protein 1 (UPF1): multitalented entertainer in RNA decay. Drug Discov. Ther., 6, 55-61.
-
(2012)
Drug Discov. Ther.
, vol.6
, pp. 55-61
-
-
Imamachi, N.1
Tani, H.2
Akimitsu, N.3
-
72
-
-
49949105213
-
The multiple lives of NMD factors: Balancing roles in gene and genome regulation
-
Isken, O., Maquat, L.E. (2008) The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nat. Rev. Genet., 9, 699-712.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 699-712
-
-
Isken, O.1
Maquat, L.E.2
|