-
1
-
-
73249121905
-
Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome
-
Addo-Quaye, C., Snyder, J. A., Park, Y. B., Li, Y. F., Sunkar, R., and Axtell, M. J. (2009). Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA 15, 2112-2121.
-
(2009)
RNA
, vol.15
, pp. 2112-2121
-
-
Addo-Quaye, C.1
Snyder, J.A.2
Park, Y.B.3
Li, Y.F.4
Sunkar, R.5
Axtell, M.J.6
-
2
-
-
71249118105
-
A loop-to-base processing mechanism undrlies the biogenesis of plant microRNAs miR319 and miR159
-
Bologna, N. G., Mateos, J. L., Bresso, E. G., and Palatnik, J. F. (2009). A loop-to-base processing mechanism undrlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J. 28, 3646-3656.
-
(2009)
EMBO J.
, vol.28
, pp. 3646-3656
-
-
Bologna, N.G.1
Mateos, J.L.2
Bresso, E.G.3
Palatnik, J.F.4
-
3
-
-
80052339278
-
Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors
-
doi: 10.1371/journal.ppat.1002176
-
Du, P., Wu, J., Zhang, J., Zhao, S., Zheng, H., Gao, G., Wei, L., and Li, Y. (2011). Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog. 7, e1002176. doi: 10.1371/journal.ppat.1002176
-
(2011)
PLoS Pathog.
, vol.7
-
-
Du, P.1
Wu, J.2
Zhang, J.3
Zhao, S.4
Zheng, H.5
Gao, G.6
Wei, L.7
Li, Y.8
-
4
-
-
34247339143
-
The N-terminal double-stranded RNA binding domains of ArabidopsisHYPONASTIC LEAVES 1 are sufficient for pre-microRNA processing
-
Feijie, W., and Yuke, H. (2007). The N-terminal double-stranded RNA binding domains of ArabidopsisHYPONASTIC LEAVES 1 are sufficient for pre-microRNA processing. Plant Cell 19, 914-925.
-
(2007)
Plant Cell
, vol.19
, pp. 914-925
-
-
Feijie, W.1
Yuke, H.2
-
5
-
-
0742323351
-
The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation
-
Han, M. H., Goud, S., Song, L., and Fedoroff, N. (2004). The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. U.S.A. 101, 1093-1098.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 1093-1098
-
-
Han, M.H.1
Goud, S.2
Song, L.3
Fedoroff, N.4
-
6
-
-
77954978134
-
Abundance of tRNA-derived small RNAs in phosphate-starved Arabidopsis roots
-
Hsieh, L. C., Lin, S. I., Kuo, H. F., and Chiou, T. J. (2010). Abundance of tRNA-derived small RNAs in phosphate-starved Arabidopsis roots. Plant Signal. Behav. 5, 537-539.
-
(2010)
Plant Signal. Behav.
, vol.5
, pp. 537-539
-
-
Hsieh, L.C.1
Lin, S.I.2
Kuo, H.F.3
Chiou, T.J.4
-
7
-
-
79955908792
-
Speciefic impact of tobamovirus infection on the Arabidopsis small RNA profile
-
doi: 10.1371/journal.pone.0019549
-
Hu, Q., Hollunder, J., Niehl, A., Korner, C. J., Gereige, D., Windels, D., Arnold, A., Kuiper, M., Vazquez, F., Pooggin, M., and Heinlein, M. (2011). Speciefic impact of tobamovirus infection on the Arabidopsis small RNA profile. PLoS ONE 6, e19549. doi: 10.1371/journal.pone.0019549
-
(2011)
PLoS ONE
, vol.6
-
-
Hu, Q.1
Hollunder, J.2
Niehl, A.3
Korner, C.J.4
Gereige, D.5
Windels, D.6
Arnold, A.7
Kuiper, M.8
Vazquez, F.9
Pooggin, M.10
Heinlein, M.11
-
8
-
-
70349939426
-
Structural insights into mechanisms of the small RNA methyltransferase HEN1
-
Huang, Y., Ji, L., Huang, Q., Vassylyev, D. G., Chen, X., and Ma, J. B. (2009). Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 461, 823-827.
-
(2009)
Nature
, vol.461
, pp. 823-827
-
-
Huang, Y.1
Ji, L.2
Huang, Q.3
Vassylyev, D.G.4
Chen, X.5
Ma, J.B.6
-
9
-
-
56449129474
-
Two cap-binding proteins CBP20 and CBP80 are involved in processing primary microRNAs
-
Kim, S., Yang, J. Y., Xu, J., Jang, I. C., Prigge, M. J., and Chua, N. H. (2008). Two cap-binding proteins CBP20 and CBP80 are involved in processing primary microRNAs. Plant Cell Physiol. 49, 1634-1644.
-
(2008)
Plant Cell Physiol.
, vol.49
, pp. 1634-1644
-
-
Kim, S.1
Yang, J.Y.2
Xu, J.3
Jang, I.C.4
Prigge, M.J.5
Chua, N.H.6
-
10
-
-
78651293534
-
miRBase: Integrating microRNA annotation and deep-sequencing data
-
Kozomara, A., and Griffiths-Jones, S. (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
11
-
-
4344637081
-
Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions
-
Kurihara, Y., and Watanabe, Y. (2004). Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. U.S.A. 101, 12753-12758.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 12753-12758
-
-
Kurihara, Y.1
Watanabe, Y.2
-
12
-
-
47249089938
-
Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana
-
Laubinger, S., Sachsenberg, T., Zeller, G., Busch, W., Lohmann, J. U., Rätsch, G., and Weigel, D. (2008). Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 105, 8795-8800.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 8795-8800
-
-
Laubinger, S.1
Sachsenberg, T.2
Zeller, G.3
Busch, W.4
Lohmann, J.U.5
Rätsch, G.6
Weigel, D.7
-
13
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li, H., and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
14
-
-
79955802124
-
Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways
-
doi: 10.1186/1471-2148-11-122
-
Li, Y., Li, C., Ding, G., and Jin, Y. (2011). Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways. BMC Evol. Biol. 11, 122. doi: 10.1186/1471-2148-11-122
-
(2011)
BMC Evol. Biol.
, vol.11
, pp. 122
-
-
Li, Y.1
Li, C.2
Ding, G.3
Jin, Y.4
-
15
-
-
0037144457
-
Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
-
Llave, C., Xie, Z., Kasschau, K. D., and Carrington, J. C. (2002). Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053-2056.
-
(2002)
Science
, vol.297
, pp. 2053-2056
-
-
Llave, C.1
Xie, Z.2
Kasschau, K.D.3
Carrington, J.C.4
-
16
-
-
33749254470
-
SERRATE: A new player on the plant microRNA scene
-
Lobbes, D., Rallapalli, G., Schmidt, D. D., Martin, C., and Clarke, J. (2006). SERRATE: a new player on the plant microRNA scene. EMBO Rep. 7, 1052-1058.
-
(2006)
EMBO Rep.
, vol.7
, pp. 1052-1058
-
-
Lobbes, D.1
Rallapalli, G.2
Schmidt, D.D.3
Martin, C.4
Clarke, J.5
-
17
-
-
76049118057
-
miR319a targeting of TCP4 is critical for petal growth and development inArabidopsis
-
Nag, A., King, S., and Jack, T. (2009). miR319a targeting of TCP4 is critical for petal growth and development inArabidopsis. Proc. Natl. Acad. Sci. U.S.A. 106, 22534-22539.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 22534-22539
-
-
Nag, A.1
King, S.2
Jack, T.3
-
18
-
-
0141493493
-
Control of leaf morphogenesis by microRNAs
-
Palatnik, J. F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J. C., and Weigel, D. (2003). Control of leaf morphogenesis by microRNAs. Nature 18, 257-263.
-
(2003)
Nature
, vol.18
, pp. 257-263
-
-
Palatnik, J.F.1
Allen, E.2
Wu, X.3
Schommer, C.4
Schwab, R.5
Carrington, J.C.6
Weigel, D.7
-
19
-
-
34250832061
-
Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319
-
Palatnik, J. F., Wollmann, H., Schommer, C., Schwab, R., Boisbouvier, J., Rodriguez, R., Warthmann, N., Allen, E., Dezulian, T., Huson, D., Carrington, J. C., and Weigel, D. (2007). Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev. Cell 13, 115-125.
-
(2007)
Dev. Cell
, vol.13
, pp. 115-125
-
-
Palatnik, J.F.1
Wollmann, H.2
Schommer, C.3
Schwab, R.4
Boisbouvier, J.5
Rodriguez, R.6
Warthmann, N.7
Allen, E.8
Dezulian, T.9
Huson, D.10
Carrington, J.C.11
Weigel, D.12
-
20
-
-
67650156804
-
Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing
-
Pant, B. D., Musialak-Lange, M., Nuc, P., May, P., Buhtz, A., Kehr, J., Walther, D., and Scheible, W. R. (2009). Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol. 150, 1541-1555.
-
(2009)
Plant Physiol.
, vol.150
, pp. 1541-1555
-
-
Pant, B.D.1
Musialak-Lange, M.2
Nuc, P.3
May, P.4
Buhtz, A.5
Kehr, J.6
Walther, D.7
Scheible, W.R.8
-
21
-
-
48549102479
-
Functional identification ofArabidopsis stress regulatory genes using the controlled cDNA overexpression system
-
Papdi, C., Abraham, E., Joseph, M. P., Popescu, C., Koncz, C., and Szabados, L. (2008). Functional identification ofArabidopsis stress regulatory genes using the controlled cDNA overexpression system. Plant Physiol. 147, 528-542.
-
(2008)
Plant Physiol.
, vol.147
, pp. 528-542
-
-
Papdi, C.1
Abraham, E.2
Joseph, M.P.3
Popescu, C.4
Koncz, C.5
Szabados, L.6
-
22
-
-
14844339653
-
Nuclear processing and export of microRNAs in Arabidopsis
-
Park, M. Y., Wu, G., Gonzalez-Sulser, A., Vaucheret, H., and Poethig, R. S. (2005). Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 102, 3691-3696.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 3691-3696
-
-
Park, M.Y.1
Wu, G.2
Gonzalez-Sulser, A.3
Vaucheret, H.4
Poethig, R.S.5
-
23
-
-
0037015239
-
Carpel factory, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana
-
Park, W., Li, J., Song, R., Messing, J., and Chen, X. (2002). Carpel factory, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12, 1484-1495.
-
(2002)
Curr. Biol.
, vol.12
, pp. 1484-1495
-
-
Park, W.1
Li, J.2
Song, R.3
Messing, J.4
Chen, X.5
-
24
-
-
0036645146
-
MicroRNAs in plants
-
Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B., and Bartel, D. P. (2002). MicroRNAs in plants. Genes Dev. 16, 1616-1626.
-
(2002)
Genes Dev.
, vol.16
, pp. 1616-1626
-
-
Reinhart, B.J.1
Weinstein, E.G.2
Rhoades, M.W.3
Bartel, B.4
Bartel, D.P.5
-
25
-
-
33846926826
-
ABA induction of miR159 controls transcripts levels of two MYB factors during Arabidopsis seed germination
-
Reyes, J. L., and Chua, N. H. (2007). ABA induction of miR159 controls transcripts levels of two MYB factors during Arabidopsis seed germination. Plant J. 49, 592-606.
-
(2007)
Plant J.
, vol.49
, pp. 592-606
-
-
Reyes, J.L.1
Chua, N.H.2
-
26
-
-
54749156380
-
Control of jasmonate biosynthesis and senescence by miR319 targets
-
doi: 10.1371/journal.pbio.0060230
-
Schommer, C., Palatnik, J. F., Aggarwal, P., Chételat, A., Cubas, P., Farmer, E. E., Nath, U., and Weigel, D. (2008). Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol. 6, e230. doi: 10.1371/journal.pbio.0060230
-
(2008)
PLoS Biol.
, vol.6
-
-
Schommer, C.1
Palatnik, J.F.2
Aggarwal, P.3
Chételat, A.4
Cubas, P.5
Farmer, E.E.6
Nath, U.7
Weigel, D.8
-
27
-
-
84857692673
-
Transfer RNA-derived fragments: Origins, processing, and functions
-
Sobala, A., and Hutvagner, G. (2011). Transfer RNA-derived fragments: origins, processing, and functions. Wiley Interdiscip. Rev. RNA 2, 853-862.
-
(2011)
Wiley Interdiscip. Rev. RNA
, vol.2
, pp. 853-862
-
-
Sobala, A.1
Hutvagner, G.2
-
28
-
-
66249128639
-
Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs
-
Szarzynska, B., Sobkowiak, L., Pant, B. D., Balazadeh, S., Scheible, W. R., Mueller-Roeber, B., Jarmolowski, A., and Szweykowska-Kulinska, Z. (2009). Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs. Nucleic Acids Res. 37, 3083-3093.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 3083-3093
-
-
Szarzynska, B.1
Sobkowiak, L.2
Pant, B.D.3
Balazadeh, S.4
Scheible, W.R.5
Mueller-Roeber, B.6
Jarmolowski, A.7
Szweykowska-Kulinska, Z.8
-
29
-
-
67649386471
-
Small RNAs derived from snoRNAs
-
Taft, R. J., Glazov, E. A., Lassmann, T., Hayashizaki, Y., Carninci, P., and Mattick, J. S. (2009). Small RNAs derived from snoRNAs. RNA 15, 1233-1240.
-
(2009)
RNA
, vol.15
, pp. 1233-1240
-
-
Taft, R.J.1
Glazov, E.A.2
Lassmann, T.3
Hayashizaki, Y.4
Carninci, P.5
Mattick, J.S.6
-
30
-
-
80052458531
-
Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
-
Valen, E., Preker, P., Andersen, P. R., Zhao, X., Chen, Y., Ender, C., Dueck, A., Meister, G., Sandelin, A., and Jensen, T. H. (2011). Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nat. Struct. Mol. Biol. 18, 1075-1082.
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 1075-1082
-
-
Valen, E.1
Preker, P.2
Andersen, P.R.3
Zhao, X.4
Chen, Y.5
Ender, C.6
Dueck, A.7
Meister, G.8
Sandelin, A.9
Jensen, T.H.10
-
31
-
-
56649102410
-
Evolution of Arabidopsis MIR genes generates novel microRNA classes
-
Vazquez, F., Blevins, T., Ailhas, J., Boller, T., and Meins, F. Jr. (2008). Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res. 36, 6429-6438.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 6429-6438
-
-
Vazquez, F.1
Blevins, T.2
Ailhas, J.3
Boller, T.4
Meins Jr., F.5
-
32
-
-
1542350745
-
The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing
-
Vazquez, F., Gasciolli, V., Crété, P., and Vaucheret, H. (2004). The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol. 14, 346-351.
-
(2004)
Curr. Biol.
, vol.14
, pp. 346-351
-
-
Vazquez, F.1
Gasciolli, V.2
Crété, P.3
Vaucheret, H.4
-
33
-
-
0342927487
-
Activation tagging in Arabidopsis
-
Weigel, D., Ahn, J. F., Blazquez, M. A., Borevitz, J. O., Christensen, S. K., Fankhauser, C., Ferrandiz, C., Karadailsky, I., Malancharuvil, E. J., Neff, M. M., Nguyen, J. T., Sato, S., Wang, Z. Y., Xia, Y., Dixon, R. A., Harrison, M. J., Lamb, C. J., Yanofsky, M. F., and Chory, J. (2000). Activation tagging in Arabidopsis. Plant Physiol. 122, 1003-1014.
-
(2000)
Plant Physiol.
, vol.122
, pp. 1003-1014
-
-
Weigel, D.1
Ahn, J.F.2
Blazquez, M.A.3
Borevitz, J.O.4
Christensen, S.K.5
Fankhauser, C.6
Ferrandiz, C.7
Karadailsky, I.8
Malancharuvil, E.J.9
Neff, M.M.10
Nguyen, J.T.11
Sato, S.12
Wang, Z.Y.13
Xia, Y.14
Dixon, R.A.15
Harrison, M.J.16
Lamb, C.J.17
Yanofsky, M.F.18
Chory, J.19
-
34
-
-
33748314483
-
SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis
-
Yang, L., Liu, Z., Lu, F., Dong, A., and Huang, H. (2006a). SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J. 47, 841-850.
-
(2006)
Plant J.
, vol.47
, pp. 841-850
-
-
Yang, L.1
Liu, Z.2
Lu, F.3
Dong, A.4
Huang, H.5
-
35
-
-
32644454064
-
HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide
-
Yang, Z., Ebright, Y. W., Yu, B., and Chen, X. (2006b). HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res. 34, 667-675.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 667-675
-
-
Yang, Z.1
Ebright, Y.W.2
Yu, B.3
Chen, X.4
-
36
-
-
48249158259
-
The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis
-
Yu, B., Bi, L., Zheng, B., Ji, L., Chevalier, D., Agarwal, M., Ramachandran, V., Li, W., Lagrange, T., Walker, J. C., and Chen, X. (2008). The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl. Acad. Sci. U.S.A. 105, 10073-10078.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 10073-10078
-
-
Yu, B.1
Bi, L.2
Zheng, B.3
Ji, L.4
Chevalier, D.5
Agarwal, M.6
Ramachandran, V.7
Li, W.8
Lagrange, T.9
Walker, J.C.10
Chen, X.11
-
37
-
-
78650516640
-
Multiple distinct small RNAs originate from the same micro RNA precursors
-
Zhang, W., Gao, S., Zhou, X., Xia, J., Chellappan, P., Zhou, X., Zhang, X., and Jin, H. (2010). Multiple distinct small RNAs originate from the same micro RNA precursors. Genome Biol. 11, R81.
-
(2010)
Genome Biol.
, vol.11
-
-
Zhang, W.1
Gao, S.2
Zhou, X.3
Xia, J.4
Chellappan, P.5
Zhou, X.6
Zhang, X.7
Jin, H.8
-
38
-
-
77951974552
-
DNA methylation mediated by a micro RNA pathway
-
Zhou, H., Zhang, Q., Zhang, J., Ni, F., Liu, C., and Qi, Y. (2010). DNA methylation mediated by a micro RNA pathway. Mol. Cell 38, 465-475.
-
(2010)
Mol. Cell
, vol.38
, pp. 465-475
-
-
Zhou, H.1
Zhang, Q.2
Zhang, J.3
Ni, F.4
Liu, C.5
Qi, Y.6
|