| [1] | De Lozanne A (2003) The role of BEACH proteins in Dictyostelium. Traffic 4: 6–12. pmid:12535270 doi: 10.1034/j.1600-0854.2003.40102.x
|
| [2] | Saedler R, Jakoby M, Marin B, Galiana-Jaime E, Hulskamp M (2009) The cell morphogenesis gene SPIRRIG in Arabidopsis encodes a WD/BEACH domain protein. Plant J 59: 612–621. doi: 10.1111/j.1365-313X.2009.03900.x. pmid:19392685
|
| [3] | Nagle DL, Karim MA, Woolf EA, Holmgren L, Bork P, et al. (1996) Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome. Nat Genet 14: 307–311. pmid:8896560 doi: 10.1038/ng1196-307
|
| [4] | Barbosa MD, Nguyen QA, Tchernev VT, Ashley JA, Detter JC, et al. (1996) Identification of the homologous beige and Chediak-Higashi syndrome genes. Nature 382: 262–265. pmid:8717042 doi: 10.1038/382262a0
|
| [5] | Perou CM, Moore KJ, Nagle DL, Misumi DJ, Woolf EA, et al. (1996) Identification of the murine beige gene by YAC complementation and positional cloning. Nat Genet 13: 303–308. pmid:8673129 doi: 10.1038/ng0796-303
|
| [6] | Introne W, Boissy RE, Gahl WA (1999) Clinical, molecular, and cell biological aspects of Chediak-Higashi syndrome. Mol Genet Metab 68: 283–303. pmid:10527680 doi: 10.1006/mgme.1999.2927
|
| [7] | Wang JW, Gamsby JJ, Highfill SL, Mora LB, Bloom GC, et al. (2004) Deregulated expression of LRBA facilitates cancer cell growth. Oncogene 23: 4089–4097. pmid:15064745 doi: 10.1038/sj.onc.1207567
|
| [8] | Castermans D, Wilquet V, Parthoens E, Huysmans C, Steyaert J, et al. (2003) The neurobeachin gene is disrupted by a translocation in a patient with idiopathic autism. J Med Genet 40: 352–356. pmid:12746398 doi: 10.1136/jmg.40.5.352
|
| [9] | Cullinane AR, Schaffer AA, Huizing M (2013) The BEACH is hot: a LYST of emerging roles for BEACH-domain containing proteins in human disease. Traffic 14: 749–766. doi: 10.1111/tra.12069. pmid:23521701
|
| [10] | Wang N, Wu WI, De Lozanne A (2002) BEACH family of proteins: phylogenetic and functional analysis of six Dictyostelium BEACH proteins. J Cell Biochem 86: 561–570. pmid:12210762 doi: 10.1002/jcb.10254
|
| [11] | Khodosh R, Augsburger A, Schwarz TL, Garrity PA (2006) Bchs, a BEACH domain protein, antagonizes Rab11 in synapse morphogenesis and other developmental events. Development 133: 4655–4665. pmid:17079274 doi: 10.1242/dev.02650
|
| [12] | Burgess A, Mornon JP, de Saint-Basile G, Callebaut I (2009) A concanavalin A-like lectin domain in the CHS1/LYST protein, shared by members of the BEACH family. Bioinformatics 25: 1219–1222. doi: 10.1093/bioinformatics/btp151. pmid:19289442
|
| [13] | Xu J, Chua NH (2009) Arabidopsis decapping 5 is required for mRNA decapping, P-body formation, and translational repression during postembryonic development. Plant Cell 21: 3270–3279. doi: 10.1105/tpc.109.070078. pmid:19855049
|
| [14] | Xu J, Yang JY, Niu QW, Chua NH (2006) Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Plant Cell 18: 3386–3398. pmid:17158604 doi: 10.1105/tpc.106.047605
|
| [15] | Gazzani S, Lawrenson T, Woodward C, Headon D, Sablowski R (2004) A link between mRNA turnover and RNA interference in Arabidopsis. Science 306: 1046–1048. pmid:15528448 doi: 10.1126/science.1101092
|
| [16] | Souret FF, Kastenmayer JP, Green PJ (2004) AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell 15: 173–183. pmid:15260969 doi: 10.1016/j.molcel.2004.06.006
|
| [17] | Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, et al. (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 14: 854–866. doi: 10.1016/j.devcel.2008.04.005. pmid:18486559
|
| [18] | Rymarquis LA, Souret FF, Green PJ (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. doi: 10.1261/rna.2467911. pmid:21224377
|
| [19] | Lykke-Andersen J (2002) Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol 22: 8114–8121. pmid:12417715 doi: 10.1128/mcb.22.23.8114-8121.2002
|
| [20] | van Dijk E, Cougot N, Meyer S, Babajko S, Wahle E, et al. (2002) Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J 21: 6915–6924. pmid:12486012 doi: 10.1093/emboj/cdf678
|
| [21] | Wang Z, Jiao X, Carr-Schmid A, Kiledjian M (2002) The hDcp2 protein is a mammalian mRNA decapping enzyme. Proc Natl Acad Sci U S A 99: 12663–12668. pmid:12218187 doi: 10.1073/pnas.192445599
|
| [22] | Parker R, Sheth U (2007) P bodies and the control of mRNA translation and degradation. Mol Cell 25: 635–646. pmid:17349952 doi: 10.1016/j.molcel.2007.02.011
|
| [23] | Jonas S, Izaurralde E (2013) The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Genes Dev 27: 2628–2641. doi: 10.1101/gad.227843.113. pmid:24352420
|
| [24] | Eulalio A, Behm-Ansmant I, Izaurralde E (2007) P bodies: at the crossroads of post-transcriptional pathways. Nat Rev Mol Cell Biol 8: 9–22. pmid:17183357 doi: 10.1038/nrm2080
|
| [25] | Franks TM, Lykke-Andersen J (2008) The control of mRNA decapping and P-body formation. Mol Cell 32: 605–615. doi: 10.1016/j.molcel.2008.11.001. pmid:19061636
|
| [26] | Segui B, Cuvillier O, Adam-Klages S, Garcia V, Malagarie-Cazenave S, et al. (2001) Involvement of FAN in TNF-induced apoptosis. J Clin Invest 108: 143–151. pmid:11435466 doi: 10.1172/jci200111498
|
| [27] | Tchernev VT, Mansfield TA, Giot L, Kumar AM, Nandabalan K, et al. (2002) The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins. Mol Med 8: 56–64. pmid:11984006
|
| [28] | Filimonenko M, Isakson P, Finley KD, Anderson M, Jeong H, et al. (2010) The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell 38: 265–279. doi: 10.1016/j.molcel.2010.04.007. pmid:20417604
|
| [29] | Hocking LJ, Mellis DJ, McCabe PS, Helfrich MH, Rogers MJ (2010) Functional interaction between sequestosome-1/p62 and autophagy-linked FYVE-containing protein WDFY3 in human osteoclasts. Biochem Biophys Res Commun 402: 543–548. doi: 10.1016/j.bbrc.2010.10.076. pmid:20971078
|
| [30] | Adam-Klages S, Adam D, Wiegmann K, Struve S, Kolanus W, et al. (1996) FAN, a novel WD-repeat protein, couples the p55 TNF-receptor to neutral sphingomyelinase. Cell 86: 937–947. pmid:8808629 doi: 10.1016/s0092-8674(00)80169-5
|
| [31] | Steffens A, Jaegle B, Tresch A, Hulskamp M, Jakoby M Processing-Body Movement in Arabidopsis Depends on an Interaction between Myosins and DECAPPING PROTEIN1. Plant Physiol 164: 1879–1892. doi: 10.1104/pp.113.233031. pmid:24525673
|
| [32] | Richardson LG, Howard AS, Khuu N, Gidda SK, McCartney A, et al. Protein-Protein Interaction Network and Subcellular Localization of the Arabidopsis Thaliana ESCRT Machinery. Front Plant Sci 2: 20. doi: 10.3389/fpls.2011.00020. pmid:22639582
|
| [33] | Shahriari M, Richter K, Keshavaiah C, Sabovljevic A, Huelskamp M, et al. The Arabidopsis ESCRT protein-protein interaction network. Plant Mol Biol 76: 85–96. doi: 10.1007/s11103-011-9770-4. pmid:21442383
|
| [34] | Pesch M, Schultheiss I, Digiuni S, Uhrig JF, Hulskamp M (2013) Mutual control of intracellular localisation of the patterning proteins AtMYC1, GL1 and TRY/CPC in Arabidopsis. Development 140: 3456–3467. doi: 10.1242/dev.094698. pmid:23900543
|
| [35] | Iwasaki S, Takeda A, Motose H, Watanabe Y (2007) Characterization of Arabidopsis decapping proteins AtDCP1 and AtDCP2, which are essential for post-embryonic development. FEBS Lett 581: 2455–2459. pmid:17485080 doi: 10.1016/j.febslet.2007.04.051
|
| [36] | Zurla C, Lifland AW, Santangelo PJ (2011) Characterizing mRNA interactions with RNA granules during translation initiation inhibition. PLoS One 6: e19727. doi: 10.1371/journal.pone.0019727. pmid:21573130
|
| [37] | Tudisca V, Recouvreux V, Moreno S, Boy-Marcotte E, Jacquet M, et al. (2010) Differential localization to cytoplasm, nucleus or P-bodies of yeast PKA subunits under different growth conditions. Eur J Cell Biol 89: 339–348. doi: 10.1016/j.ejcb.2009.08.005. pmid:19804918
|
| [38] | Teixeira D, Sheth U, Valencia-Sanchez MA, Brengues M, Parker R (2005) Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA 11: 371–382. pmid:15703442 doi: 10.1261/rna.7258505
|
| [39] | Kedersha N, Anderson P (2007) Mammalian stress granules and processing bodies. Methods Enzymol 431: 61–81. pmid:17923231 doi: 10.1016/s0076-6879(07)31005-7
|
| [40] | Ndimba BK, Chivasa S, Simon WJ, Slabas AR (2005) Identification of Arabidopsis salt and osmotic stress responsive proteins using two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 5: 4185–4196. pmid:16254930 doi: 10.1002/pmic.200401282
|
| [41] | Branco-Price C, Kawaguchi R, Ferreira RB, Bailey-Serres J (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot 96: 647–660. pmid:16081496 doi: 10.1093/aob/mci217
|
| [42] | Shah KH, Zhang B, Ramachandran V, Herman PK Processing body and stress granule assembly occur by independent and differentially regulated pathways in Saccharomyces cerevisiae. Genetics 193: 109–123. doi: 10.1534/genetics.112.146993. pmid:23105015
|
| [43] | Anderson P, Kedersha N (2009) RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nat Rev Mol Cell Biol 10: 430–436. doi: 10.1038/nrm2694. pmid:19461665
|
| [44] | Brengues M, Teixeira D, Parker R (2005) Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Science 310: 486–489. pmid:16141371 doi: 10.1126/science.1115791
|
| [45] | Cougot N, Babajko S, Seraphin B (2004) Cytoplasmic foci are sites of mRNA decay in human cells. J Cell Biol 165: 31–40. pmid:15067023 doi: 10.1083/jcb.200309008
|
| [46] | Andrei MA, Ingelfinger D, Heintzmann R, Achsel T, Rivera-Pomar R, et al. (2005) A role for eIF4E and eIF4E-transporter in targeting mRNPs to mammalian processing bodies. RNA 11: 717–727. pmid:15840819 doi: 10.1261/rna.2340405
|
| [47] | Sun J, Jiang H, Xu Y, Li H, Wu X, et al. (2007) The CCCH-type zinc finger proteins AtSZF1 and AtSZF2 regulate salt stress responses in Arabidopsis. Plant Cell Physiol 48: 1148–1158. pmid:17609218 doi: 10.1093/pcp/pcm088
|
| [48] | Yang Q, Chen ZZ, Zhou XF, Yin HB, Li X, et al. (2009) Overexpression of SOS (Salt Overly Sensitive) genes increases salt tolerance in transgenic Arabidopsis. Mol Plant 2: 22–31. doi: 10.1093/mp/ssn058. pmid:19529826
|
| [49] | Pandey GK, Cheong YH, Kim BG, Grant JJ, Li L, et al. (2007) CIPK9: a calcium sensor-interacting protein kinase required for low-potassium tolerance in Arabidopsis. Cell Res 17: 411–421. pmid:17486125 doi: 10.1038/cr.2007.39
|
| [50] | Yu Q, An L, Li W (2009) The CBL-CIPK network mediates different signaling pathways in plants. Plant Cell Rep 33: 203–214. doi: 10.1007/s00299-013-1507-1
|
| [51] | Lee SJ, Jung HJ, Kang H, Kim SY (2012) Arabidopsis zinc finger proteins AtC3H49/AtTZF3 and AtC3H20/AtTZF2 are involved in ABA and JA responses. Plant Cell Physiol 53: 673–686. doi: 10.1093/pcp/pcs023. pmid:22383628
|
| [52] | Strizhov N, Abraham E, Okresz L, Blickling S, Zilberstein A, et al. (1997) Differential expression of two P5CS genes controlling proline accumulation during salt-stress requires ABA and is regulated by ABA1, ABI1 and AXR2 in Arabidopsis. Plant J 12: 557–569. pmid:9351242 doi: 10.1046/j.1365-313x.1997.00557.x
|
| [53] | Balazadeh S, Siddiqui H, Allu AD, Matallana-Ramirez LP, Caldana C, et al. A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J 62: 250–264. doi: 10.1111/j.1365-313X.2010.04151.x. pmid:20113437
|
| [54] | Schult K, Meierhoff K, Paradies S, Toller T, Wolff P, et al. (2007) The nuclear-encoded factor HCF173 is involved in the initiation of translation of the psbA mRNA in Arabidopsis thaliana. Plant Cell 19: 1329–1346. pmid:17435084 doi: 10.1105/tpc.106.042895
|
| [55] | Narsai R, Howell KA, Millar AH, O'Toole N, Small I, et al. (2007) Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell 19: 3418–3436. pmid:18024567 doi: 10.1105/tpc.107.055046
|
| [56] | Schonberger J, Hammes UZ, Dresselhaus T In vivo visualization of RNA in plants cells using the lambdaN(2)(2) system and a GATEWAY-compatible vector series for candidate RNAs. Plant J 71: 173–181. doi: 10.1111/j.1365-313X.2012.04923.x. pmid:22268772
|
| [57] | Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, et al. (2009) Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324: 1729–1732. doi: 10.1126/science.1172046. pmid:19460965
|
| [58] | Li P, Banjade S, Cheng HC, Kim S, Chen B, et al. (2012) Phase transitions in the assembly of multivalent signalling proteins. Nature 483: 336–340. doi: 10.1038/nature10879. pmid:22398450
|
| [59] | Weber SC, Brangwynne CP (2012) Getting RNA and protein in phase. Cell 149: 1188–1191. doi: 10.1016/j.cell.2012.05.022. pmid:22682242
|
| [60] | Leung AK, Calabrese JM, Sharp PA (2006) Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules. Proc Natl Acad Sci U S A 103: 18125–18130. pmid:17116888 doi: 10.1073/pnas.0608845103
|
| [61] | Aizer A, Brody Y, Ler LW, Sonenberg N, Singer RH, et al. (2008) The dynamics of mammalian P body transport, assembly, and disassembly in vivo. Mol Biol Cell 19: 4154–4166. doi: 10.1091/mbc.E08-05-0513. pmid:18653466
|
| [62] | Arribere JA, Doudna JA, Gilbert WV (2011) Reconsidering movement of eukaryotic mRNAs between polysomes and P bodies. Mol Cell 44: 745–758. doi: 10.1016/j.molcel.2011.09.019. pmid:22152478
|
| [63] | Sormani R, Masclaux-Daubresse C, Daniel-Vedele F, Chardon F (2011) Transcriptional regulation of ribosome components are determined by stress according to cellular compartments in Arabidopsis thaliana. PLoS One 6: e28070. doi: 10.1371/journal.pone.0028070. pmid:22164228
|
| [64] | Matsuura H, Shinmyo A, Kato K (2008) Preferential translation mediated by Hsp81-3 5'-UTR during heat shock involves ribosome entry at the 5'-end rather than an internal site in Arabidopsis suspension cells. J Biosci Bioeng 105: 39–47. doi: 10.1263/jbb.105.39. pmid:18295718
|
| [65] | Proud CG (2007) Signalling to translation: how signal transduction pathways control the protein synthetic machinery. Biochem J 403: 217–234. pmid:17376031 doi: 10.1042/bj20070024
|
| [66] | Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J (2008) Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J 56: 743–755. doi: 10.1111/j.1365-313X.2008.03642.x. pmid:18665916
|
| [67] | Nicolai M, Roncato MA, Canoy AS, Rouquie D, Sarda X, et al. (2006) Large-scale analysis of mRNA translation states during sucrose starvation in arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol 141: 663–673. pmid:16632591 doi: 10.1104/pp.106.079418
|
| [68] | Kawaguchi R, Girke T, Bray EA, Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J 38: 823–839. pmid:15144383 doi: 10.1111/j.1365-313x.2004.02090.x
|
| [69] | Chiba Y, Mineta K, Hirai MY, Suzuki Y, Kanaya S, et al. (2013) Changes in mRNA stability associated with cold stress in Arabidopsis cells. Plant Cell Physiol 54: 180–194. doi: 10.1093/pcp/pcs164. pmid:23220693
|
| [70] | An FM, Chan MT (2012) Transcriptome-wide characterization of miRNA-directed and non-miRNA-directed endonucleolytic cleavage using Degradome analysis under low ambient temperature in Phalaenopsis aphrodite subsp. formosana. Plant Cell Physiol 53: 1737–1750. doi: 10.1093/pcp/pcs118. pmid:22904110
|
| [71] | Zhou X, Wang G, Sutoh K, Zhu JK, Zhang W (2008) Identification of cold-inducible microRNAs in plants by transcriptome analysis. Biochim Biophys Acta 1779: 780–788. doi: 10.1016/j.bbagrm.2008.04.005. pmid:18471443
|
| [72] | Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14: 836–843. doi: 10.1261/rna.895308. pmid:18356539
|
| [73] | de Souza N, Vallier LG, Fares H, Greenwald I (2007) SEL-2, the C. elegans neurobeachin/LRBA homolog, is a negative regulator of lin-12/Notch activity and affects endosomal traffic in polarized epithelial cells. Development 134: 691–702. pmid:17215302 doi: 10.1242/dev.02767
|
| [74] | Lim A, Kraut R (2009) The Drosophila BEACH family protein, blue cheese, links lysosomal axon transport with motor neuron degeneration. J Neurosci 29: 951–963. doi: 10.1523/JNEUROSCI.2582-08.2009. pmid:19176804
|
| [75] | Albers CA, Cvejic A, Favier R, Bouwmans EE, Alessi MC, et al. (2011) Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome. Nat Genet 43: 735–737. doi: 10.1038/ng.885. pmid:21765411
|
| [76] | Kypri E, Schmauch C, Maniak M, De Lozanne A (2007) The BEACH protein LvsB is localized on lysosomes and postlysosomes and limits their fusion with early endosomes. Traffic 8: 774–783. pmid:17488289 doi: 10.1111/j.1600-0854.2007.00567.x
|
| [77] | Coller J, Parker R (2005) General translational repression by activators of mRNA decapping. Cell 122: 875–886. pmid:16179257 doi: 10.1016/j.cell.2005.07.012
|
| [78] | Decker CJ, Teixeira D, Parker R (2007) Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae. J Cell Biol 179: 437–449. pmid:17984320 doi: 10.1083/jcb.200704147
|
| [79] | Reijns MA, Alexander RD, Spiller MP, Beggs JD (2008) A role for Q/N-rich aggregation-prone regions in P-body localization. J Cell Sci 121: 2463–2472. doi: 10.1242/jcs.024976. pmid:18611963
|
| [80] | Kshirsagar M, Parker R (2004) Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae. Genetics 166: 729–739. pmid:15020463 doi: 10.1534/genetics.166.2.729
|
| [81] | Deshmukh MV, Jones BN, Quang-Dang DU, Flinders J, Floor SN, et al. (2008) mRNA decapping is promoted by an RNA-binding channel in Dcp2. Mol Cell 29: 324–336. doi: 10.1016/j.molcel.2007.11.027. pmid:18280238
|
| [82] | She M, Decker CJ, Svergun DI, Round A, Chen N, et al. (2008) Structural basis of dcp2 recognition and activation by dcp1. Mol Cell 29: 337–349. doi: 10.1016/j.molcel.2008.01.002. pmid:18280239
|
| [83] | Floor SN, Jones BN, Hernandez GA, Gross JD (2010) A split active site couples cap recognition by Dcp2 to activation. Nat Struct Mol Biol 17: 1096–1101. doi: 10.1038/nsmb.1879. pmid:20711189
|
| [84] | Floor SN, Borja MS, Gross JD (2012) Interdomain dynamics and coactivation of the mRNA decapping enzyme Dcp2 are mediated by a gatekeeper tryptophan. Proc Natl Acad Sci U S A 109: 2872–2877. doi: 10.1073/pnas.1113620109. pmid:22323607
|
| [85] | Nissan T, Rajyaguru P, She M, Song H, Parker R (2010) Decapping activators in Saccharomyces cerevisiae act by multiple mechanisms. Mol Cell 39: 773–783. doi: 10.1016/j.molcel.2010.08.025. pmid:20832728
|
| [86] | Borja MS, Piotukh K, Freund C, Gross JD (2011) Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition. RNA 17: 278–290. doi: 10.1261/rna.2382011. pmid:21148770
|
| [87] | Fromm SA, Truffault V, Kamenz J, Braun JE, Hoffmann NA, et al. (2012) The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex. EMBO J 31: 279–290. doi: 10.1038/emboj.2011.408. pmid:22085934
|
| [88] | Rajyaguru P, She M, Parker R (2012) Scd6 targets eIF4G to repress translation: RGG motif proteins as a class of eIF4G-binding proteins. Mol Cell 45: 244–254. doi: 10.1016/j.molcel.2011.11.026. pmid:22284680
|
| [89] | Sweet T, Kovalak C, Coller J (2012) The DEAD-box protein Dhh1 promotes decapping by slowing ribosome movement. PLoS Biol 10: e1001342. doi: 10.1371/journal.pbio.1001342. pmid:22719226
|
| [90] | Sheth U, Parker R (2003) Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300: 805–808. pmid:12730603 doi: 10.1126/science.1082320
|
| [91] | Romero-Santacreu L, Moreno J, Perez-Ortin JE, Alepuz P (2009) Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae. RNA 15: 1110–1120. doi: 10.1261/rna.1435709. pmid:19369426
|
| [92] | Yoon JH, Parker R (2011) Genome-wide role of P-bodies mRNP in mRNA decay of Saccharomyces cerevisiae. Faseb Journal 25.
|
| [93] | Olszewski PK, Rozman J, Jacobsson JA, Rathkolb B, Stromberg S, et al. (2012) Neurobeachin, a regulator of synaptic protein targeting, is associated with body fat mass and feeding behavior in mice and body-mass index in humans. PLoS Genet 8: e1002568. doi: 10.1371/journal.pgen.1002568. pmid:22438821
|
| [94] | Montfort A, de Badts B, Douin-Echinard V, Martin PG, Iacovoni J, et al. (2009) FAN stimulates TNF(alpha)-induced gene expression, leukocyte recruitment, and humoral response. J Immunol 183: 5369–5378. doi: 10.4049/jimmunol.0803384. pmid:19786552
|
| [95] | Bent A (2006) Arabidopsis thaliana floral dip transformation method. Methods Mol Biol 343: 87–103. pmid:16988336 doi: 10.1385/1-59745-130-4:87
|
| [96] | Claeys H, Van Landeghem S, Dubois M, Maleux K, Inze D (2014) What Is Stress? Dose-Response Effects in Commonly Used in Vitro Stress Assays. Plant Physiol 165: 519–527. pmid:24710067 doi: 10.1104/pp.113.234641
|
| [97] | Guo J, Wang J, Xi L, Huang WD, Liang J, et al. (2009) RACK1 is a negative regulator of ABA responses in Arabidopsis. J Exp Bot 60: 3819–3833. doi: 10.1093/jxb/erp221. pmid:19584117
|
| [98] | Warming S, Costantino N, Court DL, Jenkins NA, Copeland NG (2005) Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res 33: e36. pmid:15731329 doi: 10.1093/nar/gni035
|
| [99] | Haubert D, Gharib N, Rivero F, Wiegmann K, Hosel M, et al. (2007) PtdIns(4,5)P-restricted plasma membrane localization of FAN is involved in TNF-induced actin reorganization. EMBO J 26: 3308–3321. pmid:17599063 doi: 10.1038/sj.emboj.7601778
|
| [100] | Feys BJ, Wiermer M, Bhat RA, Moisan LJ, Medina-Escobar N, et al. (2005) Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and signals within an ENHANCED DISEASE SUSCEPTIBILITY1 complex in plant innate immunity. Plant Cell 17: 2601–2613. pmid:16040633 doi: 10.1105/tpc.105.033910
|
| [101] | Gietz RD, Schiestl RH, Willems AR, Woods RA (1995) Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure. Yeast 11: 355–360. pmid:7785336 doi: 10.1002/yea.320110408
|
| [102] | Yang Y, Li R, Qi M (2000) In vivo analysis of plant promoters and transcription factors by agroinfiltration of tobacco leaves. The Plant journal: for cell and molecular biology 22: 543–551. doi: 10.1046/j.1365-313x.2000.00760.x
|
| [103] | Mathur J, Mathur N, Kirik V, Kernebeck B, Srinivas BP, et al. (2003) Arabidopsis CROOKED encodes for the smallest subunit of the ARP2/3 complex and controls cell shape by region specific fine F-actin formation. Development 130: 3137–3146. pmid:12783786 doi: 10.1242/dev.00549
|
| [104] | Horstman A, Tonaco IA, Boutilier K, Immink RG A cautionary note on the use of split-YFP/BiFC in plant protein-protein interaction studies. Int J Mol Sci 15: 9628–9643. doi: 10.3390/ijms15069628. pmid:24886811
|
| [105] | Fazekas Z, Petras M, Fabian A, Palyi-Krekk Z, Nagy P, et al. (2008) Two-sided fluorescence resonance energy transfer for assessing molecular interactions of up to three distinct species in confocal microscopy. Cytometry A 73: 209–219. pmid:18044751 doi: 10.1002/cyto.a.20489
|
| [106] | Zhang H, Deng X, Miki D, Cutler S, La H, et al. (2012) Sulfamethazine suppresses epigenetic silencing in Arabidopsis by impairing folate synthesis. Plant Cell 24: 1230–1241. doi: 10.1105/tpc.112.096149. pmid:22447685
|
| [107] | Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140. doi: 10.1093/bioinformatics/btp616. pmid:19910308
|
| [108] | Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, et al. (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell and Environment 32: 1211–1229. doi: 10.1111/j.1365-3040.2009.01978.x
|
| [109] | Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. Bmc Bioinformatics 10: 48. doi: 10.1186/1471-2105-10-48. pmid:19192299
|
| [110] | Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, et al. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant Journal 37: 914–939. pmid:14996223 doi: 10.1111/j.1365-313x.2004.02016.x
|
