Functional analysis of the microtubule-interacting transcriptome

Molecular Biology of the Cell

Volumn 22, Issue 22, 2011, Pages 4312-4323

  Sharp, Judith A ^a,b   Plant, Joshua J ^a,b   Ohsumi, Toshiro K ^a,b   Borowsky, Mark ^a,b   Blower, Michael D ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAMMA TUBULIN; MESSENGER RNA; MITOCHONDRIAL RNA; PROTEIN; TPX2 PROTEIN; TRANSCRIPTOME; UNCLASSIFIED DRUG; XRHAMM PROTEIN;

ANIMAL CELL; ARTICLE; CELL COMPARTMENTALIZATION; CELL DIVISION; CHROMOSOME; CONTROLLED STUDY; GENE FUNCTION; MICROTUBULE; MITOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN LOCALIZATION; REGULATORY MECHANISM; RNA INTERFERENCE; RNA SEQUENCE; SPINDLE POLE BODY; XENOPUS; XENOPUS TROPICALIS;

ANIMALS; BASE SEQUENCE; CELL CYCLE; CELL CYCLE PROTEINS; CELL DIVISION; CHROMOSOMAL PROTEINS, NON-HISTONE; MICROTUBULE-ASSOCIATED PROTEINS; MICROTUBULES; MITOSIS; MITOTIC SPINDLE APPARATUS; NUCLEAR PROTEINS; PHOSPHOPROTEINS; RNA INTERFERENCE; RNA, MESSENGER; RNA, SMALL INTERFERING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME; TUBULIN; XENOPUS; XENOPUS PROTEINS;

ANURA; XENOPUS LAEVIS; XENOPUS TROPICALIS;

EID: 81755172055     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E11-07-0629     Document Type: Article

References (68)

1. Aizer A, Brody Y, Ler LW, Sonenberg N, Singer RH, Shav-Tal Y (2008). The dynamics of mammalian P body transport, assembly, and disassembly in vivo. Mol Biol Cell 19, 4154-4166.
2. Besse F, Ephrussi A (2008). Translational control of localized mRNAs: restricting protein synthesis in space and time. Nat Rev Mol Cell Biol 9, 971-80.
3. Blower MD, Feric E, Weis K, Heald R (2007). Genome-wide analysis demonstrates conserved localization of messenger RNAs to mitotic microtubules. J Cell Biol 179, 1365-1373.
4. Bonneau AM, Sonenberg N (1987). Involvement of the 24-kDa cap-binding protein in regulation of protein synthesis in mitosis. J Biol Chem 262, 11134-11139.
5. Bouckson-Castaing V, Moudjou M, Ferguson DJ, Mucklow S, Belkaid Y, Milon G, Crocker PR (1996). Molecular characterisation of ninein, a new coiled-coil protein of the centrosome. J Cell Sci 109, 179-190. (Pubitemid 26038842)
6. Brown KS, Blower MD, Maresca TJ, Grammer TC, Harland RM, Heald RJ (2007). Xenopus tropicalis egg extracts provide insight into scaling of the mitotic spindle. J Cell Biol 176, 765-770. (Pubitemid 46425536)
7. Cha BJ, Koppetsch BS, Theurkauf WE (2001). In vivo analysis of Drosophila bicoid mRNA localization reveals a novel microtubule-dependent axis specification pathway. Cell 106, 35-46. (Pubitemid 32709956)
8. Cloonan N et al. (2008). Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5, 613-619. (Pubitemid 351911866)
9. Compton DA, Szilak I, Cleveland DW (1992). Primary structure of NuMA, an intranuclear protein that defines a novel pathway for segregation of proteins at mitosis. J Cell Biol 116, 1395-1408.
10. Condeelis J, Singer RH (2005). How and why does β-actin mRNA target. Biol Cell 97, 97-110. (Pubitemid 40220716)
11. Cooke CA, Heck MM, Earnshaw WC (1987). The inner centromere protein (INCENP) antigens: movement from inner centromere to midbody during mitosis. J Cell Biol 105, 2053-2067. (Pubitemid 18019057)
12. Cornelis S, Bruynooghe Y, Denecker G, Van Huffel S, Tinton S, Beyaert R (2000). Identification and characterization of a novel cell cycle-regulated internal ribosome entry site. Mol Cell 5, 597-605.
13. Doxsey SJ, Stein P, Evans L, Calarco PD, Kirschner M (1994). Pericentrin, a highly conserved centrosome protein involved in microtubule organization. Cell 76, 639-650. (Pubitemid 24070649)
14. Eliscovich C, Peset I, Vernos I, Mendez R (2008). Spindle-localized CPE-mediated translation controls meiotic chromosome segregation. Nat Cell Biol 10, 858-865. (Pubitemid 351927714)
15. Ellison TR, Mathisen PM, Miller L (1985). Developmental changes in keratin patterns during epidermal maturation. Dev Biol 112, 329-337. (Pubitemid 16160562)
16. Eystathioy T, Chan EKL, Tenenbaum SA, Keene JD, Griffith K, Fritzler MJ (2002). A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. Mol Biol Cell 13, 1338-1351. (Pubitemid 34309627)
17. Eystathioy T, Jakymiw A, Chan EK, Seraphin B, Cougot N, Fritzler MJ (2003). The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLsm4 in cytoplasmic GW bodies. RNA 9, 1171-1173. (Pubitemid 37151671)
18. Felix MA, Antony C, Wright M, Maro B (1994). Centrosome assembly in vitro: role of gamma-tubulin recruitment in Xenopus sperm aster formation. J Cell Biol 124, 19-31. (Pubitemid 24054607)
19. Fry AM, Descombes P, Twomey C, Bacchieri R, Nigg EA (2000). The NIMA-related kinase X-Nek2B is required for efficient assembly of the zygotic centrosome in Xenopus laevis. J Cell Sci 113, 1973-1984. (Pubitemid 30386501)
20. Funabiki H, Murray AW (2000). The Xenopus chromokinesin Xkid is essential for metaphase chromosome alignment and must be degraded to allow anaphase chromosome movement. Cell 102, 411-424.
21. Gergeley F, Karlsson C, Still I, Cowell J, Kilmartin J, Raff JW (2000). The TACC domain identifies a family of centrosomal proteins that can interact with microtubules. Proc Natl Acad Sci USA 97, 14352-14357. (Pubitemid 32016579)
22. Groen AC, Cameron LA, Coughlin M, Miyamoto DT, Mitchison TJ, Ohi R (2004). XRHAMM functions in ran-dependent microtubule nucleation and pole formation during anastral spindle assembly. Curr Biol 14, 1801-1811. (Pubitemid 39408769)
23. Groisman I, Huang YS, Mendez R, Cao Q, Theurkauf W, Richter JD (2000). CPEB, maskin, and cyclin B1 mRNA at the mitotic apparatus: implications for local translational control of cell division. Cell 103, 435-437.
24. Hannak E, Heald R (2006). Investigating mitotic spindle assembly and function in vitro using Xenopus laevis egg extracts. Nat Protoc 1, 2305-2314.
25. Hellsten U et al. (2010). The genome of the Western clawed frog Xenopus tropicalis. Science 328, 633-636.
26. Henschel A, Buchholz F, Habermann B (2004). DEQOR: a web-based tool for the design and quality control of siRNAs. Nucleic Acids Res 32, W113-W120. (Pubitemid 38997311)
27. Holt CE, Bullock SL (2009). Subcellular mRNA localization in animal cells and why it matters. Science 326, 1212-1216.
28. Huang DW, Sherman BT, Lempicki RA (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57.
29. Johnstone O, Lasko P (2001). Translational regulation and RNA localization in Drosophila oocytes and embryos. Annu Rev Genet 35, 365-406. (Pubitemid 34032981)
30. Kindler S, Wang H, Richter D, Tiedge H (2005). RNA transport and local control of translation. Annu Rev Cell Dev Biol 21, 223-245. (Pubitemid 41740634)
31. Kingsley EP, Chan XY, Duan Y, Lambert JD (2007). Widespread RNA segregation in a spiralian embryo. Evol Dev 9, 527-539. (Pubitemid 350045751)
32. Kislauskis EH, Zhu X, Singer RH (1997). β-Actin messenger RNA localization and protein synthesis augment cell motility. J Cell Biol 136, 1263-1270. (Pubitemid 27421914)
33. Kittler R et al. (2007). Genome-wide resources of endoribonuclease- prepared short interfering RNAs for specific loss-of-function studies. Nat Methods 4, 337-44. (Pubitemid 46766979)
34. Knorz VJ, Spalluto C, Lessard M, Purvis TL, Adigun FF, Collin GB, Hanley NA, Wilson DI, Hearn T (2010). Centriolar association of ALMS1 and likely centrosomal functions of the ALMS-motif-containing proteins C10orf90 and KIAA1731. Mol Biol Cell 21, 3617-3629.
35. Latham VM, Kislauskis EH, Singer RH, Ross AF (1994). Beta-actin mRNA localization is regulated by signal transduction mechanisms. J Cell Biol 126, 1211-1219.
36. Latham VM, Yu EH, Tullio AN, Adelstein RS, Singer RH (2001). A Rho-dependent signaling pathway operating through myosin localizes beta-actin mRNA in fibroblasts. Curr Biol 11, 1010-1016. (Pubitemid 32632715)
37. Lecuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, Krause HM (2007). Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131, 174-187. (Pubitemid 47498530)
38. Liu Y, Vikis HG, Yi Y, Futamura M, Wang Y, You M (2007). Degradation of lung adenoma susceptibility 1, a major candidate mouse lung tumor modifier, is required for cell cycle progression. Cancer Res 67, 10207-10213. (Pubitemid 350070793)
39. Lund E, Sheets MD, Imboden SB, Dahlberg JE (2011). Limiting Ago protein restricts RNAi and microRNA biogenesis during early development in Xenopus laevis. Genes Dev 25, 1121-1131.
40. Mackay AM, Eckley DM, Chue C, Earnshaw WC (1993). Molecular analysis of the INCENPs (inner centromere proteins): separate domains are required for association with microtubules during interphase and with the central spindle during anaphase. J Cell Biol 123, 373-385. (Pubitemid 23313962)
41. Martin KC, Ephrussi A (2009). mRNA localization: gene expression in the spatial dimension. Cell 136, 719-730.
42. Messitt TJ, Gagnon JA, Kreiling JA, Pratt CA, Yoon YJ, Mowry KM (2008). Multiple kinesin motors coordinate cytoplasmic RNA transport on a subpopulation of microtubules in Xenopus oocytes. Dev Cell 15, 426-436.
43. Miller S, Yasuda M, Coats JK, Jones Y, Martone ME, Mayford M (2002). Disruption of dendritic translation of CaMKIIa impairs stabilization of synaptic plasticity and memory consolidation. Neuron 36, 507-519. (Pubitemid 35291097)
44. Montero LP, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, Jacobs-Wagner C (2010). Spatial organization of the flow of genetic information in bacteria. Nature 466, 77-81.
45. Moser JJ, Fritzler MJ (2010). Cytoplasmic ribonucleoprotein (RNP bodies and their relationship to GW/P bodies. Int J Biochem Cell Biol 42, 828-843.
46. Oleynikov Y, Singer RH (2003). Real-time visualization of ZBP1 association with beta-actin mRNA during transcription and localization. Curr Biol 13, 199-207. (Pubitemid 36178297)
47. Pfaff KL, Straub CT, Chiang K, Bear DM, Zhou Y, Zon LI (2007). The Zebra fish cassiopeia mutant reveals that SIL is required for mitotic spindle organization. Mol Cell Biol 27, 5887-5897. (Pubitemid 47257841)
48. Prescott DM, Bender MA (1962). Synthesis of RNA and protein during mitosis in mammalian tissue culture cells. Exp Cell Res 26, 260-268.
49. Pyronnet S, Dostie J, Sonenberg N (2001). Suppression of cap-dependent translation in mitosis. Genes Dev 15, 2083-2093. (Pubitemid 32762052)
50. Pyronnet S, Pradayrol L, Sonenberg N (2000). A cell cycle-dependent internal ribosome entry site. Mol Cell 5, 607-616.
51. Raff JW, Whitfield WG, Glover DM (1990). Two distinct mechanisms localise cyclin B transcripts in syncytial Drosophila embryos. Development 110, 1249-1261. (Pubitemid 120009494)
52. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011). Integrative genomics viewer. Nat Biotechnol 29, 24-26.
53. Sampath SC, Ohi R, Leismann O, Salic A, Pozniakovski A, Funabiki H (2004). The chromosomal passenger complex is required for chromatin-induced microtubule stabilization and spindle assembly. Cell 118, 187-202. (Pubitemid 38962575)
54. Shestakova EA, Singer RH, Condeelis J (2001). The physiological significance of beta-actin mRNA localization in determining cell polarity and directional motility. Proc Natl Acad Sci USA 98, 7045-7050. (Pubitemid 32567900)
55. Stearns T, Kirschner M (1994). In vitro reconstitution of centrosome assembly and function: the central role of γ-tubulin. Cell 76, 623-637. (Pubitemid 24070648)
56. Sundell CL, Singer RH (1991). Requirement of microfilaments in sorting of actin messenger RNA. Science 253, 1275-1277. (Pubitemid 21917276)
57. Suprenant KA (1993). Microtubules, ribosomes, and RNA: evidence for cytoplasmic localization and translational regulation. Cell Motil Cytoskeleton 179, 1365-1373.
58. Trapnell C, Pachter L, Salzberg SL (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111.
59. Wang Z, Gerstein M, Snyder M (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10, 57-63.
60. Weil TT, Forrest KM, Gavis ER (2006). Localization of bicoid mRNA in late oocytes is maintained by continual active transport. Dev Cell 11, 251-262. (Pubitemid 44138499)
61. Wilker EW et al. (2007). 14-3-3sigma controls mitotic translation to facilitate cytokinesis. Nature 446, 329-332. (Pubitemid 46426148)
62. Wittman T, Wilm M, Karsenti E, Vernos I (2000). TPX2, a novel Xenopus MAP involved in spindle pole organization. J Cell Biol 149, 1405-1418. (Pubitemid 30437615)
63. Yang CH, Lambie EJ, Snyder M (1992). NuMA: an unusually long coiled-coil related protein in the mammalian nucleus. J Cell Biol 116, 1303-1317.
64. Yang D, Buchholz F, Huang Z, Goga A, Chen C, Brodsky FM, Bishop JM (2002). Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc Natl Acad Sci USA 99, 9942-9947. (Pubitemid 34831152)
65. Yang Z, Jakymiw A, Wood MR, Eystathioy T, Rubin RL, Fritzler MJ, Chan EKL (2004). Gw182 is critical for the stability of GW bodies expressed during the cell cycle and cell proliferation. J Cell Sci 117, 5567-5578. (Pubitemid 40012203)
66. Yin Y et al. (2009). The Talpid3 gene (KIAA0586) encodes a centrosomal protein that is essential for primary cilia formation. Development 136, 655-664.
67. Yisraeli JK, Sokol S, Melton DA (1990). A two-step model for the localization of maternal mRNA in Xenopus oocytes: involvement of microtubules and microfilaments in the translocation and anchoring of Vg1 mRNA. Development 108, 289-298.
68. Zimyanin VL, Belaya K, Pecreaux P, Gilchrist MJ, Clark A, Davis I, St Johnston D (2008). In vivo imaging of oskar mRNA transport reveals the mechanism of posterior localization. Cell 134, 843-853.