Integral Nuclear Pore Proteins Bind to Pol III-Transcribed Genes and Are Required for Pol III Transcript Processing in C. elegans

Molecular Cell

Volumn 51, Issue 6, 2013, Pages 840-849

  Ikegami, Kohta ^a   Lieb, JasonD ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; ENDONUCLEASE; GLYCINE TRANSFER RNA; KARYOPHERIN BETA; NUCLEOPORIN; NUCLEOPORIN 13; NUCLEOPORIN 3; RNA POLYMERASE II; SMALL NUCLEOLAR RNA; TRANSFER RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; CAENORHABDITIS ELEGANS; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; EMBRYO; ENZYME ACTIVITY; GENE SILENCING; HIGH THROUGHPUT SEQUENCING; NONHUMAN; NUCLEAR PORE; PROTEIN BINDING; RNA PROCESSING; TRANSCRIPTION REGULATION; WILD TYPE; YEAST;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; KARYOPHERINS; NUCLEAR PORE; NUCLEAR PORE COMPLEX PROTEINS; RNA POLYMERASE III; RNA, SMALL NUCLEOLAR; RNA, TRANSFER; TRANSCRIPTION, GENETIC;

CAENORHABDITIS ELEGANS;

EID: 84884596364     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2013.08.001     Document Type: Article

References (32)

1. Akhtar A., Gasser S.M. The nuclear envelope and transcriptional control. Nat. Rev. Genet. 2007, 8:507-517.
2. Alber F., Dokudovskaya S., Veenhoff L.M., Zhang W., Kipper J., Devos D., Suprapto A., Karni-Schmidt O., Williams R., Chait B.T., et al. The molecular architecture of the nuclear pore complex. Nature 2007, 450:695-701.
3. Barbezier N., Canino G., Rodor J., Jobet E., Saez-Vasquez J., Marchfelder A., Echeverría M. Processing of a dicistronic tRNA-snoRNA precursor: combined analysis invitro and invivo reveals alternate pathways and coupling to assembly of snoRNP. Plant Physiol. 2009, 150:1598-1610.
4. Bayliss R., Littlewood T., Stewart M. Structural basis for the interaction between FxFG nucleoporin repeats and importin-beta in nuclear trafficking. Cell 2000, 102:99-108.
5. Blobel G. Gene gating: a hypothesis. Proc. Natl. Acad. Sci. USA 1985, 82:8527-8529.
6. Brown C.R., Kennedy C.J., Delmar V.A., Forbes D.J., Silver P.A. Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. Genes Dev. 2008, 22:627-639.
7. Capelson M., Liang Y., Schulte R., Mair W., Wagner U., Hetzer M.W. Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell 2010, 140:372-383.
8. Castaño J.G., Tobian J.A., Zasloff M. Purification and characterization of an endonuclease from Xenopus laevis ovaries which accurately processes the 3' terminus of human pre-tRNA-Met(i) (3' pre-tRNase). J.Biol. Chem. 1985, 260:9002-9008.
9. Cohen M., Tzur Y.B., Neufeld E., Feinstein N., Delannoy M.R., Wilson K.L., Gruenbaum Y. Transmission electron microscope studies of the nuclear envelope in Caenorhabditis elegans embryos. J.Struct. Biol. 2002, 140:232-240.
10. Egloff S., Murphy S. Cracking the RNA polymerase II CTD code. Trends Genet. 2008, 24:280-288.
11. Fernández-Tornero C., Böttcher B., Rashid U.J., Steuerwald U., Flörchinger B., Devos D.P., Lindner D., Müller C.W. Conformational flexibility of RNA polymerase III during transcriptional elongation. EMBO J. 2010, 29:3762-3772.
12. Frenkiel-Krispin D., Maco B., Aebi U., Medalia O. Structural analysis of a metazoan nuclear pore complex reveals a fused concentric ring architecture. J.Mol. Biol. 2010, 395:578-586.
13. Galy V., Mattaj I.W., Askjaer P. Caenorhabditis elegans nucleoporins Nup93 and Nup205 determine the limit of nuclear pore complex size exclusion invivo. Mol. Biol. Cell 2003, 14:5104-5115.
14. Grandi P., Dang T., Pané N., Shevchenko A., Mann M., Forbes D., Hurt E. Nup93, a vertebrate homologue of yeast Nic96p, forms a complex with a novel 205-kDa protein and is required for correct nuclear pore assembly. Mol. Biol. Cell 1997, 8:2017-2038.
15. Grossman E., Medalia O., Zwerger M. Functional architecture of the nuclear pore complex. Annu. Rev. Biophys. 2012, 41:557-584.
16. Hachet V., Busso C., Toya M., Sugimoto A., Askjaer P., Gönczy P. The nucleoporin Nup205/NPP-3 is lost near centrosomes at mitotic onset and can modulate the timing of this process in Caenorhabditis elegans embryos. Mol. Biol. Cell 2012, 23:3111-3121.
17. Ikegami K., Egelhofer T.A., Strome S., Lieb J.D. Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. Genome Biol. 2010, 11:R120. 10.1186/gb-2010-11-12-r120.
18. Kalverda B., Pickersgill H., Shloma V.V., Fornerod M. Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 2010, 140:360-371.
19. Krull S., Thyberg J., Björkroth B., Rackwitz H.-R., Cordes V.C. Nucleoporins as components of the nuclear pore complex core structure andTpr as the architectural element of the nuclear basket. Mol. Biol. Cell 2004, 15:4261-4277.
20. Kruszka K., Barneche F., Guyot R., Ailhas J., Meneau I., Schiffer S., Marchfelder A., Echeverría M. Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by RNase Z. EMBO J. 2003, 22:621-632.
21. Lee C.Y., Lee A., Chanfreau G. The roles of endonucleolytic cleavage and exonucleolytic digestion in the 5'-end processing of S. cerevisiae box C/D snoRNAs. RNA 2003, 9:1362-1370.
22. Li T., He H., Wang Y., Zheng H., Skogerbø G., Chen R. Invivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs. BMC Mol. Biol. 2008, 9:71.
23. Noma K.-I., Cam H.P., Maraia R.J., Grewal S.I.S. A role for TFIIIC transcription factor complex in genome organization. Cell 2006, 125:859-872.
24. Rabut G., Doye V., Ellenberg J. Mapping the dynamic organization of the nuclear pore complex inside single living cells. Nat. Cell Biol. 2004, 6:1114-1121.
25. Ródenas E., González-Aguilera C., Ayuso C., Askjaer P. Dissection of the NUP107 nuclear pore subcomplex reveals a novel interaction with spindle assembly checkpoint protein MAD1 in Caenorhabditis elegans. Mol. Biol. Cell 2012, 23:930-944.
26. Rohner S., Kalck V., Wang X., Ikegami K., Lieb J.D., Gasser S.M., Meister P. Promoter- and RNA polymerase II-dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans. J.Cell Biol. 2013, 200:589-604.
27. Savas J.N., Toyama B.H., Xu T., Yates J.R., Hetzer M.W. Extremely long-lived nuclear pore proteins in the rat brain. Science 2012, 335:942.
28. Schrader N., Stelter P., Flemming D., Kunze R., Hurt E., Vetter I.R. Structural basis of the nic96 subcomplex organization in the nuclear pore channel. Mol. Cell 2008, 29:46-55.
29. Schramm L., Hernandez N. Recruitment of RNA polymerase III to its target promoters. Genes Dev. 2002, 16:2593-2620.
30. Strambio-De-Castillia C., Niepel M., Rout M.P. The nuclear pore complex: bridging nuclear transport and gene regulation. Nat. Rev. Mol. Cell Biol. 2010, 11:490-501.
31. Vaquerizas J.M., Suyama R., Kind J., Miura K., Luscombe N.M., Akhtar A. Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome. PLoS Genet. 2010, 6:e1000846. 10.1371/journal.pgen.1000846.
32. Xiao T., Wang Y., Luo H., Liu L., Wei G., Chen X., Sun Y., Chen X., Skogerbø G., Chen R. A differential sequencing-based analysis of the C. elegans noncoding transcriptome. RNA 2012, 18:626-639.