A Bioinformatic Search for Nucleoporin Regulators

Transcript

1. A Bioinformatic Search for Nucleoporin Regulators David Barsky
2. Nuclear Pore Complexes (NPC) are large protein complexes embedded in the nuclear envelope that mediate the movement of macromolecules between the nucleus and the cytoplasm [1]. Review of Literature
3. A notable subcomplex, the Y-complex, forms the structural scaffold of the NPC and is believed to be involved in mRNA export [2], nuclear pore assembly [3], and cell division [4]. Review of Literature
4. Components (known as nucleoporins) of the Y- complex are very stable in adult animals, suggesting that they may be transcribed primarily in dividing stem and progenitor cells during development [5]. Introduction
5. In the absence of NUP133 (A member of the Y- complex), neural progenitor cells are blocked from completing differentiation, and mutant embryos die between embryonic day E9.5 and E10.5 [6]. Review of Literature
6. Using bioinformatic technologies, transcriptional regulators of nucleoporins would be identified. Research Goals
7. •The initial focus was on genomic sequences 2000 base pairs upstream of each nucleoporin gene and in the 5' untranslated regions. Methods
8. •The University of California, Santa Cruz (UCSC) genome browser was used to examine the upstream and 5’ UTR segments sequence conservation, searching specifically for transcription factor binding sites. Methods
9. •The University of California, Santa Cruz (UCSC) genome browser was used to examine the upstream and 5’ UTR segments sequence conservation, searching specifically for transcription factor binding sites. Methods
10. •Transfac determined where transcription factors bound upstream of nucleoporins. From there, it was decided to focus on the NUP107–160 subcomplex members due to extensive research on its functionality. Methods
11. •For all conclusions, the minSUM stringency was used. Mouse Genome Informatics (MGI) was used to collect information regarding each transcription factor’s expression pattern and the phenotype associated with its genetic knockout. Methods
12. Results (Human)
13. Results (Mouse)
14. •The presence of RFX1 and YY1 binding sites upstream of members of the NUP107–160 subcomplex suggest that RFX1 and YY1 might regulate the expression of NUP107–160. •RFX1 and YY1 are expressed early in development, primarily in embryonic stem cells, and are critical for development. Discussion
15. •RFX1 and YY1 could be knocked out, and the resulting embryos could be analyzed for the presence of members of the NUP107–160 subcomplex. If a nucleoporin is missing, it would indicate that RFX1 and YY1 regulate that specific nucleoporin’s expression. Future Research
16. 1. Feldherr CM. 1962. The nuclear annuli as pathways for nucleocytoplasmic exchanges. J.Cell Biol.14:65–72 2. Vasu, S., Shah, S., Orjalo, A., Park, M., Fischer, W.H., and Forbes, D.J. (2001). Novel vertebrate nucleoporins Nup133 and Nup160 play a role in mRNA export. J. Cell Biol. 155, 339–353. 3. Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E: Modular self-assembly of a Y- shaped multi protein complex from seven nucleoporins. EMBO J 2002, 21:387-397. 4. Khmelinskii A, Meurer M, Knop M, Schiebel E: Artificial tethering to nuclear pores promotes partitioning of extrachromosomal DNA during yeast asymmetric cell division. Curr Biol 2011, 21:R17-R18. 5. D’Angelo MA, Raices M, Panowski SH, Hetzer MW: Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in post mitotic cells. Cell 2009, 136:284-295. 6. Lupu, F., Alves, A., Anderson, K., Doye, V., and Lacy, E. (2008). Nuclear pore composition regulates neural stem/progenitor cell differentiation in the mouse embryo. Dev. Cell 14, 831–842. References