S-5
References for Supplementary
Archer, S. K., Inchaustegui, D., Queiroz, R. &Clayton, C. (2011). The cell cycle regulated transcriptome of Trypanosoma brucei. PLoS One 6(3): e18425.
Barth, S., Shalem, B., Hury, A., Tkacz, I. D., Liang, X. H., Uliel, S., Myslyuk, I., Doniger, T., Salmon-Divon, M., Unger, R. &Michaeli, S. (2008). Elucidating the role of C/D snoRNA in rRNA processing and modification in Trypanosoma brucei. Eukaryot Cell 7(1): 86-101.
Bates, E. J., Knuepfer, E. &Smith, D. F. (2000). Poly(A)-binding protein I of Leishmania: functional analysis and localisation in trypanosomatid parasites. Nucleic Acids Res 28(5): 1211-1220.
Batista, J. A., Teixeira, S. M., Donelson, J. E., Kirchhoff, L. V. &de Sa, C. M. (1994). Characterization of a Trypanosoma cruzi poly(A)-binding protein and its genes. Mol Biochem Parasitol 67(2): 301-312.
Blom, D., Burg, J., Breek, C. K., Speijer, D., Muijsers, A. O. &Benne, R. (2001). Cloning and characterization of two guide RNA-binding proteins from mitochondria of Crithidia fasciculata: gBP27, a novel protein, and gBP29, the orthologue of Trypanosoma brucei gBP21. Nucleic Acids Res 29(14): 2950-2962.
D'Orso, I. &Frasch, A. C. (2001). TcUBP-1, a developmentally regulated U-rich RNA-binding protein involved in selective mRNA destabilization in trypanosomes. J Biol Chem 276(37): 34801-34809.
D'Orso, I. &Frasch, A. C. (2002). TcUBP-1, an mRNA destabilizing factor from trypanosomes, homodimerizes and interacts with novel AU-rich element- and Poly(A)-binding proteins forming a ribonucleoprotein complex. J Biol Chem 277(52): 50520-50528.
De Gaudenzi, J., Frasch, A. C. &Clayton, C. (2005). RNA-binding domain proteins in Kinetoplastids: a comparative analysis. Eukaryot Cell 4(12): 2106-2114.
Dunbar, D. A., Wormsley, S., Lowe, T. M. &Baserga, S. J. (2000). Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei. Sequence conservation and implications for 2'-O-ribose methylation of rRNA. J Biol Chem 275(19): 14767-14776.
Holetz, F. B., Correa, A., Avila, A. R., Nakamura, C. V., Krieger, M. A. &Goldenberg, S. (2007). Evidence of P-body-like structures in Trypanosoma cruzi. Biochem Biophys Res Commun 356(4): 1062-1067.
Hotchkiss, T. L., Nerantzakis, G. E., Dills, S. C., Shang, L. &Read, L. K. (1999). Trypanosoma brucei poly(A) binding protein I cDNA cloning, expression, and binding to 5 untranslated region sequence elements. Mol Biochem Parasitol 98(1): 117-129.
Ismaili, N., Perez-Morga, D., Walsh, P., Cadogan, M., Pays, A., Tebabi, P. &Pays, E. (2000). Characterization of a Trypanosoma brucei SR domain-containing protein bearing homology to cis-spliceosomal U1 70 kDa proteins. Mol Biochem Parasitol 106(1): 109-120.
Jensen, B. C., Sivam, D., Kifer, C. T., Myler, P. J. &Parsons, M. (2009). Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei. BMC Genomics 10: 482.
Jensen, B. C., Wang, Q., Kifer, C. T. &Parsons, M. (2003). The NOG1 GTP-binding protein is required for biogenesis of the 60 S ribosomal subunit. J Biol Chem 278(34): 32204-32211.
Kabani, S., Fenn, K., Ross, A., Ivens, A., Smith, T. K., Ghazal, P. &Matthews, K. (2009). Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei. BMC Genomics 10: 427.
Kolev, N. G., Franklin, J. B., Carmi, S., Shi, H., Michaeli, S. &Tschudi, C. (2010). The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog 6(9): e1001090.
Manful, T., Fadda, A. &Clayton, C. (2011). The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA degradation. RNA 17(11): 2039-2047.
Nilsson, D., Gunasekera, K., Mani, J., Osteras, M., Farinelli, L., Baerlocher, L., Roditi, I. &Ochsenreiter, T. (2010). Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei. PLoS Pathog 6(8): e1001037.
Prohaska, K. &Williams, N. (2009). Assembly of the Trypanosoma brucei 60S ribosomal subunit nuclear export complex requires trypanosome-specific proteins P34 and P37. Eukaryot Cell 8(1): 77-87.
Queiroz, R., Benz, C., Fellenberg, K., Hoheisel, J. D. &Clayton, C. (2009). Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons. BMC Genomics 10: 495.
Read, L. K., Goringer, H. U. &Stuart, K. (1994). Assembly of mitochondrial ribonucleoprotein complexes involves specific guide RNA (gRNA)-binding proteins and gRNA domains but does not require preedited mRNA. Mol Cell Biol 14(4): 2629-2639.
Tanaka, K. J., Ogawa, K., Takagi, M., Imamoto, N., Matsumoto, K. &Tsujimoto, M. (2006). RAP55, a cytoplasmic mRNP component, represses translation in Xenopus oocytes. J Biol Chem 281(52): 40096-40106.
Tkacz, I. D., Gupta, S. K., Volkov, V., Romano, M., Haham, T., Tulinski, P., Lebenthal, I. &Michaeli, S. (2010). Analysis of spliceosomal proteins in Trypanosomatids reveals novel functions in mRNA processing. J Biol Chem 285(36): 27982-27999.
Vazquez, M. P., Mualem, D., Bercovich, N., Stern, M. Z., Nyambega, B., Barda, O., Nasiga, D., Gupta, S. K., Michaeli, S. &Levin, M. J. (2009). Functional characterization and protein-protein interactions of trypanosome splicing factors U2AF35, U2AF65 and SF1. Mol Biochem Parasitol 164(2): 137-146.
Volpon, L., D'Orso, I., Young, C. R., Frasch, A. C. &Gehring, K. (2005). NMR structural study of TcUBP1, a single RRM domain protein from Trypanosoma cruzi: contribution of a beta hairpin to RNA binding. Biochemistry 44(10): 3708-3717.
Vondruskova, E., van den Burg, J., Zikova, A., Ernst, N. L., Stuart, K., Benne, R. &Lukes, J. (2005). RNA interference analyses suggest a transcript-specific regulatory role for mitochondrial RNA-binding proteins MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei. J Biol Chem 280(4): 2429-2438.
Winstall, E., Sadowski, M., Kuhn, U., Wahle, E. &Sachs, A. B. (2000). The Saccharomyces cerevisiae RNA-binding protein Rbp29 functions in cytoplasmic mRNA metabolism. J Biol Chem 275(29): 21817-21826.