References
- Ahn, S.J., Kim, N.Y., Seo, J.S., Je, J.E., Sung, J.H., Lee, S.H., Kim, M.S., Kim, J.K., Chung, J.K., and Lee, H.H. (2009). Molecular cloning, mRNA expression and enzymatic characterization of cathepsin F from olive flounder (Paralichthys olivaceus). Comp. Biochem. Physiol. B Biochem. Mol. Biol. 154, 211-220. https://doi.org/10.1016/j.cbpb.2009.06.005
- Amit, M., Sela, N., Keren, H., Melamed, Z., Muler, I., Shomron, N., Izraeli, S., and Ast, G. (2007). Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene. BMC Mol. Biol. 8, 109. https://doi.org/10.1186/1471-2199-8-109
- Ast, G. (2004). How did alternative splicing evolve? Nat. Rev. Genet. 5, 773-782.
- Bannert, N. and Kurth, R. (2004). Retroelements and the human genome: new perspectives on an old relation. Proc. Natl. Acad. Sci. USA 101, 14572-14579. https://doi.org/10.1073/pnas.0404838101
- Carlsson, H.E., Schapiro, S.J., Farah, I., and Hau, J. (2004). Use of primates in research: a global overview. Am. J. Primatol. 63, 225-237. https://doi.org/10.1002/ajp.20054
- Chapman, H.A., Riese, R.J., and Shi, G.P. (1997). Emerging roles for cysteine proteases in human biology. Annu. Rev. Physiol. 59, 63-88. https://doi.org/10.1146/annurev.physiol.59.1.63
- Chen, M., and Manley, J.L. (2009). Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol. 10, 741-754. https://doi.org/10.1038/nrm2777
- Chou, H.H., Hayakawa, T., Diaz, S., Krings, M., Indriati, E., Leakey, M., Paabo, S., Satta, Y., Takahata, N., and Varki, A. (2002). Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution. Proc. Natl. Acad. Sci. USA 99, 11736-11741. https://doi.org/10.1073/pnas.182257399
- Cowley, M., and Oakey, R.J. (2013). Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet. 9, e1003234. https://doi.org/10.1371/journal.pgen.1003234
- Dagan, T., Sorek, R., Sharon, E., Ast, G., and Graur, D. (2004). AluGene: a database of Alu elements incorporated within proteincoding genes. Nucleic Acids Res. 32, D489-492. https://doi.org/10.1093/nar/gkh132
- DeBarry, J.D., Ganko, E.W., McCarthy, E.M., and McDonald, J.F. (2006). The contribution of LTR retrotransposon sequences to gene evolution in Mus musculus. Mol. Biol. Evol. 23, 479-481. https://doi.org/10.1093/molbev/msj076
- Deininger, P.L., and Batzer, M.A. (1999). Alu repeats and human disease. Mol. Genet. Metab. 67, 183-193. https://doi.org/10.1006/mgme.1999.2864
- Duke-Cohan, J.S., Gu, J., McLaughlin, D.F., Xu, Y., Freeman, G.J., and Schlossman, S.F. (1998). Attractin (DPPT-L), a member of the CUB family of cell adhesion and guidance proteins, is secreted by activated human T lymphocytes and modulates immune cell interactions. Proc. Natl. Acad. Sci. USA 95, 11336-11341. https://doi.org/10.1073/pnas.95.19.11336
- Gal-Mark, N., Schwartz, S., and Ast, G. (2008). Alternative splicing of Alu exons--two arms are better than one. Nucleic Acids Res. 36, 2012-2023. https://doi.org/10.1093/nar/gkn024
- Guicciardi, M.E., Leist, M., and Gores, G.J. (2004). Lysosomes in cell death. Oncogene 23, 2881-2890. https://doi.org/10.1038/sj.onc.1207512
- Han, K., Konkel, M.K., Xing, J., Wang, H., Lee, J., Meyer, T.J., Huang, C.T., Sandifer, E., Hebert, K., Barnes, E.W., et al. (2007a). Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome. Science 316, 238-240. https://doi.org/10.1126/science.1139462
- Han, K., Lee, J., Meyer, T.J., Wang, J., Sen, S.K., Srikanta, D., Liang, P., and Batzer, M.A. (2007b). Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genet. 3, 1939-1949.
- Hilgard, P., Huang, T., Wolkoff, A.W., and Stockert, R.J. (2002). Translated Alu sequence determines nuclear localization of a novel catalytic subunit of casein kinase 2. Am. J. Physiol. Cell Physiol. 283, C472-483. https://doi.org/10.1152/ajpcell.00070.2002
- Huh, J.W., Kim, Y.H., Park, S.J., Kim, D.S., Lee, S.R., Kim, K.M., Jeong, K.J., Kim, J.S., Song, B.S., Sim, B.W., et al. (2012). Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (Macaca fascicularis) for biomedical research. BMC Genomics 13, 163. https://doi.org/10.1186/1471-2164-13-163
- Jeric, B., Dolenc, I., Mihelic, M., Klaric, M., Zavasnik-Bergant, T., Guncar, G., Turk, B., Turk, V. and Stoka, V. (2013). N-terminally truncated forms of human cathepsin F accumulate in aggresome-like inclusions. Biochim. Biophys. Acta 1833, 2254-2266. https://doi.org/10.1016/j.bbamcr.2013.05.007
- Kim, T., Kim, J.O., Oh, J.G., Hong, S.E., and Kim do, H. (2014). Pressure-overload cardiac hypertrophy is associated with distinct alternative splicing due to altered expression of splicing factors. Mol. Cells 37, 81-87. https://doi.org/10.14348/molcells.2014.2337
- Kim, Y.H., Choe, S.H., Song, B.S., Park, S.J., Kim, M.J., Park, Y.H., Yoon, S.B., Lee, Y., Jin, Y.B., Sim, B.W., et al. (2016). Macaca specific exon creation event generates a novel ZKSCAN5 transcript. Gene 577, 236-243. https://doi.org/10.1016/j.gene.2015.11.051
- Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921. https://doi.org/10.1038/35057062
- Lee, J.R., Huh, J.W., Kim, D.S., Ha, H.S., Ahn, K., Kim, Y.J., Chang, K.T., and Kim, H.S. (2009). Lineage specific evolutionary events on SFTPB gene: Alu recombination-mediated deletion (ARMD), exonization, and alternative splicing events. Gene 435, 29-35. https://doi.org/10.1016/j.gene.2009.01.008
- Lev-Maor, G., Sorek, R., Shomron, N., and Ast, G. (2003). The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science 300, 1288-1291. https://doi.org/10.1126/science.1082588
- Li, J., Han, K., Xing, J., Kim, H.S., Rogers, J., Ryder, O.A., Disotell, T., Yue, B., and Batzer, M.A. (2009). Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 448, 242-249. https://doi.org/10.1016/j.gene.2009.05.013
- Luco, R.F., Pan, Q., Tominaga, K., Blencowe, B.J., Pereira-Smith, O.M., and Misteli, T. (2010). Regulation of alternative splicing by histone modifications. Science 327, 996-1000. https://doi.org/10.1126/science.1184208
- Mersch, B., Sela, N., Ast, G., Suhai, S., and Hotz-Wagenblatt, A. (2007). SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements. BMC Genet. 8, 78.
- Mola, G., Vela, E., Fernandez-Figueras, M.T., Isamat, M., and Munoz-Marmol, A.M. (2007). Exonization of Alu-generated splice variants in the survivin gene of human and non-human primates. J. Mol. Biol. 366, 1055-1063. https://doi.org/10.1016/j.jmb.2006.11.089
- Pan, Q., Shai, O., Lee, L.J., Frey, B.J., and Blencowe, B.J. (2008). Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415. https://doi.org/10.1038/ng.259
- Park, S.J., Kim, Y.H., Lee, S.R., Choe, S.H., Kim, M.J., Kim, S.U., Kim, J.S., Sim, B.W., Song, B.S., Jeong, K.J., et al. (2015a). Gain of a new exon by a lineage-specific Alu element-integration event in the BCS1L gene during primate evolution. Mol. Cells 38, 950-958. https://doi.org/10.14348/molcells.2015.0121
- Park, S.J., Kim, Y.H., Nam, G.H., Choe, S.H., Lee, S.R., Kim, S.U., Kim, J.S., Sim, B.W., Song, B.S., Jeong, K.J., et al. (2015b). Quantitative expression analysis of APP pathway and tau phosphorylation-related genes in the ICV STZ-induced non-human primate model of sporadic Alzheimer's disease. Int. J. Mol. Sci. 16, 2386-2402. https://doi.org/10.3390/ijms16022386
- Peters, J., Rittger, A., Weisner, R., Knabbe, J., Zunke, F., Rothaug, M., Damme, M., Berkovic, S.F., Blanz, J., Saftig, P., et al. (2015). Lysosomal integral membrane protein type-2 (LIMP-2/SCARB2). is a substrate of cathepsin-F, a cysteine protease mutated in type-B-Kufsdisease. Biochem. Biophys. Res. Commun. 457, 334-340. https://doi.org/10.1016/j.bbrc.2014.12.111
- Repnik, U., Stoka, V., Turk, V. and Turk, B. (2012). Lysosomes and lysosomal cathepsins in cell death. Biochim. Biophys. Acta 1824, 22-33. https://doi.org/10.1016/j.bbapap.2011.08.016
- Rhesus Macaque Genome, S., Analysis, C., Gibbs, R.A., Rogers, J., Katze, M.G., Bumgarner, R., Weinstock, G.M., Mardis, E.R., Remington, K.A., Strausberg, R.L., et al. (2007). Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-234. https://doi.org/10.1126/science.1139247
- Rossi, A., Deveraux, Q., Turk, B., and Sali, A. (2004). Comprehensive search for cysteine cathepsins in the human genome. Biol. Chem. 385, 363-372.
- Schmitz, J., and Brosius, J. (2011). Exonization of transposed elements: A challenge and opportunity for evolution. Biochimie 93, 1928-1934. https://doi.org/10.1016/j.biochi.2011.07.014
- Smith, K.R., Dahl, H.H., Canafoglia, L., Andermann, E., Damiano, J., Morbin, M., Bruni, A.C., Giaccone, G., Cossette, P., Saftig, P., et al. (2013). Cathepsin F mutations cause Type B Kufs disease, an adultonset neuronal ceroid lipofuscinosis. Hum. Mol. Genet. 22, 1417-1423. https://doi.org/10.1093/hmg/dds558
- Sorek, R., Ast, G. and Graur, D. (2002). Alu-containing exons are alternatively spliced. Genome Res. 12, 1060-1067. https://doi.org/10.1101/gr.229302
- Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729. https://doi.org/10.1093/molbev/mst197
- Tang, C.H., Lee, J.W., Galvez, M.G., Robillard, L., Mole, S.E., and Chapman, H.A. (2006). Murine cathepsin F deficiency causes neuronal lipofuscinosis and late-onset neurological disease. Mol. Cell Biol. 26, 2309-2316. https://doi.org/10.1128/MCB.26.6.2309-2316.2006
- Turk, V., Stoka, V., Vasiljeva, O., Renko, M., Sun, T., Turk, B., and Turk, D. (2012). Cysteine cathepsins: from structure, function and regulation to new frontiers. Biochim. Biophys. Acta 1824, 68-88. https://doi.org/10.1016/j.bbapap.2011.10.002
- Vazquez-Ortiz, G., Pina-Sanchez, P., Vazquez, K., Duenas, A., Taja, L., Mendoza, P., Garcia, J.A., and Salcedo, M. (2005). Overexpression of cathepsin F, matrix metalloproteinases 11 and 12 in cervical cancer. BMC Cancer 5, 68. https://doi.org/10.1186/1471-2407-5-68
- Zhang, X.H., and Chasin, L.A. (2006). Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc. Natl. Acad. Sci. USA 103, 13427-13432. https://doi.org/10.1073/pnas.0603042103
Cited by
- Reference values of hematological and biochemical parameters in young-adult cynomolgus monkey ( Macaca fascicularis ) and rhesus monkey ( Macaca mulatta ) anesthetized with ketamine hydrochloride vol.35, pp.None, 2017, https://doi.org/10.1186/s42826-019-0006-0
- Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene vol.19, pp.1, 2017, https://doi.org/10.1186/s12862-019-1530-0
- Sense-oriented Alu YRa1 elements provide a lineage-specific transcription environment for polyadenylation vol.11, pp.1, 2017, https://doi.org/10.1038/s41598-021-83360-4