Abstract
Cellular organelle fractionation, a basic technique in molecular biology, has been devised to separate various cell components, which can then be purified and analyzed biochemically. Isolation of proteins or RNAs from these fractions provides insight into fraction-specific or even organelle-specific expression, which may indicate potential modes of functionality or likelihood for a transcript to encode a protein. These findings can be further utilized to observe differences in expression between normal and diseased cell states, such as cancer. We utilize these techniques to observe expression of chimeric RNAs in these fractions. Within this chapter we describe the most frequently used cellular fractionation technique: the separation of the cytoplasmic fraction from the nuclear fraction in a cell.
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References
Yates JR 3rd, Gilchrist A, Howell KE, Bergeron JJ (2005) Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol 6:702–714
Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS, Trotter MW (2013) The effect of organelle discovery upon sub-cellular protein localisation. J Proteome 88:129–140
Dreger M (2003) Proteome analysis at the level of subcellular structures. Eur J Biochem 270:589–599
Chandramouli K, Qian PY (2009) Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. Hum Genomics Proteomics 2009
Qin F, Song Z, Babiceanu M, Song Y, Facemire L, Singh R, Adli M, Li H (2015) Discovery of CTCF-sensitive Cis-spliced fusion RNAs between adjacent genes in human prostate cells. PLoS Genet 11:e1005001
Qin F, Zhang Y, Liu J, Li H (2017) SLC45A3-ELK4 functions as a long non-coding chimeric RNA. Cancer Lett 404:53–61
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Qin, F., Shi, X., Li, H. (2020). Separation of Nuclear and Cytoplasmic Fractions for Chimeric RNA Characterization. In: Li, H., Elfman, J. (eds) Chimeric RNA. Methods in Molecular Biology, vol 2079. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9904-0_13
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DOI: https://doi.org/10.1007/978-1-4939-9904-0_13
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Publisher Name: Humana, New York, NY
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Online ISBN: 978-1-4939-9904-0
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