Multiple-choice questions

Questions for Discussion

1. As per RNA world hypothesis, RNA was the first nucleic acid to be originated to encode genetic information and was then replaced by DNA. A uniform feature of all living organisms is the use of DNA as the genetic material. Discuss the advantages and disadvantages of using DNA as the macromolecule to store genetic information.
2. Discovery of non-coding RNA in gene regulation changed the definition of a gene as a unit DNA that encodes a functional product. Discuss the advantages and disadvantages of using non-coding RNA to regulate gene expression.
3. Several high throughput molecular techniques are used in clinical diagnosis of diseases such as cancer. Discuss the advantages and disadvantages of using expression and gene arrays as diagnosis tools.
4. Discuss the disadvantages and problems of using qRT-PCR to detect and diagnose infectious diseases.
5. Discuss advantages and disadvantages of using siRNA and other non-coding RNA as therapeutics to treat chronic diseases such as cancer.

Further Reading

1.1 The protein content of different cell types is different

Gershoni JM & Palade GE (1983) Protein blotting: principles and applications. Anal Biochem 131:1–15.

Kislinger T, Cox B, Kannan A et al. (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125:173–186.

O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007–4021.

Xie F, Liu T, Qian W-J et al. (2011) Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem 286:25443–25449.

1.2 The mRNA content of different cell types is different

Lockhart DJ & Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature 405:827–836.

Thomas PS (1980) Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose. Proc Natl Acad Sci USA 77:5201–5205.

1.3 The DNA content of different cell types is generally the same

Claycomb JM & Orr-Weaver TL (2005) Developmental gene amplification: insights into DNA replication and gene expression. Trends Genet 21:149–162.

Gurdon JB (2006) From nuclear transfer to nuclear reprogramming: the reversal of cell differentiation. Annu Rev Cell Dev Biol 22:1–22.

Gurdon JB & Melton DA (2008) Nuclear reprogramming in cells. Science 322:1811–1815.

Ji P, Murata-Hori M & Lodish HF (2011) Formation of mammalian erythrocytes: chromatin condensation and enucleation. Trends Cell Biol 21:409–415.

Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517.

Steward FC (1970) From cultured cells to whole plants: the induction and control of their growth and morphogenesis. Proc R Soc Series B 175:1–30.

Wilmut I, Schnieke AE, McWhis J et al. (1997) Viable offspring derived from fetal and adult mammalian cells. Nature 385:810–813.

1.4 Transcriptional or post-transcriptional control?

Derman E, Krauter K, Walling L et al. (1981) Transcriptional control in the production of liver specific mRNAs. Cell 23:731–739.

Ecker JR, Bickmore WA, Barroso A et al. (2012) ENCODE explained. Nature 489:52–55.

The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74.

1.5 Regulatory RNAs and the regulation of gene expression

Ameres SL & Zamore PD (2013) Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol 14:475–488.

Chen X, Liang H, Zhan J et al. (2012) Secreted microRNAs: a new form of intercellular communication. Trends Cell Biol 22:125–132.

Gebert LFR and MacRae IJ (2019) Regulation of microRNA function in animals. Nature Reviews Molecular Cell Biology 20,21-37

Geisler S & Coller J (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 14:699–712.

Gil N and Ulitsky I (2020) Regulation of gene expression by cis-acting long non-coding RNAs Nature Review Genetics 21, 102-117

Ishizu H, Siomi H & Siomi MC (2012) Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines. Genes Dev 26:2361–2373.

Komatsu S., Kitai H., & Suzuki HI. (2023). Network Regulation of microRNA Biogenesis and Target Interaction. Cells, 12(2), 306. https://doi.org/10.3390/cells12020306

Kowalczyk M.S., Higgs D.R. & Gingeras T.R. (2012) RNA discrimination. Nature 482:310–311.

Kugel J.F. & Goodrich J.A. (2012) Non-coding RNAs: key regulators of mammalian transcription. Trends Biochem Sci 37:144–151.

Luaibi, A. R., Al-Saffar, M., Jalil, A. T., Rasol, M. A., Fedorovich, E. V., Saleh, M. M., & Ahmed, O. S. (2023). Long non-coding RNAs: The modulators of innate and adaptive immune cells. Pathology, Research and Practice, 241, 154295. https://doi.org/10.1016/j.prp.2022.154295Luteijn M.J. & Ketting R.F. (2013) PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat Rev Genet 14:523–534.

Pritchard C.C., Cheng H.H. & Tewari M (2012) MicroRNA profiling: approaches and considerations. Nat Rev Genet 13:358–369.

Pelechano V & Steinmetz L.M. (2013) Gene regulation by antisense transcription. Nat Rev Genet 14:880–893.

Xiol J & Pillai R.S. (2012) Outsourcing genome protection. Science 337:529–530.Yang L, Froberg J.E. & Lee J.T. (2014) Long noncoding RNAs: fresh perspectives into the RNA world. Trends Biochem Sci 39:35–43.