Readings | An RNA Safari: Exploring the Surprising Diversity of Mammalian Transcriptomes | Biology

Course readings.
WEEK #	TOPICS	READINGS
1	Introduction and Course Overview See the Lecture Summary	No Readings
2	In the Beginning: Ribosomes and Ribosomal RNA See the Lecture Summary	Palade, G. E. "A Small Particulate Component of the Cytoplasm." Journal of Biophysical and Biochemical Cytology 1, no. 1 (1954): 59–68. Palade, G. E., and Siekevitz P. "Liver Microsomes: An Integrated Morphological and Biochemical Study." Journal of Biophysical and Biochemical Cytology 2, no. 2 (1956): 171–200.
3	Careful Measuring of Unhealthy Amounts of Radioactivity: A Role for tRNAs in Polypeptide Synthesis See the Lecture Summary	Hoagland, M.B., M. L. Stephenson, et al. "A Soluble Ribonucleic Acid Intermediate in Protein Synthesis." (PDF) The Journal of Biochemistry 213, no. 1 (1958): 241–57. Presnyak, V., Alhusaini N., et al. "Codon Optimality is a Major Determinant of mRNA Stability." Cell 160, no. 6 (2015): 1111–24.
4	mRNA as an Information Shuttle See the Lecture Summary	Astrachan, L., and E. Volkin. "Properties of Ribonucleic Acid Turnover in T2-Infected Escherichia Coli." Biochemica et Biophysica Acta 29, no. 3 (1958): 536–44. S., Brenner, F. Jacob, et al. "An Unstable Intermediate Carrying Information from Genes to Ribosomes for Protein Synthesis." Nature 190 (1961): 576–81.
5	The Genomics Revolution: An Introduction to High-throughput Sequencing See the Lecture Summary	Mortazavi, A., B. A. Williams, et al. "Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq." Nature Methods 5, no. 7 (2008): 621–8. Y., Wan, K. Qu, et al. "Genome-wide Measurement of RNA Folding Energies." Molecular Cell 48, no. 2 (2012): 169–81.
6	Let's Mix it up: SnRNAs and Pre-mRNA Splicing See the Lecture Summary	Lerner, M. R., and J. A. Steitz. "Antibodies to Small Nuclear RNAs Complexed with Proteins are Produced by Patients with Systemic Lupus Erythematosus." (PDF - 1.9MB) Proceedings of the National Academy of Science 76, no. 11 (1979): 5495–9. Jia, Y., J. C. Mu, et al. "Mutation of a U2 SnRNA Gene Causes Global Disruption of Alternative Splicing and Neurodegeneration." Cell 148, no. 1–2 (2012): 296–308.
7	Let it Sno: Ribosomal RNA Modification Directed by SnoRNAs See the Lecture Summary	Ganot, P., M. L. Bortolin, et al. "Site-specific Pseudouridine Formation in Preribosomal RNA is Guided by Small Nucleolar RNAs." Cell 89, no. 5 (1997): 799–809. Jack, K., C. Bellodi, et al. "rRNA Pseudouridylation Defects Affect Ribosomal Ligand Binding and Translational Fidelity from Yeast to Human Cells." Molecular Cell 44, no. 4 (2011): 660–6.
8	Small is Beautiful: MicroRNAs as Ubiquitous Regulatory Molecules See the Lecture Summary	Lee, R. C., Feinbaum R. L., et al. "The C. Elegans Heterochronic Gene Lin-4 Encodes Small RNAs with Antisense Complementarity to Lin-14." Cell 75, (1993): 843–54. D., Lauressergues, J. M. Couzigou, et al. "Primary Transcripts of MicroRNAs Encode Regulatory Peptides." Nature 520, no. 7545 (2015): 90–3.
9	Running Interference: SiRNA as an Experimental Tool See the Lecture Summary	A., Fire, S. Xu, et al. "Potent and Specific Genetic Interference by Double-Stranded RNA in Caenorhabditis Elegans." Nature 391, no. 6669 (1998): 806–11. G., Hu, J. Kim, et al. "A Genome-wide SiRNA Screen Identifies a New Transcriptional Module Required for Self-Renewal." Genes and Development 23, no. 7 (2009): 837–48.
10	Protecting us from Ourselves: PiRNAs Silence Transposons in Germline Tissue See the Lecture Summary	Brennecke, J., A. A. Aravin, et al. "Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila." Cell 128, no. 6 (2007): 1089–103. C., Klattenhoff, H. Xi, et al. "The Drosophila HP1 Homolog Rhino is Required for Transposon Silencing and PiRNA Production by Dual-Strand Clusters." Cell 138, no. 6 (2009): 1137–49.
11	Who Needs Proteins?: Long Noncoding RNAs as Regulators of Gene Expression See the Lecture Summary	Chaumeil, J., P. L. Baccon, et al. "A Novel Role for Xist RNA in the Formation of a Repressive Nuclear Compartment into Which Genes are Recruited When Silenced." Genes and Development 20, no. 16 (2006): 2223–37. C. A., Klattenhoff, J. C. Scheuermann, et al. "Braveheart, A Long Noncoding RNA Required for Cardiovascular Lineage Commitment." Cell 152, no. 3 (2013): 570–83.
12	No End in Sight: Circular RNAs and their (possible) Functions See the Lecture Summary	J., Salzman, C. Gawad, et al. "Circular RNAs are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types." PLOS One 7, no. 2 (2012): e30733. S., Memczak, M. Jens, et al. "Circular RNAs are a Large Class of Animal RNAs with Regulatory Potency." Nature 495, no. 7441 (2013): 333–8.
13	A New Hope: CRISPR-Associated RNAs, Prokaryotic Defense Mechanisms, have been Transformed into a Tool for Genome Editing See the Lecture Summary	L. Cong, F. A. Ran, et al. "Multiplex Genome Engineering Using CRISPR/Cas Systems." Science 339, no. 6121 (2013): 819–22. T., Hart, M. Chandrashekhar, et al. "High–Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities." Cell 163, no. 6 (2015): 1515–26.
14	Oral Presentations and Course Discussion See the Lecture Summary	No Readings