Readings

WEEK # TOPICS READINGS
1

Introduction and Course Overview

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2

In the Beginning: Ribosomes and Ribosomal RNA

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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

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Hoagland, M.B., M. L. Stephenson, et al. This resource may not render correctly in a screen reader."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

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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

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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

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Lerner, M. R., and J. A. Steitz. This resource may not render correctly in a screen reader."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

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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

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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

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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

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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

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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

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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

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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

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