(B41 U1630, Spring, 2008)

Course Description

This course is design for senior undergraduate students and graduate students who are interesting in exploring knowledge in modern genetics.  Instructor will choose a theme for each semester and expect to discuss related papers throughout the semester.  In this semester, we will focus on microRNA.  We will start the section with a brief introduction on the historical perspectives.  Then, key references will be discussed each week ranging from the microRNA discovery, biogenesis, functions, mechanisms and evolution.  The aim of this course is to introduce students the state of art of genetics and the most advanced discovery in this field.

PrerequisiteGenetics or equivalent

LectureMonday 10:20~12:00 or 11:20~1:00*, Life Science 419

InstructorChau-Ti Ting E-mail: ctting_at_ntu.edu.tw

Office: LSB 1103 Phone: 3366 2522

Course websitehttps://ceiba.ntu.edu.tw/962Genetic_Topics/

Weekly discussion

Discussion is an essential part of the course and you should critically discuss ideas and the evidence supporting scientific ideas.  Attendance and participation in the discussions are expected and will contribute to the grade.  Everyone should read all the assigned readings before attending the discussion.  If you find a reading particularly difficult, you should feel comfortable to ask questions for clarification.  I suggest that you take notes when you read the papers and put down questions prior to each discussion.  Please turn in the questions on a sheet of A4 paper with your name on it each week. 

Term paper

You are required to write a 5-page research proposal on microRNA related issues at the end of the semester.  The topic of your proposal should be decided before midterm and a single-page outline with key references is due on April 7th.  Students are encouraged to discuss with instructor about the choice of topic, the outline of the paper, and specific questions any time as long as you make an appointment in advance.  A draft proposal can be submitted on June 10th and you will have 2 weeks to revise it before turning in on June 25th.

Syllabus

Week 1 (2/18)

General introduction

Recent Reviews

Bushati N, Cohen SM. 2007. microRNA functions. Annu Rev Cell Dev Biol. 23:175-205.

Chang TC, Mendell JT. 2007. microRNAs in vertebrate physiology and human disease. Annu Rev Genomics Hum Genet. 8:215-239.

Chapman EJ, Carrington JC. 2007. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet. 8:884-896.

Kim VN. 2005. Small RNAs: classification, biogenesis, and function. Mol Cells. 19:1-15.

Matranga C, Zamore PD. 2007 Small silencing RNAs. Curr Biol. 17:R789-93.

Zamore PD, Haley B. 2005. Ribo-gnome: the big world of small RNAs. Science. 309:1519-1524.

Week 2 & 3 (2/25*, 3/3)

Discovery of microRNA

Lee RC, Feinbaum RL, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 75:843-854.

Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 403:901-906.

Wightman B, Ha I, Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell. 75:855-862.

Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science. 294:853-858.

Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 294:858-862.

Lee RC, Ambros V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science. 294:862-864.

Ruby JG, Jan C, Player C, Axtell MJ, Lee W, et al. 2006. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell. 127:1193-1207.

Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M. 2007. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17:1865-1879.

Week 4 (3/10)

Discovery of RNA interference

Guo S and Kemphues KJ. 1995. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell. 81: 611-620.

Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE et al. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 391: 806-811.

Kennerdell JR and RW Carthew. 1998. Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the Wingless pathway. Cell. 95: 1017-1026.

Week 5 (3/17)

miRNA biogeneis

Drosha

Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. 2004. Processing of primary microRNAs by the Microprocessor complex. Nature. 432:231-235.

Landthaler M, Yalcin A, Tuschl T. 2004. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol. 14:2162-2167.

Lee Y, Ahn C, Han J, Choi H, Kim J, et al. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature. 425:415-419.

Week 6 (3/24)

miRNA biogeneis

Dicer

Forstemann K, Tomari Y, Du T, Vagin VV, Denli AM, et al. 2005. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3:e236

Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T et al. 2001. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 293:834–838.

Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ et al. 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15:2654-2659.

Saito K, Ishizuka A, Siomi H, Siomi MC. 2005. Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells. PLoS Biol. 3:e235.

Week 7 (3/31)

miRNA biogeneis

Argonaute

Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S et al. 2001. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell. 106:23-34.

Hammond SM, Boettcher S, Caudy AA, Kobayashi R, and Hannon GJ. 2001. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science. 293: 1146-1150.

Carmell MA, Xuan Z, Zhang MQ, and Hannon GJ 2002. Argonaute family: Tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes & Dev. 16:2733-2742.

Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, et al. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science. 305:1437-1441. 

Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T. 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell. 15:185-197.

Okamura K, Ishizuka A, Siomi H, Siomi MC. 2004. Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev. 18:1655-1666.

Week 8 (4/7)

Midterm (Topic and outline of mini-review/proposal due on April 7th)

Week 9 & 10 (4/14, 4/21)

microRNA functions

Mechanism

Humphreys, D. T., Westman, B. J., Martin, D. I. and Preiss, T. 2005. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc Natl Acad Sci USA. 102:16961-16966.

Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N et al. 2005. Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science. 309:1573-1576.

Biological process

Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, et al. 2003. Dicer is essential for mouse development. Nat. Genet. 35:215-217.

Forstemann K, Tomari Y, Du T, Vagin VV, Denli AM, et al. 2005. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3:e236.

Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW et al. 2005. Stem cell division is regulated by the microRNA pathway. Nature. 435:974-978.

Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ et al. 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15:2654-2659.

Wienholds E, Koudijs MJ, van Eeden FJ, Cuppen E, Plasterk RH. 2003. The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat. Genet. 35:217-218.

iab-4

Bender W. 2008. MicroRNAs in the Drosophila bithorax complex. Genes Dev. 22:14-19.

Stark A, Bushati N, Jan CH, Kheradpour P, Hodges E et al. 2008. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22:8-13.

Tyler DM, Okamura K, Chung WJ, Hagen JW, Berezikov E et al. 2008. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 22:26-36.

Week 11 & 12 (4/28*, 5/5*)

microRNA targets

Brennecke J, Stark A, Russell RB, Cohen SM. 2005. Principles of microRNA-target recognition. PLoS Biol. 3:e85.

Doench JG, Sharp PA. 2004. Specificity of microRNA target selection in translational repression. Genes Dev. 18:504-511.

Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. 2005. Combinatorial microRNA target predictions. Nat. Genet. 37:495-500.

Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 120:15-20.

Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. 2003. Prediction of mammalian microRNA targets. Cell. 115:787-798.

Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature. 433:769-773.

Rehwinkel J, Natalin P, Stark A, Brennecke J, Cohen SM et al. 2006. Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol. Cell. Biol. 26:2965-2975.

Week 13 (5/12*)

microRNA evolution

Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, et al. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science. 310:1817-1821.

Lu J, Shen Y, Wu Q, Kumar S, He B, et al. 2008. The birth and death of microRNA genes in Drosophila. Nat Genet (in press).

Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM. 2005. Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell. 123:1133-1146.

Week 14 & 15 (5/19, 5/26)

Application of RNA interference

Friedman A, Perrimon N. 2006. A functional RNAi screen for regulators of receptor tyrosine kinase and ERK signalling. Nature. 444:230-234.

Dietzl G, Chen D, Schnorrer F, Su KC, Barinova Y et al. 2007. A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature. 448:151-156.

Week 16-17 (6/2, 6/9)

Individual meeting (submit the draft of your proposal by June 10th)

Week 18 (6/16)

Student presentation & Final discussion

(submit the final version of your proposal by June 25th)