Paper assignment for the Bio 164  class

What to pick:  suggestions listed below, or pick any paper topic that involves turning gene transcription on and off!

What NOT to pick: regulation that's not at the gene level, does not affect transcription of genes, but instead affects protein phosphorylation cascades or similar processes.

The paper will offer you an opportunity to explore a topic related to this class in some detail.  It will be due the Tuesday before Thanksgiving to enable you to put in heavy effort in other classes towards the end of the term, while still keeping up with the discussion articles assigned.  The paper in this course will be about 10 pages of text, with additional pages of copied figures or tables from the articles you will use, and a page of bibliography in the format of the journal Cell.  It will be a discussion of 5 related papers from the literature (not review articles, although you may use and cite review articles as background material if you wish).  It needs to be related in some way to genetic regulation in eukaryotes. 

 I will check on the scope and applicability of the topic when you hand in your choice of topic and one supporting paper at the time assigned on the syllabus. I would be glad to discuss your ideas with you before this time if you wish.  The following are a few ideas I had, but this is supposed to be YOUR choice, so just use these as a takeoff point.  You can't use one of the assigned articles that we have discussed or will discuss for one of your 5, but you could use one for background and/or references to similar work and cite it in your paper.  There are also good review articles that might give you ideas in Trends in Genetics, Trends in Biochemistry, and Annual Reviews of Genetics (also of Biochemistry and of Cell Biology).  It's OK to cite a review article, but it cannot be one of your 5 major articles.  The paper will be due on Tuesday, November 21 at the start of class.  If you must hand it in late, please see me.  If I agree to accept it late, there will be 1/2 letter grade deducted per late day, for most reasons (starting with an A, one day late would be A-/B+, two days would be B, three days would be B-/C+ etc.).

Some possible topics for paper:

  1. Role pf transcription factors in stem cell maintenance, especially inhibitory transcription factors that form dimers with the transcription factors that should turn on differentiation genes. 

2.  Role of histone methylation in imprinting to allow either maternally or paternally inherited allele to be expressed.

3.  Role of non-coding RNA in X-inactivation.

4.  Interactions of the transcription factor p53 and telomerase in aging of mouse cells and mice.

5.  Role of small inhibitory RNA molecules in C. elegans development (or in Drosophila development).

6.  Role of p53 in regulating DNA repair (induction as a transcription factor) versus apoptosis (cell death).  Particularly interesting recent aspect: regulation by attachment of small proteins that regulate protein degradation (attachment of SUMO versus Ubiquitin, for example).

7.   Role of telomerase in human cells that are undergoing replicative senescence, or in transgenic/knockout mice.

8. Role of DNA methylation disorders at oncogenes (decreased methylation) or tumor suppressors (increased methylation) as possible causative agents of cancer.

9.  Role of nuclear matrix attachment in regulation of transcription of specific genes.

10.  Splicing of DScam (38,000 splice variants possible!) and its possible role in neuronal identity bar coding.

11.  Transcriptional regulation in the control of the eukaryotic cell cycle (G1, S, G2, M).

12.  Transcription factor control of circadian or other rhythms in some organism of choice (Drosophila, mice, Neurospora, other).

 13.  Role of Transcription Factors, chromatin structure, or both in control of some developmental biology event in a particular organism (examples: MyoD1 in muscle development, Twist in mesodermal tissue development).

 14.  Locational control of transcription factors (for example, in and out of nucleus, attached to matrix or not, etc.).

15.  Mutants of Drosophila and/or C. elegans that extend their life spans ( e.g. Methuselah in Drosophila, AGE-1 in C. elegans.)

16.  Mutants of yeast that extend their life spans, e.g. LAG2, SIR2 slight overproduction, RAS2 overproduction.
 

17.  Differential splicing of RNA as a regulatory mechanism (the human genome project summary said it was a much more major regulatory system in humans than expected, and predicted 5 differently spliced transcripts per gene).
 

18.  Role of BRCA1 and BRCA2 in breast cancer
 

19.  Regulation of asymmetry (when a cell divides, one daughter has one fate and the other daughter has a different fate) in developing organisms (Arabidopsis, C. elegans, Drosophila, mice)                               

20. Regulation of asymmetry in division of stem cells to produce a cell that will differentiate along with a cell that will remain 'stem'.

21. Regulation of X chromosome inactivation in females (interesting aspects include the role of Xist RNA and its antisense RNA, process in marsupials vs placental mammals)

 
22. Regulation of sex determination in C. elegans (including how the hermaphrodites function).
 

23.  Role of imprinting of genes so that they are differentially expressed between the two sexes in diseases of humans (Prader-Willi Syndrome, Angellman syndrome).

 
24.  Regulation of the specification of the three embryonic germ layers (ectoderm, mesoderm, and endoderm).

25.  Role of RNAi (or siRNA) in regulation of some aspect of plant or animal development.

26.  Use of two-hybrid screening and or microarray analysis of transcription to identify regulatory pathway members

27. Use of microarray analysis combined with ChIP analysis to identify regulatory sites near genes that are active in living cells; including methods to validate the high throughput data.

 
28.  Heat shock protein regulation in Drosophila.

 
29.  Effects of a particular class of transcription factors (zinc finger, Helix-loop-helix, leucine zipper, coiled coil, helix-turn-helix, etc) in regulation.

30.  Regulation of DNA repair by DNA damage: role of chromatin structure and/or transcription factors.

 
31.  Another topic you think of, in the area of eukaryotic genetic regulation (NOT signal transduction or other protein level mechanisms except as they interact with gene regulation systems)