'Studying the Role of TRIM24, TRIM28 and TRIM33 in LINE-1 Retrotransposition' - MIMM 396 Undergraduate Research Project Application Form.

INSTRUCTIONS - PROFESSORS: Please review this form. Complete or correct the sections, as applicable, from "Supervisor's Name" to "Ethics, safety, and training". Please sign and date near the bottom ("Supervisor's signature").

INSTRUCTIONS - STUDENTS: You may receive this form by email, or you may download it from www.mcgill.ca/science/research/ours/396/ after it has been posted. Either way, print and review this form. Complete or correct the sections, from "Student's Name" to "Student's Level", and sign ("Student signature). Ask your supervisor to sign her/his section near the bottom. Take it to the department corresponding to the course number; this may or may not be your own department. Do not register for a '396' course on Minerva until you receive departmental permission. Have a discussion with your supervisor about time/work expectations, keeping in mind that this is a 3-credit course (roughly, 10 hours per week for 12 weeks). Remember that a '396' course is an elective.

INSTRUCTIONS - DEPARTMENTS: After the unit chair/director/designate approves (or not) this project, please notify student. If approved, please give student permission to register on Minerva, and fax this form (with signatures) to the Office for Undergraduate Research in Science at 514-398-8102. The Office for Undergraduate Research in Science will later post the project online at https://mcgill.ca/science/research/ours/396/listing/, indicating whether the project is open for students to apply or taken.

QUESTIONS OR FEEDBACK? Contact Victor Chisholm by email, or phone 514-398-5964

Supervisor's Name: Chen Liang

Supervisor's Email: chen.liang [at] mcgill.ca

Supervisor's Phone: 514-340-8260

Supervisor's Website:

Supervisor's department: Microbiology and Immunology

Course number: MIMM396 (Microbiology)

Term: Fall 2011-2012

Project start date: Wednesday, September 1, 2011

Project end date: Tuesday, December 6, 2011

Project title: Studying the Role of TRIM24, TRIM28 and TRIM33 in LINE-1 Retrotransposition

Project description:

Transposons are elements found ubiquitously at a high copy number within the genomes of various species. In humans, transposons are estimated to comprise nearly half of the genomes. The LINE-1 (L1) element from the long interspersed nuclear element (LINE) class of transposons is the most successful element and constitutes 17% of the human genome. This element is capable of replicative transposition to new genomic locations, which may contribute to diversity but may also lead to mutations. The integrated L1 element consists of two open reading frames, these include ORF1 that is required to chaperone the RNA transcript back to the nucleus and ORF2 that encodes an endonuclease and a reverse transcriptase. At the target site knicked by the endonuclease, the RNA transcript serves as a template for reverse transcription. Subsequent ligation, second strand synthesis and the filling of gaps results in a newly integrated element.

To avoid mass mutation within the genome, factors and mechanisms must exist to silence the 80 to 100 active transposition-competent L1 elements. Proteins of the tripartite motif (TRIM) superfamily are characterized by three domains located at the N-terminus collectively known as an RBCC motif. The RING domain and the coiled coil region of this motif are known to mediate protein-protein interactions and oligomerization, respectively. The C-terminus houses distinct domains for each TRIM protein and these may confer a wide variety of functions. Related members of the transcription intermediary factor (TIF) subfamily within the TRIM superfamily, including TRIM24, TRIM28, and TRIM33, are known to repress transcription through the recruitment of both DNA binding proteins and proteins involved in chromatin modification such as histine deacetylases, histone methyltransferases and heterochromatin proteins. Members of the TIF subfamily have been shown to silence integrated retroviruses and are also known to act as tumor suppressors. These proteins may act as a bridge between the DNA binding components and the chromatin modifying components.

A retrotransposition assay will be performed in mammalian cells as a model for studying transposition in humans. We will use a construct that bears a human L1 element tagged with a GFP expression cassette where successful transcription, splicing, reverse transcription and integration are specifically required for GFP expression. Knocking down TIF proteins will be achieved through RNA interference and a higher expression of GFP from integrated L1s will be expected as a result. Through flow cytometry, the percentage of GFP expressing cells will be determined. Optimization of culturing conditions, transfection and data analysis will be required to assay the involvement (if any) of the transcription intermediary factors in L1 retrotransposition in mammalian cells.

Prerequisite: 1 term completed at McGill + CGPA of 3.0 or higher; or permission of instructor.

Grading scheme (The final report must be worth at least 50% of final grade): Final grade shall be based on laboratory performance as evaluated by the research supervisor (50%) and the final written research report (minimum 10 pages) graded by the supervisor and the course coordinator or the coordinator's delegate (50%).

Project status - This project is: Taken. The professor has no more '396' projects this term.

How students can apply: After all parts of this application form are completed, and the hard copy is signed by the professor and the student, bring this application form and your unofficial transcript to Prof. Gregory Marczynski during office hours, who will review/approve as the course coordinator for MIMM 396 (Microbiology) or MIMM 397 (Immunology).

Ethics, safety, and training: Supervisors are responsible for the ethics and safety compliance of undergraduate students. Which of the following, if any, is involved? Handling chemicals

Student's Name:

Student's McGill ID:

Student's Email (first.last [at] mail.mcgill.ca):

Student's Phone:

Student's Program:

Student's Level (U0 / U1 / U2 / U3):

Student signature - I have not applied for another '396' course in this term:

Supervisor's signature:

Date:

Unit chair/director/designate's name:

Unit chair/director/designate's signature:

Date: