1. Instructional materials summary – Harvard SI 2014 Title of teachable tidbit: “Biomedical Applications of Gene Dosage Compensation” General Topic:Molecular Gene Regulation Two sentence synopsis of tidbit:Tidbit focuses on teaching gene dosage compensation to students and having them apply this knowledge to address a biomedical issue regarding the inactivation of one copy of Chromosome 21 in trisomy 21. Type of activity (or activities):Brainstorm, index card question/reflection; group (table) activity; clicker question; take home assignment Designed for what level course and type of students? Introduction to Molecular Biology; Introduction to Genetics; Introduction to Developmental Biology; Majors; Sophomore (200) level course Materials required:Laptop with connection to projector; slide changer; laser pointer; Turningpoint software; this PPT; index cards, magic markers, large poster-size graph paper; clickers; dry erase boards Comments on out of class preparation required by students and instructor: Students: Read background content in textbook and watch video on X-inactivation/gene dosage compensation online (see links in outline); Attend class time before this session. Instructor: Prepare materials for hands-on activity by acquiring all materials above; inform teaching assistants as to their different roles during the activity. General comments:See notes on each slide List five keywords that would allow others to search for this activity in a database: Molecular Gene Regulation; Gene Dosage Compensation; X chromosome inactivation; trisomy 21; gene expression Names and institutions of group members: S. Tariq Ahmad (stahmad@colby.edu); Paul Greenwood (pggreenw@colby.edu); Terence Capellini (tcapellini@fas.harvard.edu); Amy Hansen (amyhansen@g.harvard.edu); Natalie Farny (nfarny@wpi.edu); Fabienne Furt (fabiennefurt@wpi.edu)fabiennefurt@wpi.edu Facilitators: Camille Hardiman (camille.hardiman@gmail.com) and Marvin O'Neal (marvin.oneal@stonybrook.edu) Contact person for questions:Natalie Farny (nfarny@wpi.edu)

2. Biomedical Applications of Gene Dosage Compensation Group 8 (The 21-ists) HHMI Summer Institute S. Tariq Ahmad Paul Greenwood Terence Capellini Amy HansenNatalie FarnyFabienne Furt Facilitators :Camille HardimanMarvin O’Neal

3. Course Context Course: Introduction to Molecular Biology Level: Sophomore Course (200 level) Size: 40-50 students (scalable) Pre-requisites: Introduction to Biology Molecular Gene Regulation (2 weeks) Pre-Post- Central Dogma (2 weeks) Epigenetics (2 weeks) Target Unit

4. Prior knowledge -Bloom’s taxonomy -Scientific method -DNA structure and function -Chromosomes and cell division -Central dogma -Lab methods for measuring gene expression and fluorescence localization Students will have learned:

5. Learning Goals 1)Students will understand why genes are regulated 2)Students will understand the various levels at which gene regulation can occur 3) Students will understand technological applications of gene regulation to biomedicine Molecular Gene Regulation (2 weeks) Pre-Post- Central Dogma (2 weeks) Epigenetics (2 weeks) Target Unit

6. Learning Goals 1)Students will understand why genes are regulated 2)Students will understand the various levels at which gene regulation can occur 3) Students will understand technological applications of gene regulation to biomedicine Molecular Gene Regulation (2 weeks) Pre-Post- Central Dogma (2 weeks) Epigenetics (2 weeks) Target Unit

7. Goal 3: Learning Objectives 3.1. Describe and explain the experimental tools that allow for the artificial control of gene expression 3.2. Identify a situation where manipulation of the expression of a single gene is appropriate to biomedicine (gene therapy) 3.3. Provide examples of dosage compensation in nature and biomedicine 3.4 Propose an experiment and predict the results of the experiment 3.5 Discuss ethical implications of artificially manipulating gene expression Students should be able to:

8. Goal 3: Learning Objectives 3.1. Describe and explain the experimental tools that allow for the artificial control of gene expression 3.2. Identify a situation where manipulation of the expression of a single gene is appropriate to biomedicine (gene therapy) 3.3. Provide examples of dosage compensation in nature and biomedicine 3.4 Propose an experiment and predict the results of the experiment 3.5 Discuss ethical implications of artificially manipulating gene expression Students should be able to:

9. Female cells have double the number of X chromosomes as male cells. Therefore, female cells should express twice the amount of X chromosome genes than male cells. BUT - they DON’T. XX XY Male and female cells express X chromosome genes at the same level. Take 30 seconds and brainstorm several ways that this might be achieved.

10. Mechanisms of X chromosome dosage compensation wormbook.org

11. X Chromosome Inactivation http://embryology.med.unsw.edu.au/embryology/images/thumb/3/3f/X_inacti vation_Xist.jpg/400px-X_inactivation_Xist.jpg Heterochromatin formed, genes silenced Xist gene Barr body

12. Aberrant gene dosage: What’s wrong with this karyotype?

13. What we know: 1. Normally occurring X-inactivation via XIST 2. Gene dosage problem – Trisomy 21

14. Predicting Gene Expression Aim: Investigate how formation of a Chr21 Barr body affects gene expression Method: Samples - 3 different cell types: Predict: The level of gene expression in each cell type, from the two different chromosomes. Draw your predicted gene expression data on the graph provided. Quantify gene expression from chromosomes 9 & 21 Wild type Trisomy 21 Trisomy 21 + XIST Technique :

15. The Next Challenge You accidentally have targeted Chromosome 9 with Xist instead of Chromosome 21. Which graph reflects most accurately this experimental error?

16. Gene expression level a c b d Wild type You accidentally have targeted Chromosome 9 with Xist instead of Chromosome 21. Which graph reflects most accurately this experimental error?

18. Learning Outcomes of Tidbit Proposed Proposed an experiment to apply dosage compensation to biomedical research Predicted Predicted the results of the proposed experiment Provide Provide examples of dosage compensation in nature and for biomedicine

19. In one or two paragraphs, identify and discuss two ethical implications raised by this research Ethical reflection on the implication of manipulation of gene regulation Assignment :