Course Syllabus

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Meeting Time: 

Monday 1:30-3:15 

Tuesday 9:45-11:30

Location: 

Schedules (Tentative titles)

10/14 DNA replication 1

10/20 no lecture

10/21DNA replication 2

10/27 no lecture

10/28 no lecture

11/3 Link to aging and cancer development (Dr. Herbig)

11/4 DNA damage repair (Dr. Lambert)

11/10 no lecture

11/11 Epigenetic regulation (Centromere, replication)

11/17Homologous recombination

11/18 Non-homologus endjoining 

11/24 and 25 No lectures

12/1

12/2 Evolution (from low eukaryotes/pathogens to humans), repeat sequences including Alu

12/8

12/9 Neurological diseases

12/15 Trypanosome (Dr. Kim)

12/16 

Course Description

This course explores the molecular mechanisms that govern chromosome dynamics, focusing on DNA replication, repair, centromere and telomere function, and the evolutionary processes shaping chromosome ends. Students will gain a mechanistic understanding of how genomic stability is established, maintained, and regulated.

Learning Objectives

By the end of this course, students will be able to:

1. Explain the biochemical processes of DNA replication and repair.

2. Describe how replication origins are regulated epigenetically.

3. Analyze the molecular organization and function of centromeres.

4. Evaluate mechanisms of telomere maintenance and their implications for genome stability.

5. Discuss the evolution of subtelomeric regions and their roles in adaptation and genome plasticity. Using yeast and Trypanosome as model organisms 

6. Critically read and present primary research literature in chromosome biology.

Weekly Topics (Under revision; they will be changed early September)

Week 1: Introduction to Chromosome Dynamics

• Overview of genome stability and chromosome biology

Week 2–3: Biochemistry of DNA Replication

• DNA polymerases, helicases, primases

• Leading vs. lagging strand synthesis

• Replication fidelity and checkpoints

Week 4–5: DNA Repair Pathways

• Mismatch repair, base excision repair, nucleotide excision repair

• Double-strand break repair: HR, NHEJ, and alternative pathways

Week 6: Epigenetic Regulation of Replication Origins

• Chromatin structure and nucleosome positioning

• Origin recognition complex (ORC)

• Histone modifications and replication timing

Week 7–8: Centromere Structure and Function

• DNA sequence and epigenetic identity

• CENP-A chromatin and kinetochore assembly

• Mechanisms of chromosome segregation

Week 9–10: Telomere Homeostasis

• Telomerase biochemistry and accessory factors

• Telomere replication challenges and end protection

• Telomere-binding proteins and shelterin/CST complexes

Week 11: Telomeres and Genome Instability

• Telomere dysfunction, checkpoint activation, and repair

• Links to aging and disease

Week 12: Evolution of Subtelomeres

• Subtelomeric repeats and gene families

• Recombination hotspots and genome plasticity

• Adaptive evolution and pathogenicity

Week 13: Student Presentations of Selected Papers

Week 14: Integration and Review

• Connecting replication, repair, centromere, telomere, and evolution

• Open questions and future directions

Assessments

• Participation and Discussion (Quiz)– 20%

• Weekly Reading Responses – %

• Exam (Weeks 2–8 material) – 0%

• Essay/Project – 80%