Course Syllabus

Biological Chemistry 650 - Eukaryotic Gene Transcription
Lectures: Mon 10 am – 12 noon in 4560C MSRB II
Drs Dan Bochar, Yali Dou, Yifan Liu and Tom Kerppola (course director)

 

            Biological Chemistry 650 focuses on high impact topics in selected areas of eukaryotic gene expression.  The course seeks to develop the students’ understanding of recent progress in the investigation of gene expression that is based on advances in biochemical, structural, molecular, cellular and genomic approaches. The lectures are designed to update and to complement survey courses by focusing on cutting edge discoveries and on their impact on potential future directions of the field.  The instructors make extensive use of examples from original research articles, which are assigned reading in preparation for each class. To integrate their learning throughout the semester, each student prepares a critical summary of an original research paper selected from a list of papers recommended by the instructors. For more information, please see course pages on Canvas).

                                                                                             

Sep. 10     Introductions (Faculty)
General transcription factors, RNA polymerases and transcript initiation (Bochar)

Sep. 17     Transcript elongation, termination and processing (Bochar)

Sep. 24     Nucleosome structure and dynamics (Bochar)

Oct. 1        Higher order chromatin structures and chromatin remodeling (Bochar)

Oct. 8        Transcription silencing and small RNAs (Liu)

Oct. 15      Study break – prepare outline for critical summary

Oct. 22      DNA methylation and DNA modifying enzymes (Dou) - submit outline for critical summary

Oct. 29      Chromatin modifications (Dou)

Nov. 5       Chromatin modifying enzymes (Dou)

Nov. 12     Chromatin binding proteins (Dou)

Nov. 19     Genes, genomes and transcriptomes; What is a gene? (Kerppola) - revised deadline to submit polished draft for critical summary

Nov. 26     Transcription regulatory proteins; How are they regulated? (Kerppola)

Dec. 3       Transcription factor interactions; How do they engender specificity?(Kerppola)

Dec. 10     Spatial organization of the nucleus/genome; Does location matter? (Kerppola) - submit final critical summary

 

 

Instructor contact information:

 

Dr. Dan Bochar

dbochar@gmail.com

(734) 604-1585

Office hours by appointment

 

Dr. Yali Dou

yalid@med.umich.edu

(734) 615-1315

Office hours by appointment

 

Dr. Yifan Liu

yifan@med.umich.edu

(734) 615-4239

Office hours by appointment

 

Dr. Tom Kerppola (course director)

kerppola@med.umich.edu

(734) 764-3553

Office hours before classes and by appointment

 

 

 

            The objective of the course is to help each student develop the skills and knowledge necessary to understand and to analyze current scientific literature on eukaryotic gene transcription.  The attainment of this objective by each student will be evaluated during the course using three main criteria:

1. Quizzes and/or homework will be assigned and completed before or at the beginning of each class session. Discussions of the general topics of these assignments among students are encouraged. Each student will complete their own quiz or assignment independently.
2. Students are expected to become active participants in class sessions. The quality of student comments, answers, and presentations in class will be evaluated.  Students may be assigned to work in teams or in groups to present information for the class.  If necessary, absences from the scheduled class sessions will be reported in advance by the student to the instructor of the class.  Emergencies that could not be anticipated in advance must be documented.
3. Over the course of the semester, each student will conduct a critical analysis of an original publication that is selected by the student from a set recommended by the instructors. Guidance for the preparation of this analysis will be provided in class, online, and by individual consultation with the instructors.

Each of the three main criteria will account for one third of the total points that are used to determine the grade in the class.  The final grades will be assigned by the instructors by comparing the performance of each student to all students that have been taught by the instructors in previous years in this and other classes.  Student grades are therefore not determined using a “curve” or specific percentage cut-offs for the total accumulated points.