FALL 2010


Instructor:    Gary Kunkel, Associate Professor of Biochemistry

                        406A Biochemistry



                        webpage URL:


Time, location:         Thurs. 2:20-3:10PM, Room 401/403 Biochemistry


Prerequisites:         BICH 441 and BICH/GENE 431, or concurrent enrollment; or approval of instructor



In this course, we will read and discuss papers in biochemistry and molecular genetics that cover research in gene transcription during development.  One student will be the primary discussant for a paper to be presented during each meeting.  The primary discussant should prepare a PowerPoint presentation.  As a primary discussant, you will be expected to provide background leading up to the assigned paper and discuss the impact of this paper on the field. Also, you should review the data and techniques presented in the paper.  The primary discussant will be required to meet with me prior to the presentation in order to go over any questions about the paper or its historical perspective.  In addition, the primary discussant will submit three carefully devised questions that may be used for the in-class quiz (by Tuesday at 5PM preceding your presentation).


It is very important that all class members take part in the discussion, even when you are not the primary discussant.  You will need to be prepared to discuss the papers critically (meaning, that you must read the papers before class).  If you think the data are good or bad, say so, and why.  What controls did the authors present carefully or leave out?  How does the data support various models presented in that paper or other papers that you have read?


At the end of each class session, students will take a short quiz to demonstrate understanding of the assigned paper for the day.



Grading will be allocated as follows: (100 pts total)

            performance as primary discussant                                                       40% (40 pts)

            participation in other discussions                                                           20% (20 pts)

            quizzes at end of each class session (4 pts each time)                     40% (44 pts total,

meaning up to four bonus pts)

            each unexcused absence: subtract 5 pts



Making up an excused absence: If you miss a class because of an excused absence, you can make up the quiz for that class by writing a one page summary/critique of the assigned paper for that day.  This document must be submitted no later than one week after the missed class.  It will be graded on a 4 point (maximum) scale.


Letter grades will be assigned based on the following scale: A: 90 points or higher; B: 80-89 points; C: 70-79 points; D: 60-69 points; F: less than 60 points


The American with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities.  Among other things, this legislation requires all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities.  If you believe you have a disability requiring an accommodation, please contact the Department of Student Life for Students with Disabilities in Room 126 of the Koldus Building, or call 845-1637.


Aggie Honor Code: ŇAn Aggie does not lie, cheat, or steal or tolerate those who do.Ó Academic integrity is paramount in all activities during this course.  On each quiz, you will be required to sign a statement acknowledging that you have observed this honor code.  See the Honor Council Rules and Procedures at


Schedule of classes:

September 2: organizational, introduction

September 9: Master regulators: MyoD transcription factor controls myogenesis

September 16: Master regulators: Mitfa controls pigment cell development

September 23: Enhancer for segmentation in Drosophila

September 30: No class

October 7: Wnt signaling – TCF/LEF interaction with b-catenin

October 14: Wnt signaling – b-catenin displaces Groucho repressor

October 21: Role of chromatin methylation during development – bivalent marks

October 28: Role of chromatin methylation – marking during maternal/zygotic transition

November 4: Core transcription machinery can control differentiation

November 11: Stalled RNA polymerase II at many developmental genes

November 18: Chromatin repression by PRC2 complex

November 25: No class – Happy Thanksgiving!

December 2: Peptide control of a transcriptional activator during embryogenesis


Assigned readings are posted on the course page on eLearning.