Syllabus Eukaryotic Gene Regulation (BIOLOGICAL SCIENCES 565), Spring 2014 Updated 1/20/14

Syllabus – Eukaryotic Gene Regulation (BIOLOGICAL SCIENCES 565), Spring 2014 – Updated 1/20/14

Instructor: Dr. Ava J. Udvadia Office: Lapham Hall--LAP SB80 Class Hours: TR 9:30-10:45am LAP 260 Office Hours: F 9:30 am-12:00 pm LAP SB80 (or by appointment) Phone (emergencies only): 414-382-1750 (office at SFS), 414-382-1761 (lab at SFS) Email: [email protected]

Purpose of Course It is expected that students participating in the course are comfortable with the basic concepts in cell and molecular biology that are covered in a 300 level college Genetics or Cell Biology course. The goal of this course is to provide students with a comprehensive understanding of transcriptional and post-transcriptional regulation of eukaryotic genes. This goal will be achieved using a combination of lecture, textbook readings, reviews articles, and readings from the current literature. The course will cover the process and analysis of gene regulation in eukaryotes including the roles of chromatin remodeling, noncoding RNA, DNA sequence regulatory elements, and transcription factors in mediating transcriptional regulation. Finally, the course will explore how differential gene regulation is involved in the processes of cell signaling, development, and disease.

Format The course is divided into 2 parts: lecture and literature review – both require active participation in group discussions. The lecture component of the course will be based on material from the textbook and discussion will be based on assigned homework problems. In the literature review portion, students will have the opportunity to display their comprehension of the material by participating in classroom discussions on current articles from the primary literature. The discussions will be led by students and moderated by the instructor. Students are expected to spend a minimum of 6 hours each week completing homework assignments in order to effectively participate in the group discussions that will be a part of each class.

Prerequisite BioSci 325 (P), or BioSci 315 (P)

Required Materials

Required Text:  Gene Control, by David Latchman; Garland Science (January 21, 2010) (ISBN: 0815365136)

Optional Text:  Molecular Biology 4th ed, by Robert F. Weaver; McGraw Hill 2007 (ISBN: 0073319945)

Online Materials: https://uwm.courses.wisconsin.edu/

 Access course materials through course D2L site Time Investment On average, students are expected to spend 48 hours per credit per semester on in-class activities and activities outside of the classroom. The following is a workload estimate and should be used as a guideline. Time spent on any given assignment as well as total time required to adequately learn the material will vary from individual to individual. Students are assessed on their performance on graded assignments and not on the time put into the course.

Total hours: 3 credits x 48 hours = 144 hours In Class: 150 minutes x 15 weeks = 37.5 hours Assigned reading/homework: 6 hours/wk x 15 weeks = 90 hours Preparation of Journal Article Presentations: 16.5 hours

PAG 2 Reading Assignments Date Activity Topic Readings Jan 21 Lecture 1 Introduction to Eukaryotic Gene Latchman: Ch. 1, lecture 1 Regulation and the Toolbox goals Jan 23 Lecture 2, quiz1 Structure of Chromatin I Latchman: Ch. 2, lecture 2 goals Jan 28 Lecture 3, quiz 2 Chromatin Regulation Latchman: Ch. 3, lecture 3 goals Jan 30 Lecture 4, quiz 3 Chromatin Regulation (continued) Latchman: Ch. 3, lecture 4 goals Feb 4 Lecture 5, quiz 4 The process of transcription Latchman: Ch. 4, lecture 5 goals Feb 6 Lecture 6, quiz 5 Regulatory cis-acting elements Latchman: Ch. 4, lecture 6 goals Feb 11 Lecture 7, quiz 6 Transcription Factors: DNA Latchman: Ch. 5, lecture 7 binding motifs goals Feb 13 Lecture 8, quiz 7 Transcription Factors: Latchman: Ch. 5, lecture 8 Transactivation domains goals Feb 18 Lecture 9, quiz 8 Post-transcriptional Processes Latchman: Ch. 6, lecture 9 goals Feb 20 Lecture 10, quiz Post-transcriptional Regulation Latchman: Ch. 7, lecture 10 9 goals Feb 25 Lecture 11, quiz Gene control and cellular Latchman Ch. 8, lecture 11 10 signaling pathways goals Feb 27 Exam Practice Eukaryotic Gene Regulation Latchman chapters 1-8; Review, quiz 11 lecture goals, your notes Mar 4 Midterm Exam Material from Lectures 1-11 Latchman chapters 1-8; lecture goals, your notes Mar 6 Discussion Answers to Midterm Exam Mar 11 Tutorial 1. PubMed literature search Manual for PubMed 2. Critical reading of primary research articles Mar 13 How to read a Nucleosome eviction and Luebben, W.R., Sharma, N., Deadline for paper activated transcription require and Nyborg, J.K. (2010). GS paper p300 acetylation of histone H3 Proc Natl Acad Sci U S A topic lysine 14. 107: 19254-19259. approval Mar 16-23 Spring Recess Spring Recess Spring Recess Mar 25 Paper preview: TBA TBA Mar 27 Paper TBA TBA discussion: Apr 1 Paper preview: TBA TBA

3 Apr 3 Paper TBA TBA discussion: Apr 8 Paper preview: TBA TBA GS paper outline due Apr 10 Paper TBA TBA discussion:

Apr 15 Paper preview: TBA TBA

Apr 17 Paper TBA TBA discussion:

Apr 22 Paper preview: TBA TBA GS review papers due Apr 24 Paper TBA TBA discussion:

Apr 29 Graduate TBA TBA Student Lectures

May 1 Graduate TBA TBA Student Lectures May 6 Graduate TBA TBA Student Lectures May 8 Graduate TBA TBA Student Lectures May 15 FINAL EXAM Lapham 260, 10am - noon Lapham 260, 10am - noon 10 am - noon

Class Objectives

1. Learn the different mechanisms that regulate eukaryotic gene expression.

2. Apply this knowledge to understanding articles from the current primary literature.

3. Understand the methods that are used to study the regulation of eukaryotic gene expression.

4. Critically read, discuss, and present scientific findings even when they are outside your primary field of interest.

5. Learn how to give and receive constructive criticism on scientific communications.

PAG 4 Requirements

1. Complete reading assignments as noted on the syllabus prior to each class.

2. Complete written homework assignments as specified in directions prior to each class. See specific directions on D2L under heading ”Assignments”.

3. Participate in classroom discussions of homework questions or reading assignments from the current primary literature.

4. Lead discussion of an assigned primary research paper. See specific directions on D2L under heading ”Assignments”.

5. Graduate students only: 5000-8000 word term paper on topic of choice approved by instructor. 30 minute lecture on the topic. See specific directions on D2L under heading ”Assignments”.

6. Complete peer reviews of graduate student papers. See specific directions on D2L under heading ”Assignments”.

7. Take midterm and final exams.

Homework Policy Homework is assigned to help direct your reading of the chapters or articles and to facilitate “active learning” and meaningful classroom discussions. Completion of homework and participation in subsequent classroom discussions is essential for the successful completion of the course. Be prepared to spend, on average, 3 hours per assignment. Homework assignments are described in detail in the D2L handout “Daily Assignments”. In order to receive credit for homework, you must make a good faith effort to correctly answer all homework questions in your own words (e.g. “I don’t know” or “I didn’t understand” or copying from the text are not acceptable answers). Incomplete homework is worth 0 points. Answers to homework will be part of the classroom discussion. You must participate in the class discussion in order to receive full credit for the homework. If you are absent from class, but submitted the homework on time you will receive 2 points for the homework. Since answers are discussed in class, homework submitted after class is not accepted. Homework that is submitted late, but before class will receive half credit if you are in class. Because preparation for class is essential for effective classroom discussion, a minimum of 75% of total homework points is required. Averaging less than 75% in homework points will result in a 5 point deduction from your overall weighted average grade. Students with at least 95% in homework points at the time of the midterm will earn 5 bonus points toward the midterm exam. Students with at least 95% in homework points between the midterm and final exams will earn 5 bonus points toward the final exam.

Examination Policy There will be 1 midterm and a final examination. Exams will be in “blue book” format and consist of essay and/or short answer questions. Partial credit will be given for partially correct answers. Students will be examined on their ability to apply their knowledge of eukaryotic gene regulation to a given research problem. Students are expected to know how to form testable hypotheses, propose appropriate approaches, and be able to articulate possible outcomes and interpretations that could result from their proposed approaches. Requests for make-up exams in the event of an emergency should be made as soon as possible and must be supported by documentation (e.g. physician’s order, accident report). Make- up exams will be oral or written, at the discretion of the instructor. In order to qualify for a make-up exam for religious observances or other unavoidable absences (e.g. scientific conference attendance or graduate school interview), you must notify Dr. Udvadia at least 2 weeks before the scheduled 5 examination time and provide appropriate documentation for absence. The final exam will be given on the date found in the schedule of classes.

Exam Date Time Place___

Midterm Exam Feb 27, 2014 9:30 – 10:45 am LAP260 Final Exam May 15, 2014 10 am- noon LAP260

Grading Policy Grades will be calculated on the basis of 2 exams, participation (homework and class discussion), and journal article presentations (undergrads) or term papers & lectures (grad students only). Your final grade will be weighted as follows.

Graduate students: Undergraduate students:

Homework/Discussion* 5% 5% Midterm Exam 20% 20% Paper Preview Presentation - 20% Journal Club Presentation - 20% Lecture 20% - Term Paper 20% - Final Exam 35% 35%

* Students must have points in each category to pass the course. Students completing less than 75% of the homework points will be penalized 5 points from the total weighted average grade of the course.

Grading Scale 93-100 A 90-92 A- 87-89 B+ 83-86 B 80-82 B- 77-79 C+ 70-76 C 60-69 D

Expectations of students in Bio Sci 565 1. I expect you to have an adult level of maturity, self-motivation, and a strong desire to learn the material in this course. 2. I expect you to have passed the pre-requisite courses with a C or better and to have college level writing and speaking skills. 3. I expect you to show up for every lecture, on time. 4. I expect that you will prepare for lecture by completing the reading assignments before class. 5. I expect you to upload written assignments to D2L on time. 6. I expect you to take notes during lecture. PAG 6 7. I expect you to utilize the study materials provided to you on the D2L site. 8. I expect that you will spend at least 6 hours/week outside of class studying the material for this class. a. Reading assignments should be completed ahead of lecture. b. Lecture notes and reading assignments should be reviewed with a study partner or group at least once/week. c. Any concepts that are unclear to you after reading and reviewing should be discussed with the professor at office hours (schedule alternative appointment if you have a class/work conflict with office hours). 9. I expect you to ask questions when you are confused and to volunteer to answer questions I ask at the beginning of and during the lectures. 10. I expect you to prepare for exam reviews by studying the material ahead of time and by asking specific questions at the review session.

I am here to guide you in studying Mechanisms of Eukaryotic Gene Regulation. Meeting the expectations outlined above will ensure that you learn the material to the best of your ability.

Registration Policy

Last day to drop class without “W” appearing on academic record is Feb 17, 2013. No drops will be allowed after March 14, 2013, except for exceptional non-academic reasons. This course may not be taken with an audit or credit/no credit status. In the event of excess enrollment, priority will be given to students who are registering for the course for the first time.

Attendance Policy: This success of this course is heavily dependent on student participation and interaction therefore attendance is required.

Cell Phone Policy: Please refrain from texting or talking on the phone during lectures and discussions.

Academic Conduct Policy: There is absolutely no tolerance for any kind of cheating or plagiarism on any of the assignments (including homework) in this class. The University has a responsibility to promote academic honesty and integrity and to develop procedures to deal effectively with instances of academic dishonesty. Students are responsible for the honest completion and representation of their work, for the appropriate citation of sources, and for respect of others’ academic endeavors. Students caught plagiarizing will receive a reprimand and a zero for the assignment at a minimum and may be subject to more serious sanctions by the University. This course follows the guidelines and procedures detailed in the description of Student Academic Disciplinary Procedures found in Regents Policy Statements, UWS Chapter 14 and UWM Faculty Document #1686 and can be found online at http://www.uwm.edu/Dept/Acad_Aff/policy/academicmisconduct.html.

Firearms Policy: Accommodations for Students with Disabilities: If you need special accommodations to meet the requirements of this course, please A. No Firearms contact the Student Accessibility Center (Mitchell Hall Room 112, 229- or Dangerous 6287, http://www.sac.uwm.edu) and inform the instructor Weapons in UWM Buildings Individuals are prohibited from carrying firearms and dangerous weapons into buildings or portions of buildings that are owned, occupied, or controlled by UWM. UWM shall place signs in prominent places near all of the entrances to UWM buildings notifying the UWM community and visitors of this ban. This ban on firearms and dangerous weapons inside UWM 7 buildings applies equally to Licensees. This ban does not apply to firearms or dangerous weapons carried solely within motor vehicles that might be parked in UWM parking facilities except as provided in IV.B of this Policy (below).

B. No Firearms within 1000 Feet of Schools Individuals are prohibited from possessing firearms, except for a handgun carried in a concealed manner by a Licensee, outside of UWM buildings, on any portion of UWM buildings or grounds that falls within 1,000 feet of any school (defined above) (e.g. Hartford Elementary School), including within vehicles parked in UWM parking facilities within this zone. These areas are known as “Gun-Free School Zones.” Maps showing the Gun-Free School Zone surrounding Hartford Elementary School and other schools nearby UWM buildings are attached as Appendix A. UWM shall place signs in prominent places on UWM grounds falling within these zones notifying the campus community and visitors of the ban.