Syllabus for BIOL 532-001, Fall 2015

Recent Discoveries in Molecular Biology:

Novel RegulatoryRNAs in the Eukaryotic Transcriptome

Thursdays, 2:00- 4:45 pm

202 Wilson Hall

Instructor: Dr. Lillie Searles ()

Office: 508 Fordham Hall

Prerequisites: BIOL 202 and either BIOL 205 or a 400-level BIOL course

Course Objectives:

  • To learn about some of the exciting new developments in molecular and cellular biology
  • To develop critical thinking skills by analyzing experimental data in primary research articles
  • To develop scientific communication skills through leading and participating in class discussions

Course Overview: Genomic studies performed in recent years have revealed that the eukaryotic transcriptome, i.e., the complete set of RNA molecules produced by a given cell, is much more complex than expected. For example, many transcripts with no obvious coding potential originate from intergenic regions, which were previously thought to be transcriptionally silent. Research efforts currently underway have the goal of defining the mechanisms that regulate these transcriptional events and defining the functions of these novel noncoding RNAs. The functional studies performed to date indicate that these noncoding RNAs mediate a variety of important regulatory processes. In this course, we will read and discuss some recent papers on this topic. This will involve learning about modern experimental approaches that were probably not discussed in previous classes.Also, a good deal of our time together will be devoted to analyzing and interpreting experimental data. You are not expected to have extensive prior experience with this type of analysis.

Format: This is a seminar course, designed for advanced undergraduate students and graduate students. The class will meet once a week for 2.5 hours. During each class meeting, we will discuss an assigned research article in depth. The entire class is required to read each paper before class and participate in the discussion of the experiments. Teams of two or threestudents will lead each class discussion, and each student will serve in this role at least twice during the semester. (The actual number of times will depend on the class enrollment).

Discussion Leader Responsibilities:

  • At least 3 days before your presentation, meet with Dr. Searles in her office for about 1 hour to discuss the research article. (This meeting is encouraged, but not required.) At that time, you will have the opportunity to resolve any questionspertaining to the paper or relevant background information.
  • Prepare a PowerPoint presentation that covers the relevant background and other information needed to understand the experiments described in the paper. The PowerPoint presentation should also include slides of the figures from the paper, and these slides will provide the basis for the discussion. A final slide should summarize the main points and suggest questions that might be addressed in future experiments.
  • Come to class well-prepared to lead the discussion. You are expected to demonstrate a thorough understanding of the experiments in the paper, even though other students will contribute to explaining and discussing them.

Reading assignments: For each class, a primary research paper and usually one other relevant article, such as a review article or perspectives paper will be posted on sakai.unc.edu. The review/perspective articles are intended to provide a context for the research paper, and, therefore, should be especially useful to discussion leaders.On rare occasions, two closely-related research papers will be assigned and discussed in class.

Exams: There will be two exams during the semester, a mid-term and a final exam, and most of the exam questions will be answered as short essays. Both will be open-note exams, i.e., you are permitted to refer to your notes, the research articles, and other class materials in answering the questions. Each exam will have an out-of-class component (part 1), and an in-class component (part 2). Part 1 of each exam will be completed outside of class and is due on the day of the exam. It will involve reading a new paper and answering several questions about the paper. Part 2of the exam will completed in class, and itwill be based on the papers that we previously read and discussed in class. The final exam is not cumulative, i.e., onlythe papers discussed after the mid-term exam will be included.

Grading:

Presenting and leading discussions40%

Participation in weekly discussions*20%

Midterm exam20%

Final exam20%

* You will be given periodic feedback about your level of participation.

Session # / Date / Topic/Paper
1 / 08/20 / Overview of the class; sign-up to lead class discussions; introduction to long noncoding RNAs and genomic techniques
Long Noncoding RNAs
2 / 08/27 / XistRNA and X-chromosome inactivation in mammals, part 1: Mechanism of XistRNA spreading along the X-chromosome
3 / 09/03 / XistRNA and X-chromosome inactivation in mammals, part 2: Xist-mediated transcriptional silencing
4 / 09/10 / HOTAIR RNA and HOTTIP: regulators of HOX gene expression
5 / 09/17 / HOTAIR RNA and cancer
6 / 09/24 / LincRNA-p21 and the p53 tumor suppressorpathway
7 / 10/01 / TINCR and control of somatic tissue differentiation
8 / 10/08 / Mid-term Exam
10/15 / Fall Break—no class
Short Noncoding RNAs
9 / 10/22 / miRNA mir10b and cancer
10 / 10/29 / miRNAs and the regulation of development in Drosophila
11 / 11/05 / small RNAs and the silencing of repeated and foreign genes
CRISPR/Cas9 as a genome editing tool
12 / 11/12 / RNA-guided human genome editing via Cas9
13 / 11/19 / Potential use of the CRISPR/Cas9 system as an HIV defense tool
11/26 / Thanksgiving Break—no class
14 / 12/05 at
noon / Final exam

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