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MICa 8014

MICa 8014, Small RNA Biology

Spring Semester 2015
Thursdays, 1:30-3:00 pm, 2-580 Moos Tower

Course Coordinator: Subbaya Subramanian, Ph.D.
11-212 Moos Tower

Course Description:

Small RNAs especially microRNAs have emerged as a major regulators of gene expression. Recently, microRNAs have been demonstrated for their potential use in diagnosis and prognosis of various disease conditions including cancers. Recent advances in understanding the biology of miRNA biogenesis and function have contributed to a greater extent in deciphering the molecular mechanism(s) of disease development and progression. The goals of the course are to expose the PhD students to the biology of small RNAs and their role in health and disease. Further, the course will highlight the recent advances in the research methodologies and next generation approaches to understand the small RNA function and gene regulatory networks. 

Who this course is designed for:
The course is designed for 2nd year graduate students in the MICaB Graduate Program However, it is also open to biology graduate program students at a similarly advanced level in other doctoral graduate programs such as GCD and MBB. These students may register with instructor’s approval.  Postdoctoral fellows may want to audit this course. 

Student Performance Objectives:
After completing this course students are expected to:

1. Understand post-transcriptional gene regulation.
2. Develop methods to study small RNA biology.
3. Develop skills of analytical thinking to determine small RNA function.
4. Understand translational research using small RNAs and
 5. Independently develop ideas and presenting them clearly in oral presentations.
     Each session will comprise of a lecture and two 15 min student presentations.


  • One take-home exam 50%
  • In class participation and 15 min presentation 25%
  • Final in class quiz 25%

There will be 1 take home problem set, worth 25% of the final grade.  The take home exam will consist of a paper to read and 3 questions related to the paper.  We expect a 2 page written answer to these questions – possibly with illustration(s) to help explain your points.  Please email your take home exam answers to Dr. Subramanian AND turn in a printed copy.

25% of the grade will be based on an in class presentation on a recent published manuscript describing a breakthrough in the small RNA filed. Students can use power point and data projector or overhead transparencies.  Please have your paper choice ok’ed by Dr. Subramanian.

For the final 50% of the grade students will be based on the performance in the class quiz. 30 objective type questions will be given to students.  

January 22
 Introduction to gene regulation & microRNA biogenesis 
Dr. Subree Subramanian

January 29
Small RNAs: evolutionary conservation and types
Dr. Subree Subramanian

February 5
RNAi vs microRNAs: Fundamentals and concepts
Dr. Subree Subramanian

February 12
Competing endogenous RNAs
Dr. Subree Subramanian

February 19
Virus and bacterial encoded RNAs
Dr. Gary Dunny

February 26
Microbial small RNAs paper discussion
Dr. Gary Dunny

March 5
Small RNAs in development and differentiation
Dr. Ann Rougvie

March 12
microRNA based biomarkers and clinical applications
Dr. Clifford Steer

March 19
Spring Break

March 26
Student presentations and assignments

April 2
OncomiRs, microRNAs in cancer
Dr. Subree Subramanian

April 9
microRNAs and angiogenesis
Dr. Ramki Sundaram

April 16
microRNAs and pharmacogenomics
Dr. Brian VanNess

April 23
Student presentations/assignments

April 30
Circulating RNAs
Dr. Reena Kartha

May 7
Bioinformatics and applications to understand small RNA
Dr. Anne Sarver


Student presentations
Quality of background:
Hypothesis description:
Experimental design:
Suggestions and future work:

Text and Reference Materials:

1. MicroRNAs: From Basic Science to Disease Biology, by Krishnarao Appasani, Sidney Altman, and Victor R. Ambros

2. microRNA: Biology, Function & Expression (Nuts & Bolts series) by Neil J. Clarke; Philippe Sanseau.

3. Lecturers will provide pertinent reading materials (usually a published peer-reviewed paper) at least 2 days before their first lecture