PSS6325 - Epigenetic Mechanisms

Instructuor

Dr. Benildo G. de los Reyes

Professor of Plant Genomics and Bayer CropScience Endowed Chair
Graduate Programs Director
Department of Plant and Soil Science
Texas Tech University

Experimental Sciences Building
Room 215, Mail Stop 2122
Lubbock, TX 79409-2122
Phone: +1 (806) 834-6421; Fax: 806-742-0775
Email: benildo.reyes@ttu.edu

Text Book

Allis CD, Caparros ML, Jenuwein T, Reinberg D (2015) Epigenetics, 2nd Edition, Cold Spring Harbor Laboratory Press, ISBN:978-1-936113-59-0 or newer edition if available.

Lecture hand-outs and power point slides will be accessible to students in electronic or other forms. Supplementary printed reading materials will also be provided as necessary.

Course Description

Prerequisites: Consent of instructor; 3-credits, lecture

Epigenetics is the study of phenotypic expression that cannot be fully explained by Mendelian principles of heredity, and by DNA sequence variation among individuals. The core of this science is rooted from intrinsically and extrinsically determined processes that lead to dynamic changes in chromatin structure, DNA methylation, RNA- directed gene regulation and genome modification, and how these processes bring about heritable phenotypic variation at the somatic and/or germ levels. During the last decade, the study of epigenetic mechanisms has become a critical aspect in understanding how plants and animals develop and adapt to environmental changes and diseases, providing another layer of complexity to the flow of genetic information as classically defined by the central dogma of molecular biology.

This course opens with discussions of the basic concepts and overview of classical examples of epigenetic phenomena in eukaryotes. The initial part of the course will set the framework to examine the various molecular mechanisms that have recently been uncovered in a number of eukaryotic models including yeast, Arabidopsis, maize, C. elegans, Drosophila, and mouse. Molecular mechanisms involving histone modification and chromatin remodeling, DNA modification by cytosine methylation, genomic imprinting, paramutation, transposable element-induced gene silencing, position effect variegation, post-transcriptional gene silencing by small regulatory RNA molecules, and RNA-directed DNA methylation are highlighted in context of the current understanding of genome structure, function, regulation and evolution in plants and animals.

Purpose of the course

Fundamental principles governing the functions of genes and genomes as defined by the central dogma of molecular biology have greatly advanced our understanding of the cellular processes associated with growth, development, and responses to biotic and abiotic stimuli. During the last several decades, the study of epigenetic mechanisms has expanded the realm of how genes and genomes function to define the phenotype, beyond the scope of the central dogma. This topic is not covered in-depth by traditional courses in genetics, molecular biology, physiology, and biochemistry. Epigenetics is now considered as the critical piece of the puzzle to fully understand the finer details of 'genotype x environment interaction' that lead to phenotypic expression in plants and animals. Therefore, it is critically important for the continuous advancement of biotechnology and its various applications in agriculture (plant and animal breeding, health, nutrition, and production) and human medicine. Under these contexts, PSS 6325 aims to provide graduate students engaged in any aspect of plant and animal biological research enabled by the genomics paradigm, with a platform for understanding the recent paradigm shifts brought about by epigenetics, and not directly addressed by the central dogma. Successful completion of this course fulfills the requirements for graduate degrees (M.S., Ph.D.) in any basic or applied disciplines of plant and animal biosciences including genetics, biochemistry, molecular biology, plant/animal breeding, plant/animal/human nutrition, agronomy, horticulture and plant/animal conservation sciences. It can also be used to fulfill elective courses for graduate students in the areas of bioinformatics, biotechnology, and bioengineering.

Expected learning outcomes

This course is a platform for learning the fundamental differences of epigenetic regulatory mechanisms from genetic regulatory mechanisms, at a level sufficient to allow comprehension of both the conceptual and technical aspects of research papers that are rapidly accumulating in this vibrant area of research in modern biology. Upon successful completion of this course, students will be able to:

1. Recognize the fundamental differences between genetic and epigenetic mechanisms and their significance to basic processes of growth, development, and responses to biotic and abiotic stimuli at the cellular and whole organismal levels.
2. Interpret molecular biological and genomic data from research literature addressing questions about epigenetic mechanisms in plants and/or animals.
3. Formulate original questions and/or hypotheses relevant to epigenetically regulated processes in plants and/or animals, and design experiments addressing those questions and/or hypotheses.
4. Demonstrate the ability to articulate and explain their ideas of epigenetic mechanisms to other scientists.

Methods for assessing the learning outcomes

Expected learning outcomes will be assessed using a combination of approaches that includes the following:

1. For each topic, individual students will be assigned to make an oral presentation on a research paper on epigenetic mechanisms that was recently published in any research journal. Papers must be chosen by the students themselves and must be approved by the instructor prior to class presentation at least one week before the scheduled presentation. Students will also write a brief synthesis, analysis, and critique of the research paper which must include their own interpretation, conclusions, questions that were left hanging, and how those questions should be addressed with further research.
2. Students will take a one-on-one oral exam with the instructor after the completion of the theoretical aspects of modules 1, 2, 3, and 4 (midterm). Questions for this oral exam will include conceptual, problem-solving and/or integration types of questions.
3. Students will write a research proposal on an original idea addressing an important question/hypothesis on epigenetic mechanisms either on a plant or animal study system, in the style and format of either NSF, NIH or USDA-AFRI programs.
4. Students will orally present and defend the ideas behind their research proposal to a mock panel of experts consisting of invited guests from the faculty, postdocs and senior graduate students.