Department of Biomedical Engineering

GBE 406 | Course Introduction and Application Information

Course Name

Gene Control and Epigenetics

Code	Semester	Theory (hour/week)	Application/Lab (hour/week)	Local Credits	ECTS
GBE 406	FALL	2	2	3	6

Prerequisites	None
Course Language	English
Course Type	ELECTIVE_COURSE
Course Level	First Cycle
Mode of Delivery	Face-To-Face
Teaching Methods and Techniques of the Course	Discussion Group work Problem solving Case study Q&A Lecture/Presentation
National Occupational Classification Code	-
Course Coordinator	Doç. Dr. Cihangir Yandım
Course Lecturer(s)	Doç. Dr. Cihangir Yandım
Assistant(s)	-

Course Objectives

The aim of this course is to teach the effects of gene control and epigenetic mechanisms on pluripotency and reprogramming, their role in cell division and cell differentiation, and how errors in these mechanisms lead to diseases. It is also aimed to give techniques related to gene control and measurement of epigenetic mechanisms.

Learning Outcomes

The students who succeeded in this course;

Name	Description	PC Sub	* Contribution Level
Name	Description	PC Sub	1	2	3	4	5
LO1	Will be able to explain the concept of epigenetics and its multi-layered mechanisms,	1.2		X
LO2	Will be able to discuss epigenetic mechanisms through specific examples,	1.2		X
LO3	Will be able to explain silencing methods at the transcription level,	4		X
LO4	Will be able to choose techniques that can analyze the relationship between epigenetics and human diseases,	4		X
LO5	Will be able to interpret the results of methods measuring epigenetic markers.	5.1	X

Course Description

This course explains the gene control mechanisms that affect development and deteriorate in disease. The course covers epigenetic markers and related techniques to identify differences in gene regulation.

Related Sustainable Development Goals

Course Category	Core Courses
	Major Area Courses	X
	Supportive Courses
	Media and Managment Skills Courses
	Transferable Skill Courses

WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES

Week	Subjects	Required Materials	Learning Outcome
1	Introduction	Epigenetics, Cold Spring Harbor Laboratory Press, 2015 - Chapter 1	LO1
2	Circuit elements of a gene	Molecular Biology of the Cell 6th edition, Garland-Norton, 2015 - Chapter 1	LO1
3	RNA polymerase and fundamentals of gene control	Molecular Biology of the Cell 6th edition, Garland-Norton, 2015. -Chapter 6. Transcription Regulation at the Core: Similarities Among Bacterial, Archaeal, and Eukaryotic RNA Polymerases, Decker and Hinton, Annual Reviews, 2013.	LO3
4	Chromatin and chromsome architecture	Molecular Biology of the Cell 6th edition, Garland-Norton, 2015. - Chapter 4.	LO1
5	Histone modifications	Epigenetics, Cold Spring Harbor Laboratory Press, 2015.- Chapters 4,5,6. Lateral Thinking: How Histone Modifications Regulate Gene Expression, Lawrence et al., Trends in Genetics, 2016.	b844e03f-e191-4b1f-982c-37cd80d63801
6	Dynamics of chromatin remodeling	Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes, Clapier et al. , Nature Reviews, 2017.	LO4
7	Chromatin balance and gene insulation	Heterochromatin effects in Friedreich's ataxia and sexual dimorphism. C. Yandım, PhD Thesis, Imperial College London, 2012. Gene Regulation and Epigenetics in Friedreich's ataxia. Yandım et al. J of Neurochem., 2013.	LO2
8	Midterm		-
9	Nuclear architecture	Biogenesis and function of nuclear bodies, Mao et al, Trends in Genetics, 2011.	LO1
10	DNA methylation and epigenetic reprogramming	Principles of DNA methylation and their implications for biology and medicine, Dor and Cedar., Lancet, 2018.	LO4
11	RNA interference	Strategies for silencing human disease using RNA interference, Kim and Rossi, Nature Reviews, 2007.	LO3
12	Epigenetic memory	Mechanisms of epigenetic memory, D'Urso and Brickner, Trends in Genetics, 2014.	LO5
13	Induced pluripotency	Epigenetics, Cold Spring Harbor Laboratory Press, 2015. - Chapter 28	LO2
14	Epigenetics and human disease	Epigenetics, Cold Spring Harbor Laboratory Press, 2015- Chapter 33.	LO5
15	Review		-
16	Final exam		-

Course Notes/Textbooks

Human Molecular Genetics by Strachan and Read (2018) Garland Science. ISBN: 0815345895

Suggested Readings/Materials

Chromosome Architecture and Genome Organization by Bernardi (2015) PLoS One
Heterochromatin effects in Friedrich's ataxia and sexual dimorphism (2012) PhD Thesis by C. Yandım
Transcription Regulation at the Core: similarities among bacterial archaeal and eukaryotic RNA polymerases by Decker and Hinton (2013) Annual Reviews
Lateral thinking: how histone modifications regulate gene expression by Lawrence et al. (2016) Trends in Genetics
Principles of DNA methylation and their implications for biology and medicine by Dor and Cedar (2018) The Lancet
Molecular mechanisms of RNA interference by Wilson and Doudna (2013) Annual Reviews.

EVALUATION SYSTEM

Semester Activities	Number	Weighting	LO1	LO2	LO3	LO4	LO5
Homework / Assignments	4	40		X	X	X	X
Midterm	1	30	X	X			X
Final Exam	1	30	X		X	X
Total	6	100

ECTS / WORKLOAD TABLE

Semester Activities	Number	Duration (Hours)	Workload
Participation	-	-	-
Theoretical Course Hours	16	2	32
Laboratory / Application Hours	16	2	32
Study Hours Out of Class	14	2	28
Field Work	-	-	-
Quizzes / Studio Critiques	-	-	-
Portfolio	-	-	-
Homework / Assignments	4	5	20
Presentation / Jury	-	-	-
Project	-	-	-
Seminar / Workshop	-	-	-
Oral Exams	-	-	-
Midterms	1	34	34
Final Exam	1	34	34
		Total	180

COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP

#	PC Sub	Program Competencies/Outcomes	* Contribution Level
#	PC Sub	Program Competencies/Outcomes	1	2	3	4	5
1	Engineering Knowledge: Knowledge of mathematics, science, basic engineering, computation, and related engineering discipline-specific topics; the ability to apply this knowledge to solve complex engineering problems.
	1	Mathematics
	2	Science		LO1 LO2
	3	Basic Engineering
	4	Computation
	5	Related engineering discipline-specific topics
	6	The ability to apply this knowledge to solve complex engineering problems
2	Problem Analysis: Ability to identify, formulate and analyze complex engineering problems using basic knowledge of science, mathematics and engineering, and considering the UN Sustainable Development Goals relevant to the problem being addressed.
3	Engineering Design: The ability to devise creative solutions to complex engineering problems; the ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions.
	1	Ability to design creative solutions to complex engineering problems
	2	Ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions
4	Use of Techniques and Tools: Ability to select and use appropriate techniques, resources, and modern engineering and computing tools, including estimation and modeling, for the analysis and solution of complex engineering problems, while recognizing their limitations.			LO3 LO4
5	Research and Investigation: Ability to use research methods to investigate complex engineering problems, including literature research, designing and conducting experiments, collecting data, and analyzing and interpreting results.
	1	Literature research for the study of complex engineering problems	LO5
	2	Designing experiments
	3	Ability to use research methods, including conducting experiments, collecting data. analyzing and interpreting results
6	Global Impact of Engineering Practices: Knowledge of the impacts of engineering practices on society, health and safety, economy, sustainability, and the environment, within the context of the UN Sustainable Development Goals; awareness of the legal implications of engineering solutions.
	1	Knowledge of the impacts of engineering practices on society, health and safety, economy, sustainability, and the environment, within the context of the UN Sustainable Development Goals
	2	Awareness of the legal implications of engineering solutions
7	Ethical Behavior: Acting in accordance with the principles of the engineering profession, knowledge about ethical responsibility; awareness of being impartial, without discrimination, and being inclusive of diversity.
	1	Acting in accordance with the principles of the engineering profession, knowledge about ethical responsibility ethical responsibility
	2	Awareness of being impartial and inclusive of diversity, without discriminating on any subject
8	Individual and Teamwork: Ability to work effectively, individually and as a team member or leader on interdisciplinary and multidisciplinary teams (face-to-face, remote or hybrid).
	1	Ability to work individually and within the discipline
	2	Ability to work effectively as a team member or leader in multidisciplinary teams (face-to-face, remote or hybrid)
9	Verbal and Written Communication: Taking into account the various differences of the target audience (such as education, language, profession) on technical issues.
	1	Ability to communicate verbally
	2	Ability to communicate effectively in writing
10	Project Management: Knowledge of business practices such as project management and economic feasibility analysis; awareness of entrepreneurship and innovation.
	1	Knowledge of business practices such as project management and economic feasibility analysis
	2	Awareness of entrepreneurship and innovation
11	Lifelong Learning: Lifelong learning skills that include being able to learn independently and continuously, adapting to new and developing technologies, and thinking questioningly about technological changes.