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Lahore University of Management Sciences

BIO 521 – Gene regulation and Epigenetics


Fall 2018
Instructor Muhammad Tariq, Amir Faisal
Room No. 9-315 A
Office Hours TBA
Email m.tariq@lums.edu.pk
Telephone 8218
Secretary/TA Iqra Manzoor
TA Office Hours -
Course URL (if any) -

Course Basics
Credit Hours 3
Lecture(s) Nbr of Lec(s) Per Week Duration
Recitation (per week) Nbr of Rec (s) Per Duration
Week
Lab (if any ) per week Nbr of Session(s) Per Duration
Week
Tutorial (per week) Nbr of Tut(s) Per Duration
Week

Course Distribution
Core -
Elective Biology Major Elective
Open for Student Category Anyone who fulfills pre-requisites (Juniors, Seniors, MS/PhD)
Closed for Student Category

COURSE DESCRIPTION
Students will be introduced to latest discoveries in the field of gene regulation which include transcriptional, post-transcriptional and translational
levels to regulate genes. Basic nuts and bolts of epigenetics will be explained linked to genome organization in the form of euchromatin,
heterochromatin and different covalent modifications of chromatin and RNAi interference will be discussed in relation to gene regulation. How
chromatin structure may influence gene regulation and how chromatin states are inherited through cell cycle and how structure of chromatin
may influence processes like X inactivation, imprinting, transposon silencing are all topics to be covered. A major section of course will cover how
genes are linked to environment and how environment may influence development. Lectures will cover several research papers related to
different topics and students will be required to read at least three research papers a week which will be discussed in weekly recitation.

COURSE PREREQUISITE(S)
Following pre-reqs are only for undergraduates whereas graduate students must have taken BIO 621.
• BIO216
• BIO221

COURSE OBJECTIVES
Introduce students to latest advances in the field of gene regulation and epigenetics by including several research papers in each
• lecture. An intricate relationship between environment, gene regulation, development must be explained which should enable
• students to understand development of complex traits.

Learning Outcomes
Lahore University of Management Sciences
Students must be able to explain following concepts clearly.
• Epigenetics gene regulation, epigenetic inheritance and how environment may influence gene regulation
• Epigenetic gene regulation and development in eukaryotes
• Read and assimilate latest research articles in the field of epigenetics, should also know how to use different tools to answer
fundamental questions related to epigenetic gene regulation.

Grading Breakup and Policy

Assignment(s): 15%
Home Work:
Presentation(s): 10%
Class Participation:
Attendance:
Midterm Examination: 35%
Project:
Final Examination: 40%

Examination Detail

Yes/No: Yes
Combine Separate: Combine
Midterm
Duration: 2-3 Hrs
Exam
Preferred Date:
Exam Specifications:

Yes/No: Yes
Combine Separate: Combine
Final Exam
Duration: 3 Hrs
Exam Specifications:

COURSE OVERVIEW
Week/ Lecture/ Recommended
Topics Research papers
Module Readings
Introduction to Epigenetics: A brief overview of Chapter 2 Jablonka and Lamb 2002; Waddington
history 1953; Waddington 1956

Epigenetics: overview and concepts, tools and Chapter 3 overview and concepts Richards and Elgin 2002;
machines Epigenetics by C. D. Allis
DNA methylation: mechanisms and processes Chapter 18 Holliday and Pugh 1975; Cross et al 1994;
Epigenetics by C. D. Allis Smith and Meissner 2013; Jones 2012
(reviews)
DNA methylation in mammals Chapter 18 Li et al 1992; Ng et al 1998, Jones et 1998;
Epigenetics by C. D. Allis Weber et al 2007
DNA methylation in plants Chapter 9 Epigenetic regulation in plants Finnegan 1996, Renemus and Dellaporta
Epigenetics by C. D. Allis 1996; Cubas et al 1999
Chromatin modifications: Histone methylation, Chapter 10 Chromatin modifications Rhea et al 2002; Greer & Shi 2010
acetylation, ubiqyitylation Epigenetics by C. D. Allis
Histone variants Chapter 13 Histone variant Schwartz and Kami 2005; Ng & Gurdon
Epigenetics by C. D. Allis 2008; Raisner et al 2005; Mckittrick et al
2003
Non-coding RNAs: RNAi and heterochromatin Chapter 8 Aufsatz 2002; Meister and Tuschl 2004;
Epigenetics by C. D. Allis Lipman 2004; Volpe et al 2002
Dosage compensation in mammals: Xist, HMTs and Chapter 11
DNMTs Epigenetics by C. D. Allis
Dosage compensation in Drosophila: MSL, SXL, MOFS Chapter 16
Epigenetics by C. D. Allis
Lahore University of Management Sciences
Genomic imprinting in mammals
Genomic imprinting in plants
Epigenetic cellular memory Chapter 11 and 12 Ringrose and Paro 2004; Probst 2009
Epigenetics by C. D. Allis
Transcriptional silencing by Polycomb group proteins Chapter 11 and 12
Epigenetics by C. D. Allis
Transcriptional regulation by Trx group proteins Chapter 11 and 12
Epigenetics by C. D. Allis
Epigenetics in yeast: mating type locus, telomere
silecing
Epigenetics in Drosophila: position effect variation,
heterochromatin
Genotype to Phenotype: Ecological Dev Biology by Epel and Gilbert
Environment as Normal Agent in Producing
Phenotype

Genotype to Phenotype: Molecular Changes caused Ecological Dev Biology by Epel and Gilbert
by Environment & Transgenerational Inheritance
Environmental Assaults on Development: Ecological Dev Biology by Epel and Gilbert
Teratogenesis
Epigenetic Origin of Adult Diseases Ecological Dev Biology by Epel and Gilbert

Environment, Development and Evolution: cryptic Ecological Dev Biology by Epel and Gilbert
genetic & epigenetic variation

Prions as Epigenetic Regulatory Mechanism Ecological Dev Biology by Epel and Gilbert

Textbook(s)/Supplementary Readings

• Epigenetics by C. D. Allis, Danny Reinberg and Thomas Jenuwein


• Ecological Developmental Biology by Gilbert and Epel.