Lahore University of Management Sciences BIO621 –Genetics and Genomics Spring 2016 Instructor
Sadia Hamera (Lead), Saima Anwar, Aziz Mithani
Room No. Office Hours Email Telephone Secretary/TA TA Office Hours Course URL (if any)
[email protected],
[email protected],
[email protected] 8452, 8413 TBA TBA No
Course Basics Credit Hours Lecture(s) Recitation (per week) Lab (if any ) per week Tutorial (per week)
Course Distribution Core Elective Open for Student Category Closed for Student Category
Nbr of Lec(s) Per Week Nbr of Rec (s) Per Week Nbr of Session(s) Per Week Nbr of Tut(s) Per Week
2
Duration
75min each
1
Duration
50 min
no
Duration
no
no
Duration
no
Core course for Biology major students For any student MS students (Biology) None
COURSE DESCRIPTION
The intellectual framework of this course will introduce students the practical approaches to the functional genetics and computational genomics.
COURSE PREREQUISITE(S) • • •
None
COURSE OBJECTIVES • To orient students approach from theoretical to practical bench and emphasize them to perceive genetics from • • •
implementation view point. To blaze a trail by introducing gene silencing approaches to access functional perspectives. How to differentiate genome stability from genome maintenance and use it as a tool. To understand how to explore biological functions using various genetic and epigenetic approaches.
Lahore University of Management Sciences Grading Breakup and Policy Assignment(s): 10% Quiz(s): 10% Class Participation and Attendance: 5% Exam1: 25% Exam2: 25% Presentations: 10% Exam 3: 15% Examination Detail
Midterm Exam
Yes/No: Yes Combine Separate: Separate Duration: 3hours Preferred Date: Exam Specifications:
Final Exam
Yes/No: Yes Combine Separate: Separate Duration: 3 hours Exam Specifications:
COURSE OVERVIEW Lecture
1-3 (Saima)
Topics
Recommended Readings
Research articles
Introductory lecture. Genome organization in prokaryotes, eukaryotes and selected viruses; genome evolution; Genetics from past to future. How to think, perceive and implement and contribute their share in genetics and therapeutics.
4-6 (Sadia)
Molecular Genetics: Introduction to genetic approaches and techniques, Forward genetics, reverse genetics, Mutants screening by EMS and UV irradiation. Knock out mutants by TDNA insertions, P-elements in drosophila and ENU mutagenesis in mouse.
Chapter 11, 13: Introduction to genetic Analysis by Griffiths et al., Research articles will be discussed.
1.
2.
1.
7-8 (Sadia)
Plant Genomics and Epigenomics: DNA and histone methylation, DNA methylation pathway, tools to measure DNA methylation, Epigenetic markers like Superman, FWA study.
Introduction to genetic Analysis by Griffiths et al.,
2. 3. 4.
9-10 (Sadia)
Genome stability: Transposons Retroelements, and the maintenance of genome integrity in maize, Arabidopsis,
Chapter 13: Introduction to Genetic Analysis by Griffiths et al., in 8th edition
Identification of genes required for de novo DNA (2011) Epigenetics 6:344-354. Drosophila P elements preferentially transpose to replication origins. PNAS 2011.108: 15948-53
Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNAdirected DNA methylation. Nat Let (2006) 443:1008-12 Hypermethylated epigenetic alleles Science RNA Silencing Genes Control de Novo DNA Methylation Two-Step Recruitment of RNADirected 2006. Plos Biol 4:303
1. Mobilization of transposons by… Nature 2001:411(212-214) 2. Movers and shakers maize transposons as
Lahore University of Management Sciences
11-12 (Sadia)
Drosophila and other model organisms.
and Chapter 14 in 9th edition.
Genome Maintenance: Ubquitination:posttranslational modification, formation of ubq chains, K48 a 26S proteasome pathway and K11, K27, K63 mediated modification.
Ubiquitin and the biology of the edited by Jan-Michael Peters,J.RobinHarrisand DanielFinley cell (1998)
tools… Current opinions in plant biology 1995. 1. Regulation of p53 localization and activity by UBC13.(2006) Mol Cell Biol 26:89018913 2. A bacterial E3 ubiquitin ligase targets a host protein kinase. Nature. 2007 19; 448: 370–374
Exam 1 Human genetics: Pedigree patterns to trace genetic diseases i.e autosomal and X linked patterns of inheritance. Gene mapping, forescensic and inheritance markers including RFLPs, STRs and SNPs.
13-17 (Saima)
18-19 lectures (Sadia Hamera)
5 lectures (Aziz)
3 lectures (Aziz) 1 lecture (Aziz)
Non coding RNA: Discovery of RNAi. RNAi pathways. Long noncoding RNAs, short non coding RNAs. RNAi as tool to study genes functions. Non coding RNA roles in epigenetics. Small RNAs a defense crosstalk between host-pathogen (viruses).
Exam 2 Computational Genomics: From Microarrays to Next generation sequencing, different sequencing platforms, de novo assembly, genome re-sequencing, variance detection, identification of alternative splicing and genomic rearrangements miRNAs and Epigenome: Genome-wide mapping Of miRNA-mRNA interactions, identification of small RNA targets, bisulphite sequencing and epimutations Perspective: Beyond Genomics
Chapter 3 and 6: An introduction to Human Molecular Genetics by Jack J Pasternak Chapter 2: Introduction to genetic Analysis by Griffiths et al.,
Exercise questions will be provided in class.
Chapter 19: RNAi A guide to gene silencing. (Thomas tuschl, Gregory J Hannon, David Baulcomb Craig Pikaard labs work will be discussed)
1.
Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic.. ScienceExpress 2008. 2. Cells Small RNAs and the control of transposons and viruses in Drosophila 2009 Cell . 3. Snapshot: small rna mediated…. Cell (2007) 4. Specialization and evolution of endogenous small RNA pathways Nature 2007.
TBA
TBA
TBA
TBA
TBA
TBA
Exam 3
Textbook(s)/Supplementary Readings
I.
Introduction to Genetic Analysis by Griffiths, Wesler, Lewontin, Gelbart, Suzuki, Miller (eighth edition): Photocopies of selected chapters
II.
Chromatin and Gene Regulation: Molecular mechanisms in epigenetics by Brian M. Turner: Photocopies of selected chapters.
III.
Genetics: Analysis of genes and genomes (sixth edition) by Daniel L. Hartl and Elizabeth W. Jones: Photocopies of selected chapters
Lahore University of Management Sciences IV. V. VI.
Genetics by Monroe W. Strickberger (3rd edition). Photocopies of selected chapters An introduction to Human Molecular Genetics. Jack J Pasternak 2nd Edition.(Selected chapters) Ubiquitin and the Biology of Cell by Jan Michael Peters, Robin Harris.
