Lecture 1

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Molecular Biology Fourth Edition. Copyright © The McGraw-Hill Companies, Inc. ... Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-8. ❑ DNA transposons.
Lecture10 Transposon and Mechanisms of Transposition •Molecular Genetics I: MLGN 301 2016 7/12/2016 By Prof.Dr /Ahmed Mansour Alzohairy

Genetics Department, Zagazig University, Zagazig, Egypt

Learning objectives

Learning about: -

Transposon Mechanisms of Transposition Retrotransposons SINE and LINE

Robert F. Weaver. Molecular Biology Fourth Edition. Copyright © The McGraw-Hill Companies, Inc.

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Learning outcomes By the end of this session and practical, students are expected to be able to understand what are: - The mobile DNA element or transposable element - DNA transposons & Retrotransposon - General Principles of LINE transposition - Generation of RNA from LTR transposon - the difference from retrovirus Robert F. Weaver. Molecular Biology Fourth Edition. Copyright © The McGraw-Hill Companies, Inc.

3-3

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Transposon  DNA sequence that can move in the genome  Also called mobile DNA element or transposable element  “selfish DNA”--exist only to maintain themselves ?  Transposition: The process by which these sequences are copied and inserted into a new site in the genome  Probably had a significant influence on evolution Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

How transposon was found

 1940s, Barbara McClintock discovered the first transposable element in maize, earned a Nobel prize in 1983. Late 1960s, transposition was also found in Bacteria. Barbara McClintock http://en.wikipedia.org/wiki/Barbara_McClintock

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

“We know about the components of genomes that could be made available for such restructuring. We know nothing, however, about how the cell senses danger and instigates responses to it that are often truly remarkable” McClintock, B. (1984) Science 226, 792–801.

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Two Categories  DNA transposons  Retrotransposons “cut-and-paste”

“copy-and-paste”

 Most mobile elements in bacteria is DNA transposons  In contrast, most mobile elements in eukaryotes are retrotransposons, but eukaryotic DNA transposons also occur. Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-8

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Class1

Class2

Retrotransposon

Transposon

DNA transposons  Bacterial Insertion Sequences (IS element)  P element in Drosophila

General structure of bacterial IS elements Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-9

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

General process of transposition for DNA transposons

Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-10

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Retrotransposons  LTR retrotransposons:  Non-LTR retrotransposons: the most common type of transposons in mammals

General structure of eukaryotic LTR retrotransposons Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-11

What is the difference from retrovirus?

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Generation of RNA from LTR transposon

Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-12

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

What is the difference from retrovirus?

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Model for reverse transcription Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-13

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Model for reverse transcription Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-13

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Retrotransposons • Non-LTR retrotransposons 

long interspersed elements (LINEs) ≈6 kb in human account for 21% of the genome  short interspersed elements (SINEs) ≈300 bp in human account for 13% of the genome

Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-15

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

General Principles of LINE transposition

Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-16

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

SINEs (Short Interspersed Elements)

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy Weiner (2000) Fig 1

 Most are tRNA derived; Alu is 7SL-RNA  Nonautonomous  Dependent on other machinery- genome “parasite”  RNA Pol III  Needs LINE Endonuclease and Reverse Transcriptase for activity Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

 Average size 150-200 base pairs  Composed of 3 parts  5’ head  Body  3’ tail

Molecular Genetics I: MLGN 301 2016 name: Prof. Ahmed Mansour Alzohairy VassetzkyTrainer (2013)

Molecular Genetics I: MLGN 301 2016 http://biol.lf1.cuni.cz/ucebnice/images/rep1.gif

Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy Kramerov & Vassetzky (2005)

Transport

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy Kramerov & Vassetzky (2005)

Molecular Genetics I: Batzer MLGN 301 2016 & Deininger, Nature Reviews Trainer name: Prof. Ahmed Mansour Alzohairy Genetics (2002) Box 1

Kramerov & Vassetzky (2005)

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 “Transposons: Mobile DNA” (2012)

Trainer name: Prof. Ahmed Mansour Alzohairy

 Where there is a SINE, there is a LINE  Specificity of EN/RT of LINE dictates location  Expressed during early embryogenesis and decreases in development  Active in tumor cells  Integrates into germ lines

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

References •

• • •

• •

Batzer, M.A. & Deininger, P.L. Alu repeats and Human genomic diversity. Nature Reviews Genetics 3, 370379 (2002). Doi:10.1038/nrg798 http://www.nature.com/nrg/journal/v3/n5/box/nrg798_BX1.html Kramerov, D.A. & Vassetzky, N.S. Short Retroposons in Eukaryotic Genomes. International Review of Cytology, vol 247 (2005) doi: 10.1016/S0074-7696/05 Lodish et al., Molecular Cell Biology, 7th ed. “Transposons: Mobile DNA”. (2012) http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transposons.html Vassetzky. SINEBase (2013) http://sines.eimb.ru Weiner, A. Do all SINEs lead to LINEs? Nature Genetics 24, 332-333 (2000) doi:10.1038/74135 http://www.nature.com/ng/journal/v24/n4/full/ng0400_332.html

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Practical (to try in your own time)

Explain with drawing the differences between the two Categories of mobile DNA element ?

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Molecular Genetics I: MLGN 301 2016 Trainer name: Prof. Ahmed Mansour Alzohairy

Department of Genetics, Zagazig University, Zagazig, Egypt