Lecture 7 - Eukaryotic Transposable Elements | Genetics (Zoology) by ILLL, DU - Biotechnology Engineering (BT) PDF Download

 Page 1


  Eukaryotic Transposable Elements   
 
1 
 
Institute of Lifelong Learning, University of Delhi 
NME-Zoology 
Genetics 
Lesson : Eukaryotic Transposable Elements 
Lesson Developer: Dr. Shailly Anand  and 
Dr. Jaya Malhotra 
College/Dept: Zoology, DDU college 
Zoology, Hansraj college 
Lesson Reviewer: Dr. Shashi Chawla 
College/Dept: Department of Microbiology, Gargi College 
 
 
 
 
 
 
 
 
 
 
Page 2


  Eukaryotic Transposable Elements   
 
1 
 
Institute of Lifelong Learning, University of Delhi 
NME-Zoology 
Genetics 
Lesson : Eukaryotic Transposable Elements 
Lesson Developer: Dr. Shailly Anand  and 
Dr. Jaya Malhotra 
College/Dept: Zoology, DDU college 
Zoology, Hansraj college 
Lesson Reviewer: Dr. Shashi Chawla 
College/Dept: Department of Microbiology, Gargi College 
 
 
 
 
 
 
 
 
 
 
  Eukaryotic Transposable Elements   
 
2 
 
Institute of Lifelong Learning, University of Delhi 
Table of Contents 
? Introduction 
? General Features of Transposable Elements in Eukaryotes 
? Class I Transposons 
? LTR’s 
? Non- LTR’s 
? Class II Transposons 
 
? Examples of Transposable Elements in Eukaryotes  
? Ac – Ds system in maize 
? Experiments performed by Barbara McClintock 
? Transposable Elements in Drosophila 
? Copia elements 
? P - elements  
? Discovery 
? P – element mediated transformations 
? Transposable Elements in Humans 
? LINE Insertions 
? SINE Insertions 
 
? Summary 
? Glossary 
? Practice Questions 
? Answer to the Questions 
? References 
 
 
Page 3


  Eukaryotic Transposable Elements   
 
1 
 
Institute of Lifelong Learning, University of Delhi 
NME-Zoology 
Genetics 
Lesson : Eukaryotic Transposable Elements 
Lesson Developer: Dr. Shailly Anand  and 
Dr. Jaya Malhotra 
College/Dept: Zoology, DDU college 
Zoology, Hansraj college 
Lesson Reviewer: Dr. Shashi Chawla 
College/Dept: Department of Microbiology, Gargi College 
 
 
 
 
 
 
 
 
 
 
  Eukaryotic Transposable Elements   
 
2 
 
Institute of Lifelong Learning, University of Delhi 
Table of Contents 
? Introduction 
? General Features of Transposable Elements in Eukaryotes 
? Class I Transposons 
? LTR’s 
? Non- LTR’s 
? Class II Transposons 
 
? Examples of Transposable Elements in Eukaryotes  
? Ac – Ds system in maize 
? Experiments performed by Barbara McClintock 
? Transposable Elements in Drosophila 
? Copia elements 
? P - elements  
? Discovery 
? P – element mediated transformations 
? Transposable Elements in Humans 
? LINE Insertions 
? SINE Insertions 
 
? Summary 
? Glossary 
? Practice Questions 
? Answer to the Questions 
? References 
 
 
  Eukaryotic Transposable Elements   
 
3 
 
Institute of Lifelong Learning, University of Delhi 
Introduction 
First discovered by Barbara McClintock (1983), transposable elements, also called as the 
jumping genes, transposons or the mobile DNA are genetic elements that can hop in and 
out of the chromosomes and thus capable of changing their position. These may follow the 
cut-and-paste or the copy-and-paste mechanism but by either of the ways, they result in 
genome alterations. In addition to crossing over events, independent assortment of 
gametes, fertilization and mutations, transposable elements are responsible for bringing 
about variations in the organism. It has served as a means of creating evolutionary 
novelties in genomes without affecting its integrity. This may be a reason why the 
opportunistic attitude of evolution led to the accumulation of enormous amounts of such 
DNA elements in the genomes. They also constitute the single largest fraction of the non-
coding DNA in eukaryotic genomes (C-value). These are present in all genomes from the 
bacteria to the humans. Since these are capable of reshaping the genomes, geneticists 
exploit them as cloning tags, mutagens or vectors to carry a foreign gene into the 
organisms. 
 
General Features of Transposable Elements in Eukaryotes 
Mobile elements in eukaryotes are broadly classified as Class-I and Class-II types which 
work by copy-and-paste & cut-and-paste mechanism respectively. Each of these types has 
been briefly described in the section below. But before moving to further details, it is 
important to understand that the mobile DNA is associated with autonomous elements 
(comprise of open reading frames that encode proteins necessary for transposition) and non 
– autonomous elements (do not code for proteins that help in transposition but do so due to 
other DNA sequences present within them). 
1. Class-I Transposons: These transpose using an RNA intermediate and are also 
called as retrotransposons. The insertion of transposable elements belonging to this 
class lead to duplication of the element as it works by copy-and paste method. Class-
I transposons are further grouped as those with Long Terminal Repeats (LTR) and 
Non-LTR’s.  
  
Page 4


  Eukaryotic Transposable Elements   
 
1 
 
Institute of Lifelong Learning, University of Delhi 
NME-Zoology 
Genetics 
Lesson : Eukaryotic Transposable Elements 
Lesson Developer: Dr. Shailly Anand  and 
Dr. Jaya Malhotra 
College/Dept: Zoology, DDU college 
Zoology, Hansraj college 
Lesson Reviewer: Dr. Shashi Chawla 
College/Dept: Department of Microbiology, Gargi College 
 
 
 
 
 
 
 
 
 
 
  Eukaryotic Transposable Elements   
 
2 
 
Institute of Lifelong Learning, University of Delhi 
Table of Contents 
? Introduction 
? General Features of Transposable Elements in Eukaryotes 
? Class I Transposons 
? LTR’s 
? Non- LTR’s 
? Class II Transposons 
 
? Examples of Transposable Elements in Eukaryotes  
? Ac – Ds system in maize 
? Experiments performed by Barbara McClintock 
? Transposable Elements in Drosophila 
? Copia elements 
? P - elements  
? Discovery 
? P – element mediated transformations 
? Transposable Elements in Humans 
? LINE Insertions 
? SINE Insertions 
 
? Summary 
? Glossary 
? Practice Questions 
? Answer to the Questions 
? References 
 
 
  Eukaryotic Transposable Elements   
 
3 
 
Institute of Lifelong Learning, University of Delhi 
Introduction 
First discovered by Barbara McClintock (1983), transposable elements, also called as the 
jumping genes, transposons or the mobile DNA are genetic elements that can hop in and 
out of the chromosomes and thus capable of changing their position. These may follow the 
cut-and-paste or the copy-and-paste mechanism but by either of the ways, they result in 
genome alterations. In addition to crossing over events, independent assortment of 
gametes, fertilization and mutations, transposable elements are responsible for bringing 
about variations in the organism. It has served as a means of creating evolutionary 
novelties in genomes without affecting its integrity. This may be a reason why the 
opportunistic attitude of evolution led to the accumulation of enormous amounts of such 
DNA elements in the genomes. They also constitute the single largest fraction of the non-
coding DNA in eukaryotic genomes (C-value). These are present in all genomes from the 
bacteria to the humans. Since these are capable of reshaping the genomes, geneticists 
exploit them as cloning tags, mutagens or vectors to carry a foreign gene into the 
organisms. 
 
General Features of Transposable Elements in Eukaryotes 
Mobile elements in eukaryotes are broadly classified as Class-I and Class-II types which 
work by copy-and-paste & cut-and-paste mechanism respectively. Each of these types has 
been briefly described in the section below. But before moving to further details, it is 
important to understand that the mobile DNA is associated with autonomous elements 
(comprise of open reading frames that encode proteins necessary for transposition) and non 
– autonomous elements (do not code for proteins that help in transposition but do so due to 
other DNA sequences present within them). 
1. Class-I Transposons: These transpose using an RNA intermediate and are also 
called as retrotransposons. The insertion of transposable elements belonging to this 
class lead to duplication of the element as it works by copy-and paste method. Class-
I transposons are further grouped as those with Long Terminal Repeats (LTR) and 
Non-LTR’s.  
  
  Eukaryotic Transposable Elements   
 
4 
 
Institute of Lifelong Learning, University of Delhi 
? LTR’s – They have repeat sequences from 100kb to even higher sizes in 
direct orientation. The autonomous elements contain the gag and pol genes 
which encode for capsid like proteins and other proteins like reverse 
transcriptase, RNase, integrase etc respectively. This organization resembles 
the retroviruses. Their mode of action involves the synthesis of a transcript 
(in the nucleus) that moves to the cell cytoplasm where it serves as an mRNA 
and is reverse transcribed to cDNA (Complementary DNA). The newly 
synthesized cDNA moves back to the nucleus and gets integrated into the 
genome. Therefore, they create a copy of themselves that results in increase 
in their copy number which in turn is manifested as increased genome size in 
eukaryotes.  
? Non - LTR’s – These include the LINEs and SINEs present in the human 
genome. LINEs are autonomous elements that encode for two open reading 
frames (ORF’s) – one coding for a RNA binding protein and the other for an 
endonuclease and reverse transcriptase activity. Unlike other transcripts, 
these ORF’s are transcribed by RNA Polymerase II from the 5’ region to the 
terminator sequence that is present downstream at 3’ end. In contrast to 
above are the SINEs that represent non-autonomous elements and are 
therefore dependent on the autonomous behavior machinery of the LINES to 
increase their number in the genome. They also contain an internal promoter 
region for RNA Polymerase III. As the usual mRNA, these transcripts (of 
LINEs and SINEs) terminate in a polyadenylated tail. 
Value addition: Did you know??? 
Heading text: Mobile DNA and Gene Therapy 
Body text: Transposons that were once thought to be just a portion of the junk DNA, 
today play a significant role in biology than we ever believed. With this thought, Nancy 
Craig launched a new online journal named ‘Mobile DNA’ in 2010. She believes that 
transposition is instrumental to evolutionary change. Most transpositions are harmless but 
some may contribute to diseases. Craig assumes that these jumping elements also hold a 
prospect of serving as a tool to combat diseases by Gene Therapy. It involves the use of a 
virus/ retrovirus (a type of transposon) to introduce a healthy gene into cells with defect. 
One problem encountered with this approach was the lack of control on the gene’s target 
site of insertion. In 1999, a trial was initiated to use transposons as vehicle for gene therapy 
Page 5


  Eukaryotic Transposable Elements   
 
1 
 
Institute of Lifelong Learning, University of Delhi 
NME-Zoology 
Genetics 
Lesson : Eukaryotic Transposable Elements 
Lesson Developer: Dr. Shailly Anand  and 
Dr. Jaya Malhotra 
College/Dept: Zoology, DDU college 
Zoology, Hansraj college 
Lesson Reviewer: Dr. Shashi Chawla 
College/Dept: Department of Microbiology, Gargi College 
 
 
 
 
 
 
 
 
 
 
  Eukaryotic Transposable Elements   
 
2 
 
Institute of Lifelong Learning, University of Delhi 
Table of Contents 
? Introduction 
? General Features of Transposable Elements in Eukaryotes 
? Class I Transposons 
? LTR’s 
? Non- LTR’s 
? Class II Transposons 
 
? Examples of Transposable Elements in Eukaryotes  
? Ac – Ds system in maize 
? Experiments performed by Barbara McClintock 
? Transposable Elements in Drosophila 
? Copia elements 
? P - elements  
? Discovery 
? P – element mediated transformations 
? Transposable Elements in Humans 
? LINE Insertions 
? SINE Insertions 
 
? Summary 
? Glossary 
? Practice Questions 
? Answer to the Questions 
? References 
 
 
  Eukaryotic Transposable Elements   
 
3 
 
Institute of Lifelong Learning, University of Delhi 
Introduction 
First discovered by Barbara McClintock (1983), transposable elements, also called as the 
jumping genes, transposons or the mobile DNA are genetic elements that can hop in and 
out of the chromosomes and thus capable of changing their position. These may follow the 
cut-and-paste or the copy-and-paste mechanism but by either of the ways, they result in 
genome alterations. In addition to crossing over events, independent assortment of 
gametes, fertilization and mutations, transposable elements are responsible for bringing 
about variations in the organism. It has served as a means of creating evolutionary 
novelties in genomes without affecting its integrity. This may be a reason why the 
opportunistic attitude of evolution led to the accumulation of enormous amounts of such 
DNA elements in the genomes. They also constitute the single largest fraction of the non-
coding DNA in eukaryotic genomes (C-value). These are present in all genomes from the 
bacteria to the humans. Since these are capable of reshaping the genomes, geneticists 
exploit them as cloning tags, mutagens or vectors to carry a foreign gene into the 
organisms. 
 
General Features of Transposable Elements in Eukaryotes 
Mobile elements in eukaryotes are broadly classified as Class-I and Class-II types which 
work by copy-and-paste & cut-and-paste mechanism respectively. Each of these types has 
been briefly described in the section below. But before moving to further details, it is 
important to understand that the mobile DNA is associated with autonomous elements 
(comprise of open reading frames that encode proteins necessary for transposition) and non 
– autonomous elements (do not code for proteins that help in transposition but do so due to 
other DNA sequences present within them). 
1. Class-I Transposons: These transpose using an RNA intermediate and are also 
called as retrotransposons. The insertion of transposable elements belonging to this 
class lead to duplication of the element as it works by copy-and paste method. Class-
I transposons are further grouped as those with Long Terminal Repeats (LTR) and 
Non-LTR’s.  
  
  Eukaryotic Transposable Elements   
 
4 
 
Institute of Lifelong Learning, University of Delhi 
? LTR’s – They have repeat sequences from 100kb to even higher sizes in 
direct orientation. The autonomous elements contain the gag and pol genes 
which encode for capsid like proteins and other proteins like reverse 
transcriptase, RNase, integrase etc respectively. This organization resembles 
the retroviruses. Their mode of action involves the synthesis of a transcript 
(in the nucleus) that moves to the cell cytoplasm where it serves as an mRNA 
and is reverse transcribed to cDNA (Complementary DNA). The newly 
synthesized cDNA moves back to the nucleus and gets integrated into the 
genome. Therefore, they create a copy of themselves that results in increase 
in their copy number which in turn is manifested as increased genome size in 
eukaryotes.  
? Non - LTR’s – These include the LINEs and SINEs present in the human 
genome. LINEs are autonomous elements that encode for two open reading 
frames (ORF’s) – one coding for a RNA binding protein and the other for an 
endonuclease and reverse transcriptase activity. Unlike other transcripts, 
these ORF’s are transcribed by RNA Polymerase II from the 5’ region to the 
terminator sequence that is present downstream at 3’ end. In contrast to 
above are the SINEs that represent non-autonomous elements and are 
therefore dependent on the autonomous behavior machinery of the LINES to 
increase their number in the genome. They also contain an internal promoter 
region for RNA Polymerase III. As the usual mRNA, these transcripts (of 
LINEs and SINEs) terminate in a polyadenylated tail. 
Value addition: Did you know??? 
Heading text: Mobile DNA and Gene Therapy 
Body text: Transposons that were once thought to be just a portion of the junk DNA, 
today play a significant role in biology than we ever believed. With this thought, Nancy 
Craig launched a new online journal named ‘Mobile DNA’ in 2010. She believes that 
transposition is instrumental to evolutionary change. Most transpositions are harmless but 
some may contribute to diseases. Craig assumes that these jumping elements also hold a 
prospect of serving as a tool to combat diseases by Gene Therapy. It involves the use of a 
virus/ retrovirus (a type of transposon) to introduce a healthy gene into cells with defect. 
One problem encountered with this approach was the lack of control on the gene’s target 
site of insertion. In 1999, a trial was initiated to use transposons as vehicle for gene therapy 
  Eukaryotic Transposable Elements   
 
5 
 
Institute of Lifelong Learning, University of Delhi 
to cure Severe Combined Immuno-deficiency (SCID). The therapy was successful in 8 of the 
children but of these 4 developed leukemia because the retrovirus carrying the gene got 
integrated near an oncogene. Experimental studies are still under process to develop a 
system wherein a gene can be safely targeted to its destination site. 
Source: Author 
 
 
2. Class-II Transposons: These transposable elements do not transpose via an 
RNA intermediate and are therefore also called as DNA Transposons. They have a 
simple structure composed of short Terminal Inverted Repeat (TIR) sequences that 
are 10-40bp long and have a single gene that codes for the transposase enzyme.  
This enzyme binds and cleaves at a specific sequence that is present at the ends of 
both the autonomous and non-autonomous elements of the transposon. As a result, 
the element leaves the donor site (making it empty) and gets integrated at another 
site, now called as the target site. The hollow site created by these elements is either 
repaired precisely (gap filled by DNA polymerase and nick sealed by DNA ligase) so 
that no traces of the once present transposons exist, but in some cases, the repair 
may not be that precise. In the latter case, the imprint of the transposons at the 
donor site leads to the formation of a transposons foot print.  
 
EXAMPLES OF TRANSPOSABLE ELEMENTS IN EUKARYOTES 
Ac – Ds System in Maize  
Barbara McClintock is credited for the discovery of jumping genes in maize (Zea mays). She 
studied the broken chromosomes in maize at Cold Spring Harbor Laboratory. She planted 
corns that were self pollinated and over successive generations of such genetic breeding 
experiments, she identified that the ninth maize chromosome underwent breakage at 
specific sites. This probably was the reason for unusual color patterns in the kernels. She 
then compared the chromosome of the parent plant to the present generation and 
recognized that chromosome had certain switched positions. Her observation gave a blow to 
the belief that the genes were fixed on the chromosome. This brought in a new aspect of an 
organisms genome which rather being stationary can undergo alterations and 
rearrangement.