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Genetics Lecture No. 21.docx

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Biology 2581B
Jim Karagiannis

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Genetics Lecture No. 21: Transposable Elements & Variations In Chromosome Number th Wednesday March 27 , 2013 Transposable Elements In The Human Genome: -Barbara McClintock was the first person who really described transposable elements or “jumping genes” that move from one place to another in the genome. Transposable elements are not just limited to maize, but exist in many organisms including mammals, insects, plants, and even some bacteria. Transposable elements can be classified into two major classes: retrotransposons/retroposons (“jump” by using an RNA intermediate) and transposons (transpose DNA directly without and RNA intermediate). There are many different types of transposable elements and they range from 50 base-pairs to 10 kilobase-pairs in length. Depending on the type of transposable element and the organism, there can be one to hundreds of thousands of transposable elements present in a given genome. They are often referred to as “selfish” since they carry only information that allows only their self-perpetuation, however in some cases transposable elements are attributed with having biological functions in the host organism (e.g. maintenance of telomere length in Drosophila). -About 45% of the human genome is composed of sequences that derive from transposable elements. Most of this percentage is comprised of retrotransposon groups Non-Long Terminal Repeats (Non-LTR) like Long Interspersed Elements (LINEs) and Short Interspersed Elements (SINEs), and Long Terminal Repeats. Only a small amount of all transposable elements are DNA transposons. Copia From Drosophila: -Different organisms have different transposable elements, but even within species, the numbers and location of transposable elements can change. A probe for the copia transposable element hybridizes to multiple sites (black bands superimposed over the blue chromosomes) that differ in two different strains of Drosophila from different geographic locations. The fact that these two individuals have the copia sequences in different locations on the chromosome means that the position of these transposable elements is shifting relative to the genes (keep jumping). Retrotransposons: -The main difference between the two types of retrotransposons (non-LTRs and LTRs) is that they either have or don’t have these long terminal repeats, but the other difference is that the non-LTRs possess something reminiscent of a poly-A tail. The main thing that these retrotransposons share in common is that they typically both code for a reverse transcriptase (a DNA polymerase that synthesizes cDNA by using RNA as a template). These retrotransposons often code for other proteins like endonucleases (cleavage enzymes). Retrotransposon Movement: -In order to prove that retrotransposons jump genes by using an RNA intermediate, an experiment was conducted whereby a yeast LTR retrotransposon (Ty1) was cloned into a plasmid. This cloned plasmid was then modified by inserting a yeast intron into the reverse transcriptase gene. When this intron-containing plasmid was transformed into yeast cells, the researchers could isolate new insertions of Ty1 into the yeast genomic DNA. This was accomplished through the alternate splicing of the Ty1 mRNA (removing the intron) in order to translate it to a reverse transcriptase. The enzyme then reverse transcribes the mature Ty1 mRNA in order to make a double-stranded cDNA copy of the Ty1 retrotransposon gene after a series of steps. In this form, the copied retrotransposon can insert itself in a different part of the yeast genome. -The insertion of this double-stranded cDNA into a new genomic location involves a staggered cleavage of the target site that leaves “sticky ends.” Polymerization by DNA synthesis is necessary to fill in the sticky ended gaps, producing two copies of this 5 base-pair target DNA site. Note that this mechanism is just an overview of transposition and details can differ depending on the transposable element give. Transposon Structure & Movement: -Most transposons contain inverted repeats at their ends and encode a transposase enzyme that recognizes these inverted repeats. When transcribed and translated, the transposase cuts at the borders between the transposon and adjacent genomic DNA and also help the excised transposon integrate at a new site. The transposase-catalyzed integration of P elements (transposons) creates a duplication of 8 base-pairs present at the new target site (similar to retrotransposition). However a gap still remains when transposons are excised from their original position and this needs to be filled. After exonucleases widen the gap, cells can repair this gap using related DNA sequences as templates in two distinct ways: Using a sister chromatid or homologous chromosome containing a P element (new transposon in original position; appears as if original transposon remained) or using a homologous chromosome lacking a P element (regular DNA sequence in original position; appears as if original transposon was excised). Transposable El
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