Unit 10
Define
- Transposable Elements (Transposons)- Jumping genes.
- Autonomous- Transposons that encode their own enzymes
- Non-autonomous- Transposons that do not code for their own enzymes
- Class I Retrotransposons- Copy and paste, Utilize RNA intermediate
- Class II: DNA Transposons- CUT and paste, Moves the actual segment
- Reverse transcriptase- Enzyme that synthesizes DNA from RNA template
- RNase H- Degrades the RNA strand of the RNA-DNA hybrid molecule (Pol gene)
- Integrase- Enzyme that insertes the retroposon into the target DNA site
- Transposase- an enzyme that catalyzes the movement of a transposable element (or transposon), a segment of DNA, from one location to another within the genome
Concepts
- Detail the characteristics of Transposons- Mobile, Have autonomous and non-autonomous enzymes and flanked by short, specific repetitive DNA sequences.
- What are the 2 classes of Transposable elements in Eukaryotes- Class 1 is Retrotransposons (copy and paste) and Class 2 os DNA transposons (DNA Transposons).
- What are the 2 major groups of retrotransposons- Long Terminal Repeat (LTR) which obviously has long terminal repeats and Non-LTR retrotransposons which lack LTR but have a poly-A tail at the 3’ prime end.
- Detail the structure of LTR retrotransposons (include the internal coding regions)- Identical, direct repeats that flank the internal gene-coding regions (has the promoter for transcription and signals for reverse transcriptions and integration), they also have ORFs; a region that contains the genes necessary for transposition (reverse transcriptase and integrase). The genes are Gag gene and Pol gene. The gag gene encodes the Gag polyprotein which are structure proteins that form the virus-like particle, then the virus-like particle encapsulates the RNA and Enzymes. Lastly, the Pol gene ENCODES the polyprotein, then reverse transcription occurs blah blah blah
- Detail the mechanism used to move and integrate LTR Retrotransposons- After the packaging and stuff, Pol polyprotein is cleaved into the fuctional enzymes and then reverse transcription occurs in 2 stages. Minus strand synthesis is one of the stage, and the other is the Plus strand synthesis and then is integrate sinto the genome
- What are the 2 major types of Non-LTR retrotransposons- LINEs and SINEs
- Detail the structure of LINE retrotransposons- Do not contain long terminal repeats, but have; 5’ UTR which has the region that contains an internal promoter recognized by RNA pol II, Open Reading Frames which encodes the nesessary proteins for transposition. Lastly, 3’ UTR and the Poly-A tail which serves as the termination element.
- Detail the mechanism used to move and integrate LINE retrotransposons- LINE DNA segment is transcribed by RNA pol II into mRNA, then translated in cytoplasm to form ORF proteins, those then bind to mRNA molecule forming Ribonucleoprotein (RNP) complex and transports mRNA to the nucleus. RNP complex looks for A-T rich target sequence in the host DNA, then Endonuclease cleaves one strand of the host DNA making a single-strand nick, then First strand cDNA synthesis (priming), then Second strand synthesis and integration
- Detail the structure of SINE retrotransposons- Do not need to encode any function, they have Interal RNA Pol III promoter which has an internal promoter that is reognized by the host cells RNA Pol III for transcription, A 3’ Poly-A tail a crucial segment for engaging the LINE-encoded proteins, Structure homology; active SINEs often containing sequences that sre similar to LINEs.
- Detail the mechanism used to move and integrate LINE retrotransposons- Use a modified version of TPRT, relies on enzymes expressed by LINE retrotransposons, utilizes RNA Pol II Molecule to produce RNA molecule,
- Detail the Class II: DNA Transposons- The cut and paste method, elements move directly as DNA and do not use RNA intermediate, also does not increase the number of copies, Utilizes transposase.
- Detail the structural features of DNA transposons-
Transposase gene- central region which encodes for transposase
Terminal inverted repeats (TIRs)- Transposase gene is flanked by short, inverted repeated sequences at both ends
Target Site Duplication- Upon instertion the mechanism creates short, direct repeats of host DNA sequences that flank the inserted transposon. like a signature
- Detail the mechanisms used to move and integrate DNA transposon-
Transposase recognition- encodes enzyme transposase
Double-Stranded Cleavage- Transposase makes precise double-strand DNA cuts at outer edges of the TIRS
Donor repair site- after the transposon is removed the donor site is repaired
- What is the purpose/function of transposable elements-
Source of genetic variation,
Chromosomal restructuring,
Gene domestication,
epigenetic landscape
- Detail the Transcriptional Gene Silencing (TGS) process for regulating transposable element
movement-
Physically blocks the transcription of TE
Main Mechanisms: DNA methylation, Histone modification and Heterochromatin formation
- Detail the Post-Transcriptional Gene Silencing (PTGS) process for regulating transposable element movement- Acts on TE RNA transcripts that escape TGS