[Lecture 3.1] MGEs and Prokaryotic Transcription

UNLV FALL 2026 Campanale

What is a transposable element (TE) or transposon?

A discrete DNA sequence/region in the genome that is mobile — able to transport itself to other locations within the genome. They "jump" within the same genome but never leave the cell.

What percentage of the human genome do transposons account for?

Approximately 45% of the human genome consists of transposons or their remnants.

Have most transposons in the human genome retained their mobility?

No. Most transposons in the human genome have LOST the ability to move (lost mobility).

Do transposons leave the genome to insert elsewhere?

No. Transposons never go outside the cell. They "jump" only within the same genome.

Are transposons still independent genetic elements?

No. Although many originated from viruses, transposons are now part of the cell's genome and no longer exist as independent entities.

What are the four main characteristics of transposons in the human genome?

(1) Most have lost mobility, (2) Most do not contribute to cell activities, (3) Most are located in heterochromatin (not transcriptionally active), (4) Many are moderately repetitive sequences.

Where are most transposons located in the genome?

Most are in non-coding sequences and heterochromatin (transcriptionally silent/inactive regions).

Why are transposons considered "junk DNA"?

Most transposons are non-coding, located in heterochromatin, and don't appear to contribute to normal cell activities.

How does transposon integration differ from site-specific recombination?

Transposon integration: Can happen almost anywhere in the genome (sequence-independent). Site-specific recombination: Requires specific recognition sequences at both donor and recipient sites (site-dependent).

List three harmful effects of transposons.

(1) Genome instability, (2) Mutagenic insertions into genes, (3) Major source of mutations and polymorphisms.

What happens if a transposon inserts into a functional gene?

The gene is disrupted — the insertion interrupts the gene sequence, typically causing loss-of-function.

How can a transposon cause mutations through imprecise excision?

When a transposon jumps out of the genome imprecisely, it may take out nearby "green chunks" (exon sequences or nearby genes), causing deletions and potentially exon shuffling.

What is exon shuffling in the context of transposon excision?

When imprecise excision of a transposon removes portions of adjacent genes, the remaining exons may be rearranged or combined in new ways, potentially creating novel gene arrangements.

What is single-strand annealing (SSA) recombination?

A recombination mechanism where two transposons can pair and undergo homologous recombination, leading to deletion of sequences between them. It produces the same consequence as homologous recombination but uses transposon repeats as homology.

List three potential beneficial effects of transposons.

(1) Genome evolution — transposons create genetic variation and new gene arrangements, (2) Neural development, (3) Learning (these last two are tentative/question-marked in lecture).

How do transposons contribute to genome evolution?

Through gene duplication, exon shuffling, and creating new genetic combinations, transposons generate the variation that drives evolution.

What are the two main types of chromosome rearrangement caused by transposon recombination?

(1) Homologous recombination between copies on DIFFERENT chromosomes, (2) Alignment between copies on the SAME chromosome.

What happens during homologous recombination between transposons on different chromosomes?

On homologous chromosomes: deletion + duplication (during alignment of repeat regions in meiosis). On nonhomologous chromosomes: translocation.

What occurs when two transposons in the same orientation (direct repeats) align on the same chromosome?

Homologous recombination between the direct repeats leads to deletion of the DNA region between them. One copy of the transposon remains; one is removed along with the intervening sequence.

Is transposon-mediated chromosome rearrangement site-specific recombination?

No. Although it's homologous recombination with similar consequences, it is NOT site-specific recombination because the transposons are randomly inserted sequences that happen to align (not predetermined sites).

What two types of transposons are defined by their ability to move?

(1) Autonomous units — encode their own enzymes, (2) Non-autonomous units — lack functional enzyme genes.

Define autonomous transposons.

Autonomous transposons encode their own transposase and integrase enzymes and therefore can "jump" by themselves. They are unstable and mutagenic.

Describe non-autonomous transposons.

Non-autonomous transposons represent the majority of transposons in the human genome. They have defective genes encoding transposase/integrase and cannot move by themselves in the genome. They are stable but can only move if enzymes are supplied by OTHER transposons of the same family (trans-acting).

How do non-autonomous transposons move if they can't produce their own enzymes?

Non-autonomous transposons can only be moved by enzymes (transposase and integrase) expressed from OTHER transposons of the same family. The enzymes work in trans (from a distance) on all family members.

Why are non-autonomous transposons called "relic viruses"?

Many transposons originated from viruses but are now defective/inactive, lacking genes for the enzymes needed for independent movement — making them evolutionary remnants ("relics") of viral invaders.

Do vertebrates or plants have more active DNA-based transposons currently?

Plants. Vertebrates have very few endogenous DNA-based transposons that are currently active, while plants harbor a large number of active elements.

What enzymes are required for transposon mobility?

Transposase (cuts and pastes transposon) and integrase (catalyzes integration at new location).

What is the key difference in the NUMBER of products made during replication vs transcription?

Replication: 1 DNA copy from 1 DNA template. Transcription: MANY RNA copies from 1 DNA template (~360,000 mRNA molecules per mammalian cell from ~12,000 different genes).

Compare the permanence of products in replication vs transcription.

Replication: The new DNA copy is PERMANENT and passed on/amplified in future generations. Transcription: RNA copies are TRANSIENT — they are degraded and NOT passed on to future generations.

Why do cells make many RNA copies but only one DNA copy during replication?

DNA must be accurately duplicated once per cell division (permanence), but genes need to be frequently expressed to produce proteins at needed levels (many transient copies allow for rapid protein production).

What is the sense strand?

The sense strand (also called non-template strand) has the SAME sequence as the mRNA (with U instead of T). It is written 5' to 3' and represents how genes are written/named.

What is the antisense strand?

The antisense strand (also called template strand) is COMPLEMENTARY to the mRNA. It is the strand READ by RNA polymerase during transcription (3' to 5' direction).

If the antisense strand reads 3'-TACGCACAGCT-5', what is the mRNA sequence?

5'-AUGCGUGUCGA-3'. (Remember: RNA polymerase reads template 3'→5', synthesizes mRNA 5'→3', and uses U instead of T.)

How does a researcher know which strand is the template for a particular gene?

Genes have orientations. Forward genes use the BOTTOM strand as template. Backward genes use the TOP strand as template. For a specific gene, only ONE strand is used as the template.

Why is it important that only one strand serves as the template for a specific gene?

If both strands were used as templates, the mRNA products would be complementary to each other and unable to be translated into the same protein. Gene specificity requires one consistent template strand.

What are the four main regions of a prokaryotic gene (from 5' to 3')?

(1) Promoter/Enhancer sequences (transcription factor binding, TATA box), (2) 5'UTR (untranslated, before start codon), (3) Gene sequence between start and stop codon, (4) 3'UTR with poly-A site and transcription termination sequences.

What is the function of the promoter?

The promoter is the binding site for RNA polymerase. It is located upstream (5') of the transcription start point and is usually NOT included in the mRNA sequence.

What does the +1 position represent in a gene?

The +1 position is the transcription start point — the first base that is transcribed into RNA. Numbering goes upstream (negative numbers, -35, -10) and downstream (positive numbers).

What is a transcription terminator?

A DNA sequence that triggers the dissociation (release) of RNA polymerase, ending transcription. This sequence is unique to prokaryotes and appears in the RNA transcript.

How is the DNA sequence typically written when showing a gene?

Usually written as only the sense (non-template) strand sequence, 5' to 3'. The start point is designated +1 with no "0", sequences upstream are negative numbers, and sequences downstream are positive numbers.

What is a 5'UTR and when does it get transcribed?

5'UTR (5' untranslated region) is transcribed into RNA but NOT translated into protein. It comes after the transcription start point but before the translation start codon.

What is a 3'UTR?

The 3'UTR (3' untranslated region) contains the poly-adenylation site and transcription termination sequences. It is transcribed but not translated and ends with the transcription termination point.

What is polycistronic mRNA?

A single mRNA molecule containing MULTIPLE ORFs (open reading frames), where each ORF encodes a different protein. This allows prokaryotes to express multiple genes from one transcript. Characteristic of prokaryotes; rare in eukaryotes.

What is monocistronic mRNA?

A single mRNA molecule containing ONE ORF that encodes ONE protein. Characteristic of eukaryotes.

Why is polycistronic mRNA advantageous for prokaryotes?

It allows coordinated expression of genes involved in the same pathway or operon (e.g., bacterial operons like lac operon), enabling efficient regulation of multiple related genes from a single transcript.

What is a transcription bubble?

The region of DNA (~12-14 base pairs) where the two DNA strands are separated and RNA synthesis occurs. The bubble is maintained by RNA polymerase as it moves along the template.

Describe the three key events that occur inside the transcription bubble.

(1) DNA strands are separated/denatured, (2) RNA polymerase reads the template strand in the 3' to 5' direction, (3) RNA chain grows in the 5' to 3' direction by adding nucleotides to the free 3'-OH end.

What is the substrate for RNA synthesis in prokaryotes?

Ribonucleotide triphosphates (ATP, CTP, GTP, UTP). The triphosphate provides energy for adding the nucleotide to the growing RNA chain.

How fast does RNA polymerase synthesize RNA in prokaryotes?

Approximately 40-50 nucleotides per second (slower than DNA polymerase during replication).

Why does the transcription bubble NOT stay permanently open?

As RNA polymerase moves forward, the DNA duplex behind it reforms/re-anneals. The newly synthesized RNA is displaced into single-stranded RNA. This allows the bubble size to remain constant (~12-14 bp) rather than growing larger.

What happens to the size of the transcription bubble as RNAP moves along the template?

The bubble size REMAINS UNCHANGED at 12-14 base pairs. As the bubble moves, DNA re-forms behind while DNA ahead unwinds, maintaining constant size.

Why is the size of the transcription bubble constant?

The rate at which DNA duplex re-forms behind the moving polymerase equals the rate at which DNA unwinds ahead of it. This balance maintains constant bubble dimensions.

Can multiple RNA polymerases transcribe the same gene simultaneously?

Yes. Multiple RNAPs can transcribe simultaneously on the same gene. For highly transcribed genes, RNAPs are positioned right next to each other.

What is the "Christmas-tree" structure observed under electron microscopy?

When multiple RNA polymerases transcribe the same gene simultaneously on highly expressed genes, the visualized structure resembles a Christmas tree, with the DNA trunk and growing RNA branches extending perpendicular from it.

What happens to nucleoid-associated proteins (NAPs) during heavy transcription?

For highly transcribed genes, local NAPs (proteins that organize bacterial DNA) are completely disassembled, allowing RNA polymerases to work unimpeded.

How can active transcription sites be visualized in cells?

Using FISH (Fluorescent In Situ Hybridization) — complementary fluorescent probes bind to specific transcripts, allowing visualization of transcription sites as bright spots under fluorescence microscopy.

What do different colored spots represent in FISH visualization of active transcription?

Big bright spots = active transcription sites. Small spots = single transcripts. Different colors = transcripts from different genes (e.g., green = gene A transcripts, red = gene B transcripts, blue = nucleus).

List the three important DNA sequence elements found in the sense strand of a prokaryotic gene.

(1) Promoter — RNA polymerase binding site, upstream (5'), not in mRNA, (2) Transcription start point (+1) — first base transcribed into RNA, (3) Transcription terminator — sequence that triggers RNAP dissociation, unique to bacteria.

Why is the promoter NOT part of the mRNA sequence?

The promoter is a DNA regulatory element upstream of the transcription start point. RNA polymerase begins transcription AT position +1, so sequences upstream (including the promoter) are not transcribed into mRNA.

What does "upstream" and "downstream" mean in the context of gene sequences?

Upstream = toward the 5' end, before the transcription start point (negative numbering). Downstream = toward the 3' end, after the transcription start point (positive numbering). Direction is relative to the direction of transcription.