2: Discovery of TEs

McClintock's success

1983: Won the Nobel Prize in Med. & Physiology. Attended seminars and symposia at CSH, and was active in science until she died at age 90, in 1992.

Breakage occurs on timescale that can...

...result in variation of color in one kernel.

How do TEs add "plasticity" to genomes? (4)

1. Can move to new locations: same chromosome or different 2. Can interrupt coding regions or affect regulation 3. Cause recombination events 4. Shuttle genes

Introns can undergo ____ and exons can undergo _____.

exonization, intronization.

What is replicative transposition?

in Transposons, can produce copy that moves, leaving the original in place.

Definition of transposable elements (TEs)

Sequences that code for enzymes and/or other sequence motifs that allow them to move (transpose) themselves or get themselves moved by other transposons. Also known as: transposons, mobile elements, mobile DNA, genomic parasites, jumping genes

McClintock's technique & what she accomplished

She developed techniques for staining chromosomes of maize using textile industry dyes. Was able to distinguish its 10 chromosomes. Phenotype <-- --> karyotype

How did people receive McClintock's presentation of transposons?

She was met with "dead silence"; "puzzlement, even hostility." Skeptics: genes do not move, mutations cannot revert. Retired just as TEs were found in phages, later in bacteria, Drosophila, and everything else.

Where do some genes that affect kernel phenotype reside? What does this result in?

Some genes affecting kernel phenotype reside on the segment that breaks off. Results in pseudodominace

How do TE numbers and types vary by species? How many TE's do we have in our genome?

Species differ in number of TEs. Even closely related species differ in types of TEs in genome as well. We have 50%, other animals have different. Could play potential role in speciation.

What does Ds depend on?

Its ability to jump depended on the presence of another allele, which McClintock named "Activator" (Ac).

Figure and legend from Lynch paper

A: A PTC-containing exonic region is fortuitously spliced. B: If the region spliced has a length that is a multiple of 3, and its absence is not detrimental to the functionality of the coded protein, the exonic region may start being skipped, with its incorporation into the mature mRNA gradually decreasing, essentially undergoing a phase of alternative splicing (indicated in light blue). C: The constitutive intron (IN) is created, flanked by two constitutive exons (EX); and.. (D) may grow larger (for example, as a consequence of insertion accumulation.) E: A second constitutive intron arises downstream in a way similar to that described for the previous intron, while a process of exonization starts within the previous intron. F: The novel, initially alternatively spliced exon now becomes constitutively spliced, while the exon downstream of it acquires a PTC and may start the process of intronization. G: The intronization process of the PTC-containing exon undergoes a phase of alternative splicing, which subsequently leads to.. H: The technical loss of one intron and one exon and the creation of a single, larger intron.

Where are transposable elements?

All domains of life; all three branches, even viruses.

Who discovered transposons? What are they?

Barbara McClintock, First female president of Genetics Association of America. Transposons are DNA that can move around.

What frequently happened at chromosome 9? What did she call this?

Chromosome 9 frequently broke at a particular site. McClintock named the site where the break occurs the "Dissociator" allele, or Ds.

Definition autonomous TE

Describes a transposon that codes for the factors needed to move itself. Ex: LINE-1

Definition non-autonomous TE; what does it code for?

Describes a transposon that relies on an autonomous transposon to move it; codes for only factors that allow the active transposon to recognize it. Ex: Alu elements, SVA elements.

Target site duplication (TSDs) Are LTRs a type of TSD? What do all TEs have?

Direct repeats due to repair of overhanging strands that were cut during insertion. LTRS ARE NOT A TYPE OF TSD. ALL TES HAVE TSDS.

2 sequence motifs of TEs

Inverted repeats (IR): Different transposases recognize different IRs. Target site duplication (TSD): A type of direct repeat that results from the insertion process. All TE's have TSDs, but they differ among types.

What was puzzling about Ds?

It could move around to different loci on the same or even different chromosomes.

Why was Ac difficult to map?

It, too, moved around in the genome!

What is known as the "genetic hokey-pokey"?

Kernel phenotypes caused by transposons. Suggested that there were times the gene was disrupted and not.

What did she see in Zea mays (corn)?

Kernels within the same plant can show dominant (purple), recessive (yellow), or spotted phenotype. Some could have combinations of colors.

TEs in the human genome

LEARN TO DRAW

Retrotransposons are further divided into what? Majority are ___? Where are LTRs?

LTR and nonLTR types. Majority are nonLTR. LTRs flank the ends of retroviruses.

What are LTRs? How many nucleotides? What do they look like at time of insertion? What do they carry?

Long Terminal Repeats. Also known as the transcription factor landing strip. 1. 300-1000 nt direct repeats at both ends of retroviruses and LTR-transposons. 2. Identical at time of insertion. 3. Carry regulatory features such as promoters, enhancers, and TF binding sites.

This breakage results in ____ of traits controlled by alleles ____

Pseudodominance of traits controlled by alleles on the broken segment. Associated with kernel color phenotype.

What are the two main types of TEs? How do they differ?

RNA (retro) transposons: copy and paste DNA transposons: cut and paste (differ by method of transposition)

What are TEs with LTRs closely related to?

Retroviruses; all they are missing is an envelope gene.

What is conservative transposition?

The TE can move from original location to new.

What happened when Ds left a site?

The mutated gene's function could be restored.

What was McClintock the first to show?

The physical basis of crossing over of chromosomes (recombination). She performed this work along with Harriet Creighton, at Cornell.

3 Enzymes in TEs

Transposase: mediates DNA excision and movement to new location. Reverse transcriptase: mediates copying of RNA to DNA Integrase: mediates integration of copy into new location