320-21&22 - Eukaryotic chromosomes gene regulation...

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Eukaryotic chromosomes & gene regulation Chromosome features Ch 13.1-13.3 Transposons: mobile chromosome elements. Ch 13.4 Nucleosomes & DNA packaging Nuclease hypersensitivity Regulating gene transcription Ch 18.1-18.2 Signal transduction Epigenetics • DNA methylation; genomic imprinting Regulation after transcription Ch 18.3-18.4 Gene regulation by splicing RNA interference Ridley ch 15 “SEX” Ch 14.1
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Chromosome anatomy Telomeres enable end replication not subject to repair only one per chromosome! Centromere Chromosome functions: replication and segregation Origins of replication many per chromosome spindle microtubules kinetochore microtubule attachment
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Transposons: mobile elements in genomes Dispersed repeats… …originate as transposable elements = mobile genetic elements = transposons : = DNA segments that can move from place to place in the genome. DNA transposons Depend on recombination activity of a DNA transposase Retrotransposons . Transpose via an RNA intermediate ; require reverse transcriptase First discovered in corn ( in 1940s, at CSH, by Barbara McClintock) as “controlling elements” that could move from one locus to another. Ch 14 pp 508-514
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DNA transposons Transposase gene Autonomous element: self-sufficient Non-autonomous derivative: - transposase gene mutated or lost; moves only if enzyme supplied by another element. Inverted repeats
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Examples of DNA transposons - Insertion sequences (IS’s) in bacteria - mediate F plasmid insertion into & excision from chromosomal sites. - Ac (autonomous) & Ds (nonautonomous) elements in corn - if insertion affects kernel color, color restored on excision in somatic cells: mosaic pattern produced. - P elements in Drosophila - invaded D. melanogaster worldwide in <50 years - useful for transgenics, and as mutagen. YFG white +
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RNA transposons 1 2 LTR LTR Proof of RNA intermediate: Cloned yeast Ty1 element, added intron: Intron spliced out in new insertions! Transformed into in yeast, looked for new transposition events: Fig. 14.26
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Examples of RNA transposons Retroviruses: infectious retrotransposons LTR LTR gag pol env Most dispersed repeats in the human genome are “fossil” type 1 retrotransposons LINEs AAAAAAAA TTTTTTTT e.g. LINE-1, 1.4kb, 100,000x SINEs AAAAA TTTTT e.g. “Alu” element: 180-280 bp, 300,000x Genetic parasites - “selfish DNA”. Ridley Ch 8 - “Self-interest All SINES + LINES : c. 35% of genome!
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Nucleosomes The packaging problem 2m of DNA 5 μ m nucleus 2nm 0.2mm 200km 0.5 meter 1st level: DNA is wound on protein spools: Several further levels of coiling and looping compact DNA ~200km
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Nucleosomes 145 bp DNA histone 8- mer + Core nucleosome = DNA + histones - highly conserved proteins - many basic amino acids (Lys, His: +ve charges) - 2x (histones 2A, 2B, 3, 4): 1 histone octamer Crystal structures: 1aoi.pdb, 1eqz.pdb (Jmol viewer: http://molvis.sdsc.edu/fgij/)
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320-21&amp;22 - Eukaryotic chromosomes gene regulation...

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